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Sample records for acids phylogenetic analysis

  1. Phylogenetic analysis of beta-papillomaviruses as inferred from nucleotide and amino acid sequence data.

    PubMed

    Gottschling, Marc; Köhler, Anja; Stockfleth, Eggert; Nindl, Ingo

    2007-01-01

    Human papillomaviruses (HPV) of the beta-group seem to be involved in the pathogenesis of non-melanoma skin cancer. Papillomaviruses are host specific and are considered closely co-evolving with their hosts. Evolutionary incongruence between early genes and late genes has been reported among oncogenic genital alpha-papillomaviruses and considerably challenge phylogenetic reconstructions. We investigated the relationships of 29 beta-HPV (25 types plus four putative new types, subtypes, or variants) as inferred from codon aligned and amino acid sequence data of the genes E1, E2, E6, E7, L1, and L2 using likelihood, distance, and parsimony approaches. An analysis of a L1 fragment included additional nucleotide and amino acid sequences from seven non-human beta-papillomaviruses. Early genes and late genes evolution did not conflict significantly in beta-papillomaviruses based on partition homogeneity tests (p > or = 0.001). As inferred from the complete genome analyses, beta-papillomaviruses were monophyletic and segregated into four highly supported monophyletic assemblages corresponding to the species 1, 2, 3, and fused 4/5. They basically split into the species 1 and the remainder of beta-papillomaviruses, whose species 3, 4, and 5 constituted the sistergroup of species 2. beta-Papillomaviruses have been isolated from humans, apes, and monkeys, and phylogenetic analyses of the L1 fragment showed non-human papillomaviruses highly polyphyletic nesting within the HPV species. Thus, host and virus phylogenies were not congruent in beta-papillomaviruses, and multiple invasions across species borders may contribute (additionally to host-linked evolution) to their diversification.

  2. Analysis of Fatty Acid and Growth Profiles in Ten Shewanella spp. to Associate Phylogenetic Relationships

    DTIC Science & Technology

    2015-10-25

    microorganisms from the same genus using physiological responses. To understand these changes, a shift in fatty acid length distributions and growth of...in new associations between dissimilar Shewanella spp. based on physiology . 25-11-2015 Memorandum Office of Naval Research One Liberty Center 875 N...genus which has led to novel insight into physiological changes based on fatty acid and growth profiles that are not predicted from phylogenetic

  3. Characterization and phylogenetic analysis of a thermostable N-carbamoyl- l-amino acid amidohydrolase from Bacillus kaustophilus CCRC11223.

    PubMed

    Hu, Hui-Yu; Hsu, Wen-Hwei; Chien, Hungchien Roger

    2003-04-01

    A thermostable N-carbamoyl- l-amino acid amidohydrolase ( l-N-carbamoylase) gene composed of an 1,230-bp ORF encoding a 44.3-kDa protein was cloned from the thermophile Bacillus kaustophilus CCRC11223. This l-N-carbamoylase contained six cysteine residues that form three disulfide bridges. The purified l-N-carbamoylase was stringently l-specific and exhibited high activity in the hydrolysis of N-carbamoyl- l-homophenylalanine. N-carbamoyl derivatives of beta-alanine, beta-aminoisobutyric acids, l-tryptophan, and d-specific amino acids were not recognized as substrates. The l-N-carbamoylase required the divalent metal ions Mn(2+), Co(2+), and Ni(2+) for increasing activity. The pH and temperature optima of the enzyme were pH 7.4 and 70 degrees C, respectively. This enzyme was completely thermostable at 50 degrees C for 36 days in the presence of d- and/or l-specific substrates. Phylogenetic analysis of the available amino acid sequences of N-carbamoyl and N-acyl amino acid amidohydrolases from the three main kingdoms of life showed that they can be divided into four distinct families. The B. kaustophilus enzyme could be classified into the family of l-N-carbamoylases and some beta-ureidopropionases, but did not hydrolyze beta-ureidopropionates.

  4. Cloning and phylogenetic analysis of a fatty acid elongase gene from Nannochloropsis oculata CS179

    NASA Astrophysics Data System (ADS)

    Pan, Kehou; Ma, Xiaolei; Yu, Jianzhong; Zhu, Baohua; Yang, Guanpin

    2009-12-01

    Nannochloropsis oculata CS179, a unicellular marine microalga, is rich in long-chain polyunsaturated fatty acids (LCPUFAs). Elongase and desaturase play a key role in the biosynthesis of PUFAs. A new elongase gene, which encodes 322 amino acids, was identified via RT-PCR and 5' and 3' RACE. The sequence of the elongase gene was blast-searched in the NCBI GenBank and showed a similarity to those of the cryptosporidium. But the NJ-tree revealed that the N. oculata CS179 elongase clustered with those of the microalgae Phaeodactylum tricornutum, Ostreococcus tauri and Thalassiosira pseudonana.

  5. A Comprehensive Phylogenetic Analysis of Deadenylases

    PubMed Central

    Pavlopoulou, Athanasia; Vlachakis, Dimitrios; Balatsos, Nikolaos A.A.; Kossida, Sophia

    2013-01-01

    Deadenylases catalyze the shortening of the poly(A) tail at the messenger ribonucleic acid (mRNA) 3′-end in eukaryotes. Therefore, these enzymes influence mRNA decay, and constitute a major emerging group of promising anti-cancer pharmacological targets. Herein, we conducted full phylogenetic analyses of the deadenylase homologs in all available genomes in an effort to investigate evolutionary relationships between the deadenylase families and to identify invariant residues, which probably play key roles in the function of deadenylation across species. Our study includes both major Asp-Glu-Asp-Asp (DEDD) and exonuclease-endonuclease-phospatase (EEP) deadenylase superfamilies. The phylogenetic analysis has provided us with important information regarding conserved and invariant deadenylase amino acids across species. Knowledge of the phylogenetic properties and evolution of the domain of deadenylases provides the foundation for the targeted drug design in the pharmaceutical industry and modern exonuclease anti-cancer scientific research. PMID:24348009

  6. Phylogenetic analysis of adenovirus sequences.

    PubMed

    Harrach, Balázs; Benko, Mária

    2007-01-01

    Members of the family Adenoviridae have been isolated from a large variety of hosts, including representatives from every major vertebrate class from fish to mammals. The high prevalence, together with the fairly conserved organization of the central part of their genomes, make the adenoviruses one of (if not the) best models for studying viral evolution on a larger time scale. Phylogenetic calculation can infer the evolutionary distance among adenovirus strains on serotype, species, and genus levels, thus helping the establishment of a correct taxonomy on the one hand, and speeding up the process of typing new isolates on the other. Initially, four major lineages corresponding to four genera were recognized. Later, the demarcation criteria of lower taxon levels, such as species or types, could also be defined with phylogenetic calculations. A limited number of possible host switches have been hypothesized and convincingly supported. Application of the web-based BLAST and MultAlin programs and the freely available PHYLIP package, along with the TreeView program, enables everyone to make correct calculations. In addition to step-by-step instruction on how to perform phylogenetic analysis, critical points where typical mistakes or misinterpretation of the results might occur will be identified and hints for their avoidance will be provided.

  7. Cloning, Phylogenetic Analysis, and Distribution of Free Fatty Acid Receptor GPR120 Expression along the Gastrointestinal Tract of Housing versus Grazing Kid Goats.

    PubMed

    Ran, Tao; Li, Hengzhi; Liu, Yong; Zhou, Chuanshe; Tang, Shaoxun; Han, Xuefeng; Wang, Min; He, Zhixiong; Kang, Jinghe; Yan, Qiongxian; Tan, Zhiliang; Beauchemin, Karen A

    2016-03-23

    G-protein-coupled receptor 120 (GPR120) is reported as a long-chain fatty acid (LCFA) receptor that elicits free fatty acid (FFA) regulation on metabolism homeostasis. The study aimed to clone the gpr120 gene of goats (g-GPR120) and subsequently investigate phylogenetic analysis and tissue distribution throughout the digestive tracts of kid goats, as well as the effect of housing versus grazing (H vs G) feeding systems on GPR120 expression. Partial coding sequence (CDS) of g-GPR120 was cloned and submitted to NCBI (accession no. KU161270 ). Phylogenetic analysis revealed that g-GPR120 shared higher homology in both mRNA and amino acid sequences for ruminants than nonruminants. Immunochemistry, real-time PCR, and Western blot analysis showed that g-GPR120 was expressed throughout the digestive tracts of goats. The expression of g-GPR120 was affected by feeding system and age, with greater expression of g-GPR120 in the G group. It was concluded that the g-GPR120-mediated LCFA chemosensing mechanism is widely present in the tongue and gastrointestinal tract of goats and that its expression can be affected by feeding system and age.

  8. The evolution of polar fish hemoglobin: a phylogenetic analysis of the ancestral amino acid residues linked to the root effect.

    PubMed

    Verde, Cinzia; Parisi, Elio; di Prisco, Guido

    2003-01-01

    Originating from a benthic ancestor, the suborder Notothenioidei (the dominant fish fauna component of the Antarctic sea) underwent a remarkable radiation, which led notothenioids to fill several niches. The ecological importance of notothenioids in Antarctica and their biochemical adaptations have prompted great efforts to study their physiology and phylogeny, with special attention to the evolutionary adaptation of the oxygen-transport system. We herewith report the evolutionary history of alpha- and beta-globins under the assumption of the molecular clock hypothesis as a basis for reconstructing the phylogenetic relationships among species. These studies have been extended to fish species of other latitudes, including the Arctic region. The northern and southern polar oceans have very different characteristics; indeed, in many respects the Antarctic and Arctic ichthyofaunas are more dissimilar than similar. Our results show that the inferred phylogeny of Arctic and Antarctic globins is different. Taking advantage of the wealth of information collected on structure and function of hemoglobins, we have attempted to investigate the evolutionary history of an important physiological feature in fish, the Root effect. The results suggest that the amino acid residues reported to play a key role in the Root effect may be regarded as ancestor characters, but the lack of this effect in extant species can hardly be associated with the presence of synapomorphies.

  9. A phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius (Mycoblastaceae, lichenized Ascomycota) reveals cryptic clades correlated with fatty acid profiles

    PubMed Central

    Spribille, Toby; Klug, Barbara; Mayrhofer, Helmut

    2011-01-01

    Lichens are a prominent feature of northern conifer forests and a large number of species are thought to be circumboreal. Whether or not circumboreal lichen species really constitute monophyletic groups has seldom been tested. We investigated molecular phylogenetic patterns in the mycobiont of Mycoblastus sanguinarius, a well known epiphytic lichen species of the boreal forest, based on material collected from across the high latitude northern hemisphere. A three-locus dataset of internal transcribed spacer rDNA, translation elongation factor 1-α and replication licensing factor Mcm7 DNA sequences revealed that material treated until now as belonging to M. sanguinarius does indeed form a monophyletic group within the genus and is distinct from a strongly supported Mycoblastus affinis. The M. sanguinarius complex appears closely related to the rare Mycoblastus glabrescens, which is currently known only from the Pacific Northwest and was rediscovered during the present study. However, within M. sanguinarius s.lat. in the northern hemisphere, two deeply divergent and morphologically coherent species can be recovered, one of which matches the southern hemisphere species Mycoblastus sanguinarioides and turns out to be widespread in North America and Asia, and one of which corresponds to M. sanguinarius s.str. Both M. sanguinarius and M. sanguinarioides exhibit additional low-level genetic differentiation into geographically structured clades, the most prominent of which are distributed in East Asia/eastern North America and western North America/Europe, respectively. Individuals from these lowest-level clades are morphologically indistinguishable but chemical analyses by thin layer chromatography revealed that each clade possesses its own fatty acid profile, suggesting that chemical differentiation precedes morphological differentiation and may be a precursor to speciation. PMID:21443957

  10. Phylogenetic analysis of dicyemid mesozoans (phylum Dicyemida) from innexin amino acid sequences: dicyemids are not related to Platyhelminthes.

    PubMed

    Suzuki, Takahito G; Ogino, Kazutoyo; Tsuneki, Kazuhiko; Furuya, Hidetaka

    2010-06-01

    Dicyemid mesozoans are endoparasites, or endosymbionts, found only in the renal sac of benthic cephalopod molluscs. The body organization of dicyemids is very simple, consisting of usually 10 to 40 cells, with neither body cavities nor differentiated organs. Dicyemids were considered as primitive animals, and the out-group of all metazoans, or as occupying a basal position of lophotrochozoans close to flatworms. We cloned cDNAs encoding for the gap junction component proteins, innexin, from the dicyemids. Its expression pattern was observed by whole-mount in situ hybridization. In adult individuals, the innexin was expressed in calottes, infusorigens, and infusoriform embryos. The unique temporal pattern was observed in the developing infusoriform embryos. Innexin amino acid sequences had taxon-specific indels which enabled identification of the 3 major protostome lineages, i.e., 2 ecdysozoans (arthropods and nematodes) and the lophotrochozoans. The dicyemids show typical, lophotrochozoan-type indels. In addition, the Bayesian and maximum likelihood trees based on the innexin amino acid sequences suggested dicyemids to be more closely related to the higher lophotrochozoans than to the flatworms. Flatworms were the sister group, or consistently basal, to the other lophotrochozoan clade that included dicyemids, annelids, molluscs, and brachiopods.

  11. [Analysis phylogenetic relationship of Gynostemma (Cucurbitaceae)].

    PubMed

    Qin, Shuang-shuang; Li, Hai-tao; Wang, Zhou-yong; Cui, Zhan-hu; Yu, Li-ying

    2015-05-01

    The sequences of ITS, matK, rbcL and psbA-trnH of 9 Gynostemma species or variety including 38 samples were compared and analyzed by molecular phylogeny method. Hemsleya macrosperma was designated as outgroup. The MP and NJ phylogenetic tree of Gynostemma was built based on ITS sequence, the results of PAUP phylogenetic analysis showed the following results: (1) The eight individuals of G. pentaphyllum var. pentaphyllum were not supported as monophyletic in the strict consensus trees and NJ trees. (2) It is suspected whether G. longipes and G. laxum should be classified as the independent species. (3)The classification of subgenus units of Gynostemma plants is supported.

  12. Cloning and Phylogenetic Analysis of Brassica napus L. Caffeic Acid O-Methyltransferase 1 Gene Family and Its Expression Pattern under Drought Stress

    PubMed Central

    Lu, Kun; Yuan, Jianglian; Huang, Jieheng; Du, Hai; Li, Jiana

    2016-01-01

    For many plants, regulating lignin content and composition to improve lodging resistance is a crucial issue. Caffeic acid O-methyltransferase (COMT) is a lignin monomer-specific enzyme that controls S subunit synthesis in plant vascular cell walls. Here, we identified 12 BnCOMT1 gene homologues, namely BnCOMT1-1 to BnCOMT1-12. Ten of 12 genes were composed of four highly conserved exons and three weakly conserved introns. The length of intron I, in particular, showed enormous diversification. Intron I of homologous BnCOMT1 genes showed high identity with counterpart genes in Brassica rapa and Brassica oleracea, and intron I from positional close genes in the same chromosome were relatively highly conserved. A phylogenetic analysis suggested that COMT genes experience considerable diversification and conservation in Brassicaceae species, and some COMT1 genes are unique in the Brassica genus. Our expression studies indicated that BnCOMT1 genes were differentially expressed in different tissues, with BnCOMT1-4, BnCOMT1-5, BnCOMT1-8, and BnCOMT1-10 exhibiting stem specificity. These four BnCOMT1 genes were expressed at all developmental periods (the bud, early flowering, late flowering and mature stages) and their expression level peaked in the early flowering stage in the stem. Drought stress augmented and accelerated lignin accumulation in high-lignin plants but delayed it in low-lignin plants. The expression levels of BnCOMT1s were generally reduced in water deficit condition. The desynchrony of the accumulation processes of total lignin and BnCOMT1s transcripts in most growth stages indicated that BnCOMT1s could be responsible for the synthesis of a specific subunit of lignin or that they participate in other pathways such as the melatonin biosynthesis pathway. PMID:27832102

  13. On the analysis of phylogenetically paired designs

    PubMed Central

    Funk, Jennifer L; Rakovski, Cyril S; Macpherson, J Michael

    2015-01-01

    As phylogenetically controlled experimental designs become increasingly common in ecology, the need arises for a standardized statistical treatment of these datasets. Phylogenetically paired designs circumvent the need for resolved phylogenies and have been used to compare species groups, particularly in the areas of invasion biology and adaptation. Despite the widespread use of this approach, the statistical analysis of paired designs has not been critically evaluated. We propose a mixed model approach that includes random effects for pair and species. These random effects introduce a “two-layer” compound symmetry variance structure that captures both the correlations between observations on related species within a pair as well as the correlations between the repeated measurements within species. We conducted a simulation study to assess the effect of model misspecification on Type I and II error rates. We also provide an illustrative example with data containing taxonomically similar species and several outcome variables of interest. We found that a mixed model with species and pair as random effects performed better in these phylogenetically explicit simulations than two commonly used reference models (no or single random effect) by optimizing Type I error rates and power. The proposed mixed model produces acceptable Type I and II error rates despite the absence of a phylogenetic tree. This design can be generalized to a variety of datasets to analyze repeated measurements in clusters of related subjects/species. PMID:25750719

  14. Phylogenetic analysis of cubilin (CUBN) gene

    PubMed Central

    Shaik, Abjal Pasha; Alsaeed, Abbas H; Kiranmayee, S; Bammidi, VK; Sultana, Asma

    2013-01-01

    Cubilin, (CUBN; also known as intrinsic factor-cobalamin receptor [Homo sapiens Entrez Pubmed ref NM_001081.3; NG_008967.1; GI: 119606627]), located in the epithelium of intestine and kidney acts as a receptor for intrinsic factor – vitamin B12 complexes. Mutations in CUBN may play a role in autosomal recessive megaloblastic anemia. The current study investigated the possible role of CUBN in evolution using phylogenetic testing. A total of 588 BLAST hits were found for the cubilin query sequence and these hits showed putative conserved domain, CUB superfamily (as on 27th Nov 2012). A first-pass phylogenetic tree was constructed to identify the taxa which most often contained the CUBN sequences. Following this, we narrowed down the search by manually deleting sequences which were not CUBN. A repeat phylogenetic analysis of 25 taxa was performed using PhyML, RAxML and TreeDyn softwares to confirm that CUBN is a conserved protein emphasizing its importance as an extracellular domain and being present in proteins mostly known to be involved in development in many chordate taxa but not found in prokaryotes, plants and yeast.. No horizontal gene transfers have been found between different taxa. PMID:23390341

  15. Phylogenetic analysis of cubilin (CUBN) gene.

    PubMed

    Shaik, Abjal Pasha; Alsaeed, Abbas H; Kiranmayee, S; Bammidi, Vk; Sultana, Asma

    2013-01-01

    Cubilin, (CUBN; also known as intrinsic factor-cobalamin receptor [Homo sapiens Entrez Pubmed ref NM_001081.3; NG_008967.1; GI: 119606627]), located in the epithelium of intestine and kidney acts as a receptor for intrinsic factor - vitamin B12 complexes. Mutations in CUBN may play a role in autosomal recessive megaloblastic anemia. The current study investigated the possible role of CUBN in evolution using phylogenetic testing. A total of 588 BLAST hits were found for the cubilin query sequence and these hits showed putative conserved domain, CUB superfamily (as on 27(th) Nov 2012). A first-pass phylogenetic tree was constructed to identify the taxa which most often contained the CUBN sequences. Following this, we narrowed down the search by manually deleting sequences which were not CUBN. A repeat phylogenetic analysis of 25 taxa was performed using PhyML, RAxML and TreeDyn softwares to confirm that CUBN is a conserved protein emphasizing its importance as an extracellular domain and being present in proteins mostly known to be involved in development in many chordate taxa but not found in prokaryotes, plants and yeast.. No horizontal gene transfers have been found between different taxa.

  16. Phylogenetic analysis of honey bee behavioral evolution.

    PubMed

    Raffiudin, Rika; Crozier, Ross H

    2007-05-01

    DNA sequences from three mitochondrial (rrnL, cox2, nad2) and one nuclear gene (itpr) from all 9 known honey bee species (Apis), a 10th possible species, Apis dorsata binghami, and three outgroup species (Bombus terrestris, Melipona bicolor and Trigona fimbriata) were used to infer Apis phylogenetic relationships using Bayesian analysis. The dwarf honey bees were confirmed as basal, and the giant and cavity-nesting species to be monophyletic. All nodes were strongly supported except that grouping Apis cerana with A. nigrocincta. Two thousand post-burnin trees from the phylogenetic analysis were used in a Bayesian comparative analysis to explore the evolution of dance type, nest structure, comb structure and dance sound within Apis. The ancestral honey bee species was inferred with high support to have nested in the open, and to have more likely than not had a silent vertical waggle dance and a single comb. The common ancestor of the giant and cavity-dwelling bees is strongly inferred to have had a buzzing vertical directional dance. All pairwise combinations of characters showed strong association, but the multiple comparisons problem reduces the ability to infer associations between states between characters. Nevertheless, a buzzing dance is significantly associated with cavity-nesting, several vertical combs, and dancing vertically, a horizontal dance is significantly associated with a nest with a single comb wrapped around the support, and open nesting with a single pendant comb and a silent waggle dance.

  17. A Distance Measure for Genome Phylogenetic Analysis

    NASA Astrophysics Data System (ADS)

    Cao, Minh Duc; Allison, Lloyd; Dix, Trevor

    Phylogenetic analyses of species based on single genes or parts of the genomes are often inconsistent because of factors such as variable rates of evolution and horizontal gene transfer. The availability of more and more sequenced genomes allows phylogeny construction from complete genomes that is less sensitive to such inconsistency. For such long sequences, construction methods like maximum parsimony and maximum likelihood are often not possible due to their intensive computational requirement. Another class of tree construction methods, namely distance-based methods, require a measure of distances between any two genomes. Some measures such as evolutionary edit distance of gene order and gene content are computational expensive or do not perform well when the gene content of the organisms are similar. This study presents an information theoretic measure of genetic distances between genomes based on the biological compression algorithm expert model. We demonstrate that our distance measure can be applied to reconstruct the consensus phylogenetic tree of a number of Plasmodium parasites from their genomes, the statistical bias of which would mislead conventional analysis methods. Our approach is also used to successfully construct a plausible evolutionary tree for the γ-Proteobacteria group whose genomes are known to contain many horizontally transferred genes.

  18. Erosion of phylogenetic signal in tunicate mitochondrial genomes on different levels of analysis.

    PubMed

    Stach, Thomas; Braband, Anke; Podsiadlowski, Lars

    2010-06-01

    The molecular phylogenetic position of Tunicata and internal interrelationship of higher tunicate taxa is controversial. High substitution rates and extreme gene order variability hamper phylogenetic analyses. We describe the sequence and organization of the mitochondrial genome of the aplousobranch ascidian Clavelina lepadiformis and use mitochondrial genomes to investigate phylogenetic information content on different molecular levels of comparison. Despite agreement in phylogenetic analyses of nucleotide and amino acid sequences, split analyses revealed little phylogenetic signal. Split analyses on molecular data sets deemed increasingly conservative, demonstrated that the lack of signal pervades all levels and that it is Tunicata the taxon of interest that introduces noise in the data sets. The strongest signal present in our molecular data sets as revealed by split analyses is not present in the optimal cladograms and supports a sister group relationship between cephalochordates and craniates. Phylogenetic analysis of gene order using common interval algorithms shows that phylogenetic signal is also eroded in respect of gene positions. Even functional constraints, such as partial gene overlap as exemplified in the case of the commonly observed adjacency between cox2 and cytb are subjected to homoplasy. However, rare phylogenetic events like this hold some promise to retain phylogenetic information even in such cases of extreme variability. We therefore caution to rely on sequence analysis alone and recommend investigation into the signal content of molecular data sets in order to assess the strength of phylogenetic signal.

  19. Phylogenetic analysis of diprotodontian marsupials based on complete mitochondrial genomes.

    PubMed

    Munemasa, Maruo; Nikaido, Masato; Donnellan, Stephen; Austin, Christopher C; Okada, Norihiro; Hasegawa, Masami

    2006-06-01

    Australidelphia is the cohort, originally named by Szalay, of all Australian marsupials and the South American Dromiciops. A lot of mitochondria and nuclear genome studies support the hypothesis of a monophyly of Australidelphia, but some familial relationships in Australidelphia are still unclear. In particular, the familial relationships among the order Diprotodontia (koala, wombat, kangaroos and possums) are ambiguous. These Diprotodontian families are largely grouped into two suborders, Vombatiformes, which contains Phascolarctidae (koala) and Vombatidae (wombat), and Phalangerida, which contains Macropodidae, Potoroidae, Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae. Morphological evidence and some molecular analyses strongly support monophyly of the two families in Vombatiformes. The monophyly of Phalangerida as well as the phylogenetic relationships of families in Phalangerida remains uncertain, however, despite searches for morphological synapomorphy and mitochondrial DNA sequence analyses. Moreover, phylogenetic relationships among possum families (Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae) as well as a sister group of Macropodoidea (Macropodidae and Potoroidae) remain unclear. To evaluate familial relationships among Dromiciops and Australian marsupials as well as the familial relationships in Diprotodontia, we determined the complete mitochondrial sequence of six Diprotodontian species. We used Maximum Likelihood analyses with concatenated amino acid and codon sequences of 12 mitochondrial protein genomes. Our analysis of mitochondria amino acid sequence supports monophyly of Australian marsupials+Dromiciops and monophyly of Phalangerida. The close relatedness between Macropodidae and Phalangeridae is also weakly supported by our analysis.

  20. Open Reading Frame Phylogenetic Analysis on the Cloud

    PubMed Central

    2013-01-01

    Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

  1. Molecular detection and phylogenetic analysis of bovine astrovirus in Brazil.

    PubMed

    Candido, Marcelo; Alencar, Anna Luiza Farias; Almeida-Queiroz, Sabrina R; Buzinaro, Maria da Glória; Munin, Flavia Simone; de Godoy, Silvia Helena Seraphin; Livonesi, Marcia Cristina; Fernandes, Andrezza Maria; de Sousa, Ricardo Luiz Moro

    2015-06-01

    Bovine astrovirus (BoAstV) is associated with gastroenterical disorders such as diarrhea, particularly in neonates and immunocompromised animals. Its prevalence is >60 % in the first five weeks of the animal's life. The aim of this study was to detect and perform a phylogenetic analysis of BoAstV in Brazilian cattle. A prevalence of 14.3 % of BoAstV in fecal samples from 272 head of cattle from different Brazilian states was detected, and 11 samples were analyzed by nucleotide sequencing. The majority of positive samples were obtained from diarrheic animals (p < 0.01). Phylogenetic analysis revealed that Brazilian samples were grouped in clades along with other BoAstV isolates. There was 74.3 %-96.5 % amino acid sequence similarity between the samples in this study and >74.8 % when compared with reference samples for enteric BoAstV. Our results indicate, for the first time, the occurrence of BoAstV circulation in cattle from different regions of Brazil, prevalently in diarrheic calves.

  2. [Phylogenetic analysis of bacteria of extreme ecosystems].

    PubMed

    Romanovskaia, V A; Parfenova, V V; Bel'kova, N L; Sukhanova, E V; Gladka, G V; Tashireva, A A

    2014-01-01

    Phylogenetic analysis of aerobic chemoorganotrophic bacteria of the two extreme regions (Dead Sea and West Antarctic) was performed on the basis of the nucleotide sequences of the 16S rRNA gene. Thermotolerant and halotolerant spore-forming bacteria 7t1 and 7t3 of terrestrial ecosystems Dead Sea identified as Bacillus licheniformis and B. subtilis subsp. subtilis, respectively. Taking into account remote location of thermotolerant strain 6t1 from closely related strains in the cluster Staphylococcus, 6t1 strain can be regarded as Staphylococcus sp. In terrestrial ecosystems, Galindez Island (Antarctic) detected taxonomically diverse psychrotolerant bacteria. From ornithogenic soil were isolated Micrococcus luteus O-1 and Microbacterium trichothecenolyticum O-3. Strains 4r5, 5r5 and 40r5, isolated from grass and lichens, can be referred to the genus Frondihabitans. These strains are taxonomically and ecologically isolated and on the tree diagram form the joint cluster with three isolates Frondihabitans sp., isolated from the lichen Austrian Alps, and psychrotolerant associated with plants F. cladoniiphilus CafT13(T). Isolates from black lichen in the different stationary observation points on the south side of a vertical cliff identified as: Rhodococcus fascians 181n3, Sporosarcina aquimarina O-7, Staphylococcus sp. 0-10. From orange biofilm of fouling on top of the vertical cliff isolated Arthrobacter sp. 28r5g1, from the moss-- Serratia sp. 6r1g. According to the results, Frondihabitans strains most frequently encountered among chemoorganotrophic aerobic bacteria in the Antarctic phytocenoses.

  3. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

    PubMed Central

    Jobb, Gangolf; von Haeseler, Arndt; Strimmer, Korbinian

    2004-01-01

    Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004) are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. Conclusions TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies. PMID:15222900

  4. A phylogenetic analysis of the phylum Fibrobacteres.

    PubMed

    Jewell, Kelsea A; Scott, Jarrod J; Adams, Sandra M; Suen, Garret

    2013-09-01

    Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches.

  5. Serologic and hexon phylogenetic analysis of ruminant adenoviruses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this study were to determine the antigenic relationship among ruminant adenoviruses and determine their phylogenetic relationship based on the deduced hexon gene amino acid sequence. Results of reciprocal cross-neutralization tests demonstrated antigenic relationships in either on...

  6. Exploration of phylogenetic data using a global sequence analysis method

    PubMed Central

    Chapus, Charles; Dufraigne, Christine; Edwards, Scott; Giron, Alain; Fertil, Bernard; Deschavanne, Patrick

    2005-01-01

    Background Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets. Results Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses – in particular explicit statements of homology inherent in character matrices – the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 γ-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers. Conclusion The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis. PMID:16280081

  7. Is the fatty acid composition of freshwater zoobenthic invertebrates controlled by phylogenetic or trophic factors?

    PubMed

    Makhutova, Olesia N; Sushchik, Nadezhda N; Gladyshev, Michail I; Ageev, Alexander V; Pryanichnikova, Ekaterina G; Kalachova, Galina S

    2011-08-01

    We studied the fatty acid (FA) content and composition of ten zoobenthic species of several taxonomic groups from different freshwater bodies. Special attention was paid to essential polyunsaturated fatty acids, eicosapentaenoic acid (EPA, 20:5n-3), docosahexaenoic acid (DHA, 22:6n-3), and arachidonic acid (ARA, 20:4n-6); and the n-3/n-6 and DHA/ARA ratios, which are important for consumers of higher trophic levels, i.e., fish. The content and ratios of these FA varied significantly in the studied zoobenthic species, consequently, the invertebrates were of different nutritional quality for fish. Eulimnogammarus viridis (Crustacea) and Dendrocoelopsis sp. (Turbellaria) had the highest nutrition value for fish concerning the content of EPA and DHA and n-3/n-6 and DHA/ARA ratios. Using canonical correspondence analysis we compared the FA profiles of species of the studied taxa taking into account their feeding strategies and habitats. We gained evidence that feeding strategy is of importance to determine fatty acid profiles of zoobenthic species. However, the phylogenetic position of the zoobenthic species is also responsible and may result in a similar fatty acid composition even if species or populations inhabit different water bodies or have different feeding strategies.

  8. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    ERIC Educational Resources Information Center

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  9. A phylogenetic analysis of the megadiverse Chalcidoidea (Hymenoptera)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chalcidoidea (Hymenoptera) are extremely diverse with an estimated 500,000 species. We present the first phylogenetic analysis of the superfamily based on a cladistic analysis of both morphological and molecular data. A total of 233 morphological characters were scored for 300 taxa and 265 genera, a...

  10. Kinetic and phylogenetic analysis of plant polyamine uptake transporters.

    PubMed

    Mulangi, Vaishali; Chibucos, Marcus C; Phuntumart, Vipaporn; Morris, Paul F

    2012-10-01

    The rice gene Polyamine Uptake Transporter1 (PUT1) was originally identified based on its homology to the polyamine uptake transporters LmPOT1 and TcPAT12 in Leishmania major and Trypanosoma cruzi, respectively. Here we show that five additional transporters from rice and Arabidopsis that cluster in the same clade as PUT1 all function as high affinity spermidine uptake transporters. Yeast expression assays of these genes confirmed that uptake of spermidine was minimally affected by 166 fold or greater concentrations of amino acids. Characterized polyamine transporters from both Arabidopsis thaliana and Oryza sativa along with the two polyamine transporters from L. major and T. cruzi were aligned and used to generate a hidden Markov model. This model was used to identify significant matches to proteins in other angiosperms, bryophytes, chlorophyta, discicristates, excavates, stramenopiles and amoebozoa. No significant matches were identified in fungal or metazoan genomes. Phylogenic analysis showed that some sequences from the haptophyte, Emiliania huxleyi, as well as sequences from oomycetes and diatoms clustered closer to sequences from plant genomes than from a homologous sequence in the red algal genome Galdieria sulphuraria, consistent with the hypothesis that these polyamine transporters were acquired by horizontal transfer from green algae. Leishmania and Trypansosoma formed a separate cluster with genes from other Discicristates and two Entamoeba species. We surmise that the genes in Entamoeba species were acquired by phagotrophy of Discicristates. In summary, phylogenetic and functional analysis has identified two clades of genes that are predictive of polyamine transport activity.

  11. The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis.

    PubMed

    Perseke, Marleen; Hankeln, Thomas; Weich, Bettina; Fritzsch, Guido; Stadler, Peter F; Israelsson, Olle; Bernhard, Detlef; Schlegel, Martin

    2007-08-01

    The phylogenetic position of Xenoturbella bocki has been a matter of controversy since its description in 1949. We sequenced a second complete mitochondrial genome of this species and performed phylogenetic analyses based on the amino acid sequences of all 13 mitochondrial protein-coding genes and on its gene order. Our results confirm the deuterostome relationship of Xenoturbella. However, in contrast to a recently published study (Bourlat et al. in Nature 444:85-88, 2006), our data analysis suggests a more basal branching of Xenoturbella within the deuterostomes, rather than a sister-group relationship to the Ambulacraria (Hemichordata and Echinodermata).

  12. A Deliberate Practice Approach to Teaching Phylogenetic Analysis

    ERIC Educational Resources Information Center

    Hobbs, F. Collin; Johnson, Daniel J.; Kearns, Katherine D.

    2013-01-01

    One goal of postsecondary education is to assist students in developing expert-level understanding. Previous attempts to encourage expert-level understanding of phylogenetic analysis in college science classrooms have largely focused on isolated, or "one-shot," in-class activities. Using a deliberate practice instructional approach, we…

  13. Active Ammonia Oxidizers in an Acidic Soil Are Phylogenetically Closely Related to Neutrophilic Archaeon

    PubMed Central

    Wang, Baozhan; Zheng, Yan; Huang, Rong; Zhou, Xue; Wang, Dongmei; He, Yuanqiu

    2014-01-01

    All cultivated ammonia-oxidizing archaea (AOA) within the Nitrososphaera cluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence of Nitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth of Nitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of amoA genes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that 13CO2 assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both 13C-labeled amoA and 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strains Nitrososphaera viennensis EN76 and JG1 within the Nitrososphaera cluster. Our results provide strong evidence for the adaptive growth of Nitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated. PMID:24375137

  14. A Deliberate Practice Approach to Teaching Phylogenetic Analysis

    PubMed Central

    Hobbs, F. Collin; Johnson, Daniel J.; Kearns, Katherine D.

    2013-01-01

    One goal of postsecondary education is to assist students in developing expert-level understanding. Previous attempts to encourage expert-level understanding of phylogenetic analysis in college science classrooms have largely focused on isolated, or “one-shot,” in-class activities. Using a deliberate practice instructional approach, we designed a set of five assignments for a 300-level plant systematics course that incrementally introduces the concepts and skills used in phylogenetic analysis. In our assignments, students learned the process of constructing phylogenetic trees through a series of increasingly difficult tasks; thus, skill development served as a framework for building content knowledge. We present results from 5 yr of final exam scores, pre- and postconcept assessments, and student surveys to assess the impact of our new pedagogical materials on student performance related to constructing and interpreting phylogenetic trees. Students improved in their ability to interpret relationships within trees and improved in several aspects related to between-tree comparisons and tree construction skills. Student feedback indicated that most students believed our approach prepared them to engage in tree construction and gave them confidence in their abilities. Overall, our data confirm that instructional approaches implementing deliberate practice address student misconceptions, improve student experiences, and foster deeper understanding of difficult scientific concepts. PMID:24297294

  15. A deliberate practice approach to teaching phylogenetic analysis.

    PubMed

    Hobbs, F Collin; Johnson, Daniel J; Kearns, Katherine D

    2013-01-01

    One goal of postsecondary education is to assist students in developing expert-level understanding. Previous attempts to encourage expert-level understanding of phylogenetic analysis in college science classrooms have largely focused on isolated, or "one-shot," in-class activities. Using a deliberate practice instructional approach, we designed a set of five assignments for a 300-level plant systematics course that incrementally introduces the concepts and skills used in phylogenetic analysis. In our assignments, students learned the process of constructing phylogenetic trees through a series of increasingly difficult tasks; thus, skill development served as a framework for building content knowledge. We present results from 5 yr of final exam scores, pre- and postconcept assessments, and student surveys to assess the impact of our new pedagogical materials on student performance related to constructing and interpreting phylogenetic trees. Students improved in their ability to interpret relationships within trees and improved in several aspects related to between-tree comparisons and tree construction skills. Student feedback indicated that most students believed our approach prepared them to engage in tree construction and gave them confidence in their abilities. Overall, our data confirm that instructional approaches implementing deliberate practice address student misconceptions, improve student experiences, and foster deeper understanding of difficult scientific concepts.

  16. Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily

    PubMed Central

    Lakshmi, Balasubramanian; Mishra, Madhulika; Srinivasan, Narayanaswamy; Archunan, Govindaraju

    2015-01-01

    Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity. PMID:26263546

  17. A novel primary bile acid in the Shoebill stork and herons and its phylogenetic significance.

    PubMed

    Hagey, L R; Schteingart, C D; Ton-Nu, H-T; Hofmann, A F

    2002-05-01

    The Shoebill stork, an enigma phylogenetically, was found to contain as its dominant biliary bile acid 16alpha-hydroxychenodeoxycholic acid, a heretofore undescribed bile acid. The bile acid occurred as its taurine N-acyl amidate; structure was established by nuclear magnetic resonance (NMR) and mass spectrometry (MS). A search for this novel bile acid in other Ciconiiformes showed that it constituted >92% of biliary bile acids in five of nine herons in the Ardidae, but was absent in all other families (Ciconiidae, Threskiornithidae, Scopidae, Phoenicopteridae). The presence of this biochemical trait in the Shoebill stork and certain herons suggests that these birds are closely related.

  18. Phylogenetic and Recombination Analysis of Tomato Spotted Wilt Virus

    PubMed Central

    Yu, Jisuk; Kim, Mi-Kyeong; Choi, Hong-Soo; Kim, Kook-Hyung

    2013-01-01

    Tomato spotted wilt virus (TSWV) severely damages and reduces the yield of many economically important plants worldwide. In this study, we determined the whole-genome sequences of 10 TSWV isolates recently identified from various regions and hosts in Korea. Phylogenetic analysis of these 10 isolates as well as the three previously sequenced isolates indicated that the 13 Korean TSWV isolates could be divided into two groups reflecting either two different origins or divergences of Korean TSWV isolates. In addition, the complete nucleotide sequences for the 13 Korean TSWV isolates along with previously sequenced TSWV RNA segments from Korea and other countries were subjected to phylogenetic and recombination analysis. The phylogenetic analysis indicated that both the RNA L and RNA M segments of most Korean isolates might have originated in Western Europe and North America but that the RNA S segments for all Korean isolates might have originated in China and Japan. Recombination analysis identified a total of 12 recombination events among all isolates and segments and five recombination events among the 13 Korea isolates; among the five recombinants from Korea, three contained the whole RNA L segment, suggesting reassortment rather than recombination. Our analyses provide evidence that both recombination and reassortment have contributed to the molecular diversity of TSWV. PMID:23696821

  19. Mesoamerican tree squirrels evolution (Rodentia: Sciuridae): a molecular phylogenetic analysis.

    PubMed

    Villalobos, Federico; Gutierrez-Espeleta, Gustavo

    2014-06-01

    The tribe Sciurini comprehends the genera Sciurus, Syntheosiurus, Microsciurus, Tamiasciurus and Rheinthrosciurus. The phylogenetic relationships within Sciurus have been only partially done, and the relationship between Mesoamerican species remains unsolved. The phylogenetic relationships of the Mesoamerican tree squirrels were examined using molecular data. Sequence data publicly available (12S, 16S, CYTB mitochondrial genes and IRBP nuclear gene) and cytochrome B gene sequences of four previously not sampled Mesoamerican Sciurus species were analyzed under a Bayesian multispecies coalescence model. Phylogenetic analysis of the multilocus data set showed the neotropical tree squirrels as a monophyletic clade. The genus Sciurus was paraphyletic due to the inclusion of Microsciurus species (M. alfari and M. flaviventer). The South American species S. aestuans and S. stramineus showed a sister taxa relationship. Single locus analysis based on the most compact and complete data set (i.e. CYTB gene sequences), supported the monophyly of the South American species and recovered a Mesoamerican clade including S. aureogaster, S. granatensis and S. variegatoides. These results corroborated previous findings based on cladistic analysis of cranial and post-cranial characters. Our data support a close relationship between Mesoamerican Sciurus species and a sister relationship with South American species, and corroborates previous findings in relation to the polyphyly of Microsciurus and Syntheosciurus paraphyly.

  20. Effects of Abiotic Factors on the Phylogenetic Diversity of Bacterial Communities in Acidic Thermal Springs▿

    PubMed Central

    Mathur, Jayanti; Bizzoco, Richard W.; Ellis, Dean G.; Lipson, David A.; Poole, Alexander W.; Levine, Richard; Kelley, Scott T.

    2007-01-01

    Acidic thermal springs offer ideal environments for studying processes underlying extremophile microbial diversity. We used a carefully designed comparative analysis of acidic thermal springs in Yellowstone National Park to determine how abiotic factors (chemistry and temperature) shape acidophile microbial communities. Small-subunit rRNA gene sequences were PCR amplified, cloned, and sequenced, by using evolutionarily conserved bacterium-specific primers, directly from environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Energy-dispersive X-ray spectroscopy, X-ray diffraction, and colorimetric assays were used to analyze sediment chemistry, while an optical emission spectrometer was used to evaluate water chemistry and electronic probes were used to measure the pH, temperature, and Eh of the spring waters. Phylogenetic-statistical analyses found exceptionally strong correlations between bacterial community composition and sediment mineral chemistry, followed by weaker but significant correlations with temperature gradients. For example, sulfur-rich sediment samples contained a high diversity of uncultured organisms related to Hydrogenobaculum spp., while iron-rich sediments were dominated by uncultured organisms related to a diverse array of gram-positive iron oxidizers. A detailed analysis of redox chemistry indicated that the available energy sources and electron acceptors were sufficient to support the metabolic potential of Hydrogenobaculum spp. and iron oxidizers, respectively. Principal-component analysis found that two factors explained 95% of the genetic diversity, with most of the variance attributable to mineral chemistry and a smaller fraction attributable to temperature. PMID:17220248

  1. Phylogenetic, Molecular, and Biochemical Characterization of Caffeic Acid o-Methyltransferase Gene Family in Brachypodium distachyon

    PubMed Central

    Wu, Xianting; Wu, Jiajie; Luo, Yangfan; Bragg, Jennifer; Anderson, Olin; Vogel, John; Gu, Yong Q.

    2013-01-01

    Caffeic acid o-methyltransferase (COMT) is one of the important enzymes controlling lignin monomer production in plant cell wall synthesis. Analysis of the genome sequence of the new grass model Brachypodium distachyon identified four COMT gene homologs, designated as BdCOMT1, BdCOMT2, BdCOMT3, and BdCOMT4. Phylogenetic analysis suggested that they belong to the COMT gene family, whereas syntenic analysis through comparisons with rice and sorghum revealed that BdCOMT4 on Chromosome 3 is the orthologous copy of the COMT genes well characterized in other grass species. The other three COMT genes are unique to Brachypodium since orthologous copies are not found in the collinear regions of rice and sorghum genomes. Expression studies indicated that all four Brachypodium COMT genes are transcribed but with distinct patterns of tissue specificity. Full-length cDNAs were cloned in frame into the pQE-T7 expression vector for the purification of recombinant Brachypodium COMT proteins. Biochemical characterization of enzyme activity and substrate specificity showed that BdCOMT4 has significant effect on a broad range of substrates with the highest preference for caffeic acid. The other three COMTs had low or no effect on these substrates, suggesting that a diversified evolution occurred on these duplicate genes that not only impacted their pattern of expression, but also altered their biochemical properties. PMID:23431288

  2. Phylogenetic analysis of ALAD and MGP genes related to lead toxicity.

    PubMed

    Shaik, A P; Khan, M; Jamil, K

    2009-07-01

    Experimental studies in our laboratory have established the role of delta-aminolevulinic acid dehydratase (ALAD) and matrix gamma-carboxyglutamic acid (MGP) gene polymorphisms in the etiology of lead toxicity. Polymorphisms in these genes influenced the levels of lead in subjects exposed to this metal. In extension to our studies, we aimed to investigate the possible role of these proteins in evolution by studying the phylogenetic relationship and divergence of ALAD and MGP genes using computational phylogenetic methods. The human ALAD and MGP protein sequences from various species were retrieved from Swiss-Prot database and were compared using Basic Local Alignment Search Tool. Multiple sequence alignment was carried out using ClustalW with defaults, and phylogenetic trees for both the genes were built using neighbor-joining method as in Mega software. Our study indicated that ALAD is a highly conserved protein with the same metal binding site distributed in all the phyla (from archaea to chordates). Phylogenetic analysis of MGP gene revealed that it had an important role in the evolution of endogenous skeleton in contrast to exoskeleton of insects. Occurrence of these genes in evolution with conserved metal binding sites strengthens the role of ALAD and MGP genes in regulating heme biosynthesis and mineralization, respectively, in evolution and helps in better understanding of lead poisoning.

  3. Analysis of diversification: combining phylogenetic and taxonomic data.

    PubMed Central

    Paradis, Emmanuel

    2003-01-01

    The estimation of diversification rates using phylogenetic data has attracted a lot of attention in the past decade. In this context, the analysis of incomplete phylogenies (e.g. phylogenies resolved at the family level but unresolved at the species level) has remained difficult. I present here a likelihood-based method to combine partly resolved phylogenies with taxonomic (species-richness) data to estimate speciation and extinction rates. This method is based on fitting a birth-and-death model to both phylogenetic and taxonomic data. Some examples of the method are presented with data on birds and on mammals. The method is compared with existing approaches that deal with incomplete phylogenies. Some applications and generalizations of the approach introduced in this paper are further discussed. PMID:14667342

  4. [A phylogenetic analysis of plant communities of Teberda Biosphere Reserve].

    PubMed

    Shulakov, A A; Egorov, A V; Onipchenko, V G

    2016-01-01

    Phylogenetic analysis of communities is based on the comparison of distances on the phylogenetic tree between species of a community under study and those distances in random samples taken out of local flora. It makes it possible to determine to what extent a community composition is formed by more closely related species (i.e., "clustered") or, on the opposite, it is more even and includes species that are less related with each other. The first case is usually interpreted as a result of strong influence caused by abiotic factors, due to which species with similar ecology, a priori more closely related, would remain: In the second case, biotic factors, such as competition, may come to the fore and lead to forming a community out of distant clades due to divergence of their ecological niches: The aim of this' study Was Ad explore the phylogenetic structure in communities of the northwestern Caucasus at two spatial scales - the scale of area from 4 to 100 m2 and the smaller scale within a community. The list of local flora of the alpine belt has been composed using the database of geobotanic descriptions carried out in Teberda Biosphere Reserve at true altitudes exceeding.1800 m. It includes 585 species of flowering plants belonging to 57 families. Basal groups of flowering plants are.not represented in the list. At the scale of communities of three classes, namely Thlaspietea rotundifolii - commumties formed on screes and pebbles, Calluno-Ulicetea - alpine meadow, and Mulgedio-Aconitetea subalpine meadows, have not demonstrated significant distinction of phylogenetic structure. At intra level, for alpine meadows the larger share of closely related species. (clustered community) is detected. Significantly clustered happen to be those communities developing on rocks (class Asplenietea trichomanis) and alpine (class Juncetea trifidi). At the same time, alpine lichen proved to have even phylogenetic structure at the small scale. Alpine (class Salicetea herbaceae) that

  5. Poly (beta-L-malic acid) production by diverse phylogenetic clades of Aureobasidium pullulans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Poly (beta-L-malic acid) (PMA) is a natural biopolyester that has pharmaceutical applications and other potential uses. Here we examine PMA production by genetically diverse phylogenetic clades of the fungus A. pullulans. Thirty-six strains of A. pullulans were isolated for this study from various...

  6. Phylogenetic analysis reveals a scattered distribution of autumn colours

    PubMed Central

    Archetti, Marco

    2009-01-01

    Background and Aims Leaf colour in autumn is rarely considered informative for taxonomy, but there is now growing interest in the evolution of autumn colours and different hypotheses are debated. Research efforts are hindered by the lack of basic information: the phylogenetic distribution of autumn colours. It is not known when and how autumn colours evolved. Methods Data are reported on the autumn colours of 2368 tree species belonging to 400 genera of the temperate regions of the world, and an analysis is made of their phylogenetic relationships in order to reconstruct the evolutionary origin of red and yellow in autumn leaves. Key Results Red autumn colours are present in at least 290 species (70 genera), and evolved independently at least 25 times. Yellow is present independently from red in at least 378 species (97 genera) and evolved at least 28 times. Conclusions The phylogenetic reconstruction suggests that autumn colours have been acquired and lost many times during evolution. This scattered distribution could be explained by hypotheses involving some kind of coevolutionary interaction or by hypotheses that rely on the need for photoprotection. PMID:19126636

  7. Phylogenetic analysis of uroporphyrinogen III synthase (UROS) gene.

    PubMed

    Shaik, Abjal Pasha; Alsaeed, Abbas H; Sultana, Asma

    2012-01-01

    The uroporphyrinogen III synthase (UROS) enzyme (also known as hydroxymethylbilane hydrolyase) catalyzes the cyclization of hydroxymethylbilane to uroporphyrinogen III during heme biosynthesis. A deficiency of this enzyme is associated with the very rare Gunther's disease or congenital erythropoietic porphyria, an autosomal recessive inborn error of metabolism. The current study investigated the possible role of UROS (Homo sapiens [EC: 4.2.1.75; 265 aa; 1371 bp mRNA; Entrez Pubmed ref NP_000366.1, NM_000375.2]) in evolution by studying the phylogenetic relationship and divergence of this gene using computational methods. The UROS protein sequences from various taxa were retrieved from GenBank database and were compared using Clustal-W (multiple sequence alignment) with defaults and a first-pass phylogenetic tree was built using neighbor-joining method as in DELTA BLAST 2.2.27+ version. A total of 163 BLAST hits were found for the uroporphyrinogen III synthase query sequence and these hits showed putative conserved domain, HemD superfamily (as on 14(th) Nov 2012). We then narrowed down the search by manually deleting the proteins which were not UROS sequences and sequences belonging to phyla other than Chordata were deleted. A repeat phylogenetic analysis of 39 taxa was performed using PhyML and TreeDyn software to confirm that UROS is a highly conserved protein with approximately 85% conserved sequences in almost all chordate taxons emphasizing its importance in heme synthesis.

  8. Phylogenetic analysis of Mexican Babesia bovis isolates using msa and ssrRNA gene sequences.

    PubMed

    Genis, Alma D; Mosqueda, Juan J; Borgonio, Verónica M; Falcón, Alfonso; Alvarez, Antonio; Camacho, Minerva; de Lourdes Muñoz, Maria; Figueroa, Julio V

    2008-12-01

    Variable merozoite surface antigens of Babesia bovis are exposed glycoproteins having a role in erythrocyte invasion. Members of this gene family include msa-1 and msa-2 (msa-2c, msa-2a(1), msa-2a(2), and msa-2b). Small subunit ribosomal (ssr)RNA gene is subject to evolutive pressure and has been used in phylogenetic studies. To determine the phylogenetic relationship among B. bovis Mexican isolates using different genetic markers, PCR amplicons, corresponding to msa-1, msa-2c, msa-2b, and ssrRNA genes, were cloned and plasmids carrying the corresponding inserts were sequenced. Comparative analysis of nucleotide and deduced amino acid sequences revealed distinct degrees of variability and identity among the coding gene sequences obtained from 12 geographically different B. bovis isolates and a reference strain. Overall sequence identities of 47.7%, 72.3%, 87.7%, and 94% were determined for msa-1, msa-2b, msa-2c, and ssrRNA, respectively. A robust phylogenetic tree was obtained with msa-2b sequences. The phylogenetic analysis suggests that Mexican B. bovis isolates group in clades not concordant with the Mexican geography. However, the Mexican isolates group together in an American clade separated from the Australian clade. Sequence heterogeneity in msa-1, msa-2b, and msa-2c coding regions of Mexican B. bovis isolates present in different geographical regions can be a result of either differential evolutive pressure or cattle movement from commercial trade.

  9. Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses.

    PubMed

    Masta, Susan E; Longhorn, Stuart J; Boore, Jeffrey L

    2009-01-01

    Phylogenetic analyses based on mitochondrial DNA have yielded widely differing relationships among members of the arthropod lineage Arachnida, depending on the nucleotide coding schemes and models of evolution used. We enhanced taxonomic coverage within the Arachnida greatly by sequencing seven new arachnid mitochondrial genomes from five orders. We then used all 13 mitochondrial protein-coding genes from these genomes to evaluate patterns of nucleotide and amino acid biases. Our data show that two of the six orders of arachnids (spiders and scorpions) have experienced shifts in both nucleotide and amino acid usage in all their protein-coding genes, and that these biases mislead phylogeny reconstruction. These biases are most striking for the hydrophobic amino acids isoleucine and valine, which appear to have evolved asymmetrical exchanges in response to shifts in nucleotide composition. To improve phylogenetic accuracy based on amino acid differences, we tested two recoding methods: (1) removing all isoleucine and valine sites and (2) recoding amino acids based on their physiochemical properties. We find that these methods yield phylogenetic trees that are consistent in their support of ancient intraordinal divergences within the major arachnid lineages. Further refinement of amino acid recoding methods may help us better delineate interordinal relationships among these diverse organisms.

  10. Sequence and phylogenetic analysis of M-class genome segments of novel duck reovirus NP03

    PubMed Central

    Wang, Shao; Chen, Shilong; Cheng, Xiaoxia; Chen, Shaoying; Lin, FengQiang; Jiang, Bing; Zhu, Xiaoli; Li, Zhaolong; Wang, Jinxiang

    2015-01-01

    We report the sequence and phylogenetic analysis of the entire M1, M2, and M3 genome segments of the novel duck reovirus (NDRV) NP03. Alignment between the newly determined nucleotide sequences as well as their deduced amino acid sequences and the published sequences of avian reovirus (ARV) was carried out with DNASTAR software. Sequence comparison showed that the M2 gene had the most variability among the M-class genes of DRV. Phylogenetic analysis of the M-class genes of ARV strains revealed different lineages and clusters within DRVs. The 5 NDRV strains used in this study fall into a well-supported lineage that includes chicken ARV strains, whereas Muscovy DRV (MDRV) strains are separate from NDRV strains and form a distinct genetic lineage in the M2 gene tree. However, the MDRV and NDRV strains are closely related and located in a common lineage in the M1 and M3 gene trees, respectively. PMID:25852231

  11. Genomic characterization and phylogenetic analysis of Chinese sacbrood virus isolated from Loess Plateau, China.

    PubMed

    Yu, H; Liu, T X; Wang, D

    2016-09-23

    The complete genomic RNA of the Chinese sacbrood virus (CSBV) strain, which infects the honeybees in the Loess plateau, was sequenced and analyzed. The CSBV-SX strain contains 8705 nucleotides, which includes a single large open reading frame (99-8681 nucleotides) encoding 2860 amino acids. A novel efficient identification method was used to investigate the samples infected by CSBV. The putative amino acid sequence alignment analysis showed that, except for some normal well characterized domains such as RNA helicase, RNA protease, and RNA-dependent RNA polymerase domains, a calicivirus coat protein domain was identified at amino acids 493-564. Phylogenetic analysis indicated that CSBV-SX was closely related to CSBV-BJ, and this result was supported by nucleotide multiple sequence alignment and protein multiple sequence alignment analysis results. These differences in the CSBV-SX strain may be related to virus adaptation to the xerothermic, low relative humidity, and strong ultraviolet radiation conditions in the Loess Plateau.

  12. Phylogenetic analysis of a transfusion-transmitted hepatitis A outbreak.

    PubMed

    Hettmann, Andrea; Juhász, Gabriella; Dencs, Ágnes; Tresó, Bálint; Rusvai, Erzsébet; Barabás, Éva; Takács, Mária

    2017-02-01

    A transfusion-associated hepatitis A outbreak was found in the first time in Hungary. The outbreak involved five cases. Parenteral transmission of hepatitis A is rare, but may occur during viraemia. Direct sequencing of nested PCR products was performed, and all the examined samples were identical in the VP1/2A region of the hepatitis A virus genome. HAV sequences found in recent years were compared and phylogenetic analysis showed that the strain which caused these cases is the same as that had spread in Hungary recently causing several hepatitis A outbreaks throughout the country.

  13. Detecting Network Communities: An Application to Phylogenetic Analysis

    PubMed Central

    Andrade, Roberto F. S.; Rocha-Neto, Ivan C.; Santos, Leonardo B. L.; de Santana, Charles N.; Diniz, Marcelo V. C.; Lobão, Thierry Petit; Goés-Neto, Aristóteles; Pinho, Suani T. R.; El-Hani, Charbel N.

    2011-01-01

    This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (>70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis. PMID:21573202

  14. Phylogenetic analysis and characterization of Korean bovine viral diarrhea viruses.

    PubMed

    Oem, Jae-Ku; Hyun, Bang-Hun; Cha, Sang-Ho; Lee, Kyoung-Ki; Kim, Seong-Hee; Kim, Hye-Ryoung; Park, Choi-Kyu; Joo, Yi-Seok

    2009-11-18

    Thirty-six bovine viral disease viruses (BVDVs) were identified in bovine feces (n=16), brains (n=2), and aborted fetuses (n=18) in Korea. To reveal the genetic diversity and characteristics of these Korean strains, the sequences of their 5'-untranslated regions (5'-UTRs) were determined and then compared with published reference sequences. Neighbor-joining phylogenetic analysis revealed that most of the Korean viruses were of the BVDV subtypes 1a (n=17) or 2a (n=17). The remaining strains were of subtypes 1b (n=1) and 1n (n=1). This analysis indicates that the 1a and 2a BVDV subtypes are predominant and widespread in Korea. In addition, the prevalence of BVDV-2 was markedly higher in aborted fetuses than in other samples and was more often associated with reproductive problems and significant mortality in cattle.

  15. Phylogenetic analysis of cichlid fishes using nuclear DNA markers.

    PubMed

    Sültmann, H; Mayer, W E; Figueroa, F; Tichy, H; Klein, J

    1995-11-01

    The recent explosive adaptive radiation of cichlids in the great lakes of Africa has attracted the attention of both morphologists and molecular biologists. To decipher the phylogenetic relationships among the various taxa within the family Cichlidae is a prerequisite for answering some fundamental questions about the nature of the speciation process. In the present study, we used the random amplification of polymorphic DNA (RAPD) technique to obtain sequence differences between selected cichlid species. We then designed specific primers based on these sequences and used them to amplify template DNA from a large number of species by the polymerase chain reaction (PCR). We sequenced the amplified products and searched the sequences for indels and shared substitutions. We identified a number of such characters at three loci--DXTU1, DXTU2, and DXTU3--and used them for phylogenetic and cladistic analysis of the relationships among the various cichlid groups. Our studies assign an outgroup position to Neotropical cichlids in relation to African cichlids, provide evidence for a sister-group relationship of tilapiines to the haplochromines, group Cyphotilapia frontosa with the lamprologines of Lake Tanganyika, place Astatoreochromis alluaudi to an outgroup position with respect to other haplochromines of Lakes Victoria and Malawi, and provide additional support for the monophyly of the remaining Lake Victoria haplochromines and the Lake Malawi haplochromines. The described approach holds great promise for further resolution of cichlid phylogeny.

  16. A phylogenetic transform enhances analysis of compositional microbiota data

    PubMed Central

    Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A

    2017-01-01

    Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities. DOI: http://dx.doi.org/10.7554/eLife.21887.001 PMID:28198697

  17. Phylogenetic analysis of the Argonaute protein family in platyhelminths.

    PubMed

    Zheng, Yadong

    2013-03-01

    Argonaute proteins (AGOs) are mediators of gene silencing via recruitment of small regulatory RNAs to induce translational regression or degradation of targeted molecules. Platyhelminths have been reported to express microRNAs but the diversity of AGOs in the phylum has not been explored. Phylogenetic relationships of members of this protein family were studied using data from six platyhelminth genomes. Phylogenetic analysis showed that all cestode and trematode AGOs, along with some triclad planarian AGOs, were grouped into the Ago subfamily and its novel sister clade, here referred to as Cluster 1. These were very distant from Piwi and Class 3 subfamilies. By contrast, a number of planarian Piwi-like AGOs formed a novel sister clade to the Piwi subfamily. Extensive sequence searching revealed the presence of an additional locus for AGO2 in the cestode Echinococcus granulosus and exon expansion in this species and E. multilocularis. The current study suggests the absence of the Piwi subfamily and Class 3 AGOs in cestodes and trematodes and the Piwi-like AGO expansion in a free-living triclad planarian and the occurrence of exon expansion prior to or during the evolution of the most-recent common ancestor of the Echinococcus species studied.

  18. Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria

    USGS Publications Warehouse

    Lonergan, D.J.; Jenter, H.L.; Coates, J.D.; Phillips, E.J.P.; Schmidt, T.M.; Lovley, D.R.

    1996-01-01

    Evolutionary relationships among strictly anaerobic dissimilatory Fe(III)- reducing bacteria obtained from a diversity of sedimentary environments were examined by phylogenetic analysis of 16S rRNA gene sequences. Members of the genera Geobacter, Desulfuromonas, Pelobacter, and Desulfuromusa formed a monophyletic group within the delta subdivision of the class Proteobacteria. On the basis of their common ancestry and the shared ability to reduce Fe(III) and/or S0, we propose that this group be considered a single family, Geobacteraceae. Bootstrap analysis, characteristic nucleotides, and higher- order secondary structures support the division of Geobacteraceae into two subgroups, designated the Geobacter and Desulfuromonas clusters. The genus Desulfuromusa and Pelobacter acidigallici make up a distinct branch with the Desulfuromonas cluster. Several members of the family Geobacteraceae, none of which reduce sulfate, were found to contain the target sequences of probes that have been previously used to define the distribution of sulfate-reducing bacteria and sulfate-reducing bacterium-like microorganisms. The recent isolations of Fe(III)-reducing microorganisms distributed throughout the domain Bacteria suggest that development of 16S rRNA probes that would specifically target all Fe(III) reducers may not be feasible. However, all of the evidence suggests that if a 16S rRNA sequence falls within the family Geobacteraceae, then the organism has the capacity for Fe(III) reduction. The suggestion, based on geological evidence, that Fe(III) reduction was the first globally significant process for oxidizing organic matter back to carbon dioxide is consistent with the finding that acetate-oxidizing Fe(III) reducers are phylogenetically diverse.

  19. Phylogenetic and Structural Analysis of Polyketide Synthases in Aspergilli

    PubMed Central

    Bhetariya, Preetida J.; Prajapati, Madhvi; Bhaduri, Asani; Mandal, Rahul Shubhra; Varma, Anupam; Madan, Taruna; Singh, Yogendra; Sarma, P. Usha

    2016-01-01

    Polyketide synthases (PKSs) of Aspergillus species are multidomain and multifunctional megaenzymes that play an important role in the synthesis of diverse polyketide compounds. Putative PKS protein sequences from Aspergillus species representing medically, agriculturally, and industrially important Aspergillus species were chosen and screened for in silico studies. Six candidate Aspergillus species, Aspergillus fumigatus Af293, Aspergillus flavus NRRL3357, Aspergillus niger CBS 513.88, Aspergillus terreus NIH2624, Aspergillus oryzae RIB40, and Aspergillus clavatus NRRL1, were selected to study the PKS phylogeny. Full-length PKS proteins and only ketosynthase (KS) domain sequence were retrieved for independent phylogenetic analysis from the aforementioned species, and phylogenetic analysis was performed with characterized fungal PKS. This resulted into grouping of Aspergilli PKSs into nonreducing (NR), partially reducing (PR), and highly reducing (HR) PKS enzymes. Eight distinct clades with unique domain arrangements were classified based on homology with functionally characterized PKS enzymes. Conserved motif signatures corresponding to each type of PKS were observed. Three proteins from Protein Data Bank corresponding to NR, PR, and HR type of PKS (XP_002384329.1, XP_753141.2, and XP_001402408.2, respectively) were selected for mapping of conserved motifs on three-dimensional structures of KS domain. Structural variations were found at the active sites on modeled NR, PR, and HR enzymes of Aspergillus. It was observed that the number of iteration cycles was dependent on the size of the cavity in the active site of the PKS enzyme correlating with a type with reducing or NR products, such as pigment, 6MSA, and lovastatin. The current study reports the grouping and classification of PKS proteins of Aspergilli for possible exploration of novel polyketides based on sequence homology; this information can be useful for selection of PKS for polyketide exploration and

  20. Genomic structure of the luciferase gene and phylogenetic analysis in the Hotaria-group fireflies.

    PubMed

    Choi, Yong Soo; Bae, Jin Sik; Lee, Kwang Sik; Kim, Seong Ryul; Kim, Iksoo; Kim, Jong Gill; Kim, Keun Young; Kim, Sam Eun; Suzuki, Hirobumi; Lee, Sang Mong; Sohn, Hung Dae; Jin, Byung Rae

    2003-02-01

    The luminescent fireflies have species specific flash patterns, being recognized as sexual communication. The luciferase gene is the sole enzyme responsible for bioluminescence. We describe here the complete nucleotide sequence and the exon-intron structure of the luciferase gene of the Hotaria-group fireflies, H. unmunsana, H. papariensis and H. tsushimana. The luciferase gene of the Hotaria-group firefly including the known H. parvula spans 1950 bp and consisted of six introns and seven exons coding for 548 amino acid residues, suggesting highly conserved structure among the Hotaria-group fireflies. Although only one luciferase gene was cloned from H. papariensis, each of the two sequences of the gene was found in H. unmunsana (U1 and Uc) and H. tsushimana (T1 and T2). The amino acid sequence divergence among H. unmunsana, H. papariensis, and H. tsushimana only ranged from zero to three amino acid residues, but H. parvula differed by 10-11 amino acid residues from the other Hotaria-group fireflies, suggesting a divergent relationship of this species. Phylogenetic analysis using the deduced amino acid sequences of the luciferase gene resulted in a monophyletic group in the Hotaria excluding H. parvula, suggesting a close relationship among H. unmunsana, H. papariensis and H. tsushimana. Additionally, we also analyzed the mitochondrial cytochrome oxidase I (COI) gene of the Hotaria-group fireflies. The deduced amino acid sequence of the COI gene of H. unmunsana was identical to that of H. papariensis and H. tsushimana, but different by three positions from H. parvula. In terms of nucleotide sequences of the COI gene, intraspecific sequence divergence was sometimes larger than interspecies level, and phylogenetic analysis placed the three species into monophyletic groups unresolved among them, but excluded H. parvula. In conclusion, our results suggest that H. unmunsana, H. papariensis and H. tsushimana are very closely related or might be an identical species, at

  1. Culturable and molecular phylogenetic diversity of microorganisms in an open-dumped, extremely acidic Pb/Zn mine tailings.

    PubMed

    Tan, Gui-Liang; Shu, Wen-Sheng; Hallberg, Kevin B; Li, Fang; Lan, Chong-Yu; Zhou, Wen-Hua; Huang, Li-Nan

    2008-09-01

    A combination of cultivation-based and molecular-based approaches was used to reveal the culturable and molecular diversity of the microbes inhabiting an open-dumped Pb/Zn mine tailings that was undergoing intensive acid generation (pH 1.9). Culturable bacteria found in the extremely acidic mine tailings were Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, Sulfobacillus thermotolerans and Acidiphilium cryptum, where the number of acidophilic heterotrophs was ten times higher than that of the iron- and sulfur-oxidizing bacteria. Cloning and phylogenetic analysis revealed that, in contrast to the adjacent AMD, the mine tailings possessed a low microbial diversity with archaeal sequence types dominating the 16S rRNA gene library. Of the 141 clones examined, 132 were represented by two sequence types phylogenetically affiliated with the iron-oxidizing archaea Ferroplasma acidiphilum and three belonged to two tentative groups within the Thermoplasma lineage so far represented by only a few environmental sequences. Six clones in the library were represented by the only bacterial sequence type and were closely related to the well-described iron-oxidizer L. ferriphilum. The significant differences in the prokaryotic community structures of the extremely acidic mine tailings and the AMD associated with it highlights the importance of studying the microbial communities that are more directly involved in the iron and sulfur cycles of mine tailings.

  2. [Phylogenetic analysis and expression patterns of tropomyosin in amphioxus].

    PubMed

    Li, Xin-Yi; Lin, Yu-Shuang; Zhang, Hong-Wei

    2012-08-01

    In amphioxus, we found a mesoderm related gene, tropomyosin, which encodes a protein comprising 284 amino acid residues, sharing high identities with other known Tropomyosin proteins both in vertebrates and invertebrates. Phylogenetically, amphioxus Tropomyosin fell outside the invertebrate clade and was at the base of the vertebrate protein family clade, indicating that it may represent an independent branch. From the early neurula to the larva stage, whole-mount in situ hybridization and histological sections found transcripts of amphioxus tropomyosin gene. Weak tropomyosin expression was first detected in the wall of the archenteron at about 10 hours-post-fertilization neurula stage, while intense expression was revealed in the differentiating presumptive notochord and the muscle. Transcripts of tropomyosin were then expressed in the formed notochord and somites. Gene expression seemed to continue in these developing organs throughout the neurular stages and remained till 72-hours, during the early larval stages. In situ study still showed tropomyosin was also expressed in the neural tube, hepatic diverticulum, notochord and the spaces between myotomes in adult amphioxus. Our results indicated that tropomyosin may play an important role in both embryonic development and adult life.

  3. Phylogenetic analysis of the evolution of lactose digestion in adults.

    PubMed

    Holden, C; Mace, R

    1997-10-01

    In most of the world's population the ability to digest lactose declines sharply after infancy. High lactose digestion capacity in adults is common only in populations of European and circum-Mediterranean origin and is thought to be an evolutionary adaptation to millennia of drinking milk from domestic livestock. Milk can also be consumed in a processed form, such as cheese or soured milk, which has a reduced lactose content. Two other selective pressures for drinking fresh milk with a high lactose content have been proposed: promotion of calcium uptake in high-latitude populations prone to vitamin-D deficiency and maintainance of water and electrolytes in the body in highly and environments. These three hypotheses are all supported by the geographic distribution of high lactose digestion capacity in adults. However, the relationships between environmental variables and adult lactose digestion capacity are highly confounded by the shared ancestry of many populations whose lactose digestion capacity has been tested. The three hypotheses for the evolution of high adult lactose digestion capacity are tested here using a comparative method of analysis that takes the problem of phylogenetic confounding into account. This analysis supports the hypothesis that high adult lactose digestion capacity is an adaptation to dairying but does not support the hypotheses that lactose digestion capacity is additionally selected for either at high latitudes or in highly arid environments. Furthermore, methods using maximum likelihood are used to show that the evolution of milking preceded the evolution of high lactose digestion.

  4. Molecular analysis and phylogenetic characterization of HIV in Iran.

    PubMed

    Sarrami-Forooshani, Ramin; Das, Suman Ranjan; Sabahi, Farzaneh; Adeli, Ahmad; Esmaeili, Rezvan; Wahren, Britta; Mohraz, Minoo; Haji-Abdolbaghi, Mahboubeh; Rasoolinejad, Mehrnaz; Jameel, Shahid; Mahboudi, Fereidoun

    2006-07-01

    The rate of human immunodeficiency virus type 1 (HIV-1) infection in Iran has increased dramatically in the last few years. While the earliest cases were found in hemophiliacs, intravenous drug users are now fueling the outbreak. In this study, both the 122 clones of HIV-1 gag p17 and the 131 clones of env V1-V5 region were obtained from 61 HIV-1 seropositives belonging to these two groups in Iran. HIV-1 subtyping and phylogenetic analysis was done by heteroduplex mobility assays (HMA) and multiple clone sequencing. The result indicated all hemophiliacs are infected with HIV-1 subtype B and all intravenous drug users are infected with HIV-1 subtype A. Since intravenous drug abuse is the major transmission route in Iran, HIV-1 subtype A is likely to be the dominant viral subtype circulating in the country. The analysis of genetic distances showed subtype B viruses in Iran to be twice as heterogeneous as the subtype A viruses. In conclusion, this first molecular study of HIV-1 genotypes in Iran suggests two parallel outbreaks in distinct high-risk populations and may offer clues to the origin and spread of infection in Iran.

  5. Molecular phylogenetic analysis of mango mealybug, Drosicha mangiferae from Punjab.

    PubMed

    Banta, Geetika; Jindal, Vikas; Mohindru, Bharathi; Sharma, Sachin; Kaur, Jaimeet; Gupta, V K

    2016-01-01

    Mealybugs (Hemiptera: Pseudococcidae) are major pests of a wide range of crops and ornamental plants worldwide. Their high degree of morphological similarity makes them difficult to identify and limits their study and management. In the present study, four Indian populations of mango mealybug (mango, litchi, guava from Gurdaspur and mango from Jalandhar) were analyzed. The mtCOI region was amplified, cloned, the nucleotide sequences were determined and analysed. All the four species were found to be D. mangiferae. The population from Litchi and Mango from Gurdaspur showed 100% homologus sequence. The population of Guava-Gurdaspur and Mango-Jalandhar showed a single mutation of 'C' instead of 'T' at 18th and 196th position, respectively. Indian populations were compared with populations from Pakistan (21) and Japan (1). The phylogenetic tree resulted in two main clusters. Cluster1 represent all the 4 populations of Punjab, India, 20 of Pakistan (Punjab, Sind, Lahore, Multan, Faisalabad and Karak districts) with homologous sequences. The two population collected from Faisalabad district of Pakistan and Japan made a separate cluster 2 because the gene sequence used in analysis was from the COI-3p region. However, all the other sequence of D. mangiferae samples under study showed a low nucleotide divergence. The homologus mtCO1 sequence of Indian and Pakistan population concluded that the genetic diversity in mealybug population was quite less over a large geographical area.

  6. Inventory and Phylogenetic Analysis of Meiotic Genes in Monogonont Rotifers

    PubMed Central

    2013-01-01

    A long-standing question in evolutionary biology is how sexual reproduction has persisted in eukaryotic lineages. As cyclical parthenogens, monogonont rotifers are a powerful model for examining this question, yet the molecular nature of sexual reproduction in this lineage is currently understudied. To examine genes involved in meiosis, we generated partial genome assemblies for 2 distantly related monogonont species, Brachionus calyciflorus and B. manjavacas. Here we present an inventory of 89 meiotic genes, of which 80 homologs were identified and annotated from these assemblies. Using phylogenetic analysis, we show that several meiotic genes have undergone relatively recent duplication events that appear to be specific to the monogonont lineage. Further, we compare the expression of “meiosis-specific” genes involved in recombination and all annotated copies of the cell cycle regulatory gene CDC20 between obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of B. calyciflorus. We show that “meiosis-specific” genes are expressed in both CP and OP strains, whereas the expression of one of the CDC20 genes is specific to cyclical parthenogenesis. The data presented here provide insights into mechanisms of cyclical parthenogenesis and establish expectations for studies of obligate asexual relatives of monogononts, the bdelloid rotifer lineage. PMID:23487324

  7. Phylogenetic analysis of Indian rabies virus isolates targeting the complete glycoprotein gene.

    PubMed

    Cherian, Susan; Singh, Rajendra; Singh, K P; Manjunatha Reddy, G B; Anjaneya; Ravi Kumar, G V P P S; Sumithra, T G; Singh, R P

    2015-12-01

    Rabies a fatal viral zoonosis is endemic in India. There is no report on phylogenetic study of Indian rabies virus isolates based on the complete G gene. In the present study, a total of 25 rabies positive brain samples collected during 2001-2014 from North India (UP, MP, Delhi, Rajasthan), South India (Kerala and Karnataka) and Gujarat states belonging to six different host species were subjected to G gene amplification by RT-PCR as three overlapping fragments of 881 bp, 991 bp and 618 bp. Phylogenetic analysis revealed that all Indian rabies virus isolates are genetically closely related with Arctic-like 1a lineage viruses. However, two distinct clusters were identified namely, India South and India North. All the Indian rabies isolates had 95.5-100% homology related to geography, but not to host species. Deduced amino acids on comparison revealed two amino acid changes, aa 356 in ECTO; N→K and aa 458; M→I, which were found to distinguish between the India South and India North isolates.

  8. Functional and phylogenetic analysis of ureD in Shiga toxin-producing Escherichia coli.

    PubMed

    Steyert, Susan R; Rasko, David A; Kaper, James B

    2011-02-01

    Enterohemorrhagic Escherichia coli (EHEC) is a food-borne pathogen that can cause severe health complications and utilizes a much lower infectious dose than other E. coli pathotypes. Despite having an intact ure locus, ureDABCEFG, the majority of EHEC strains are phenotypically urease negative under tested conditions. Urease activity potentially assists with survival fitness by enhancing acid tolerance during passage through the stomach or by aiding with colonization in either human or animal reservoirs. Previously, in the EHEC O157:H7 Sakai strain, a point mutation in ureD, encoding a urease chaperone protein, was identified, resulting in a substitution of an amber stop codon for glutamine. This single nucleotide polymorphism (SNP) is observed in the majority of EHEC O157:H7 isolates and correlates with a negative urease phenotype in vitro. We demonstrate that the lack of urease activity in vitro is not solely due to the amber codon in ureD. Our analysis has identified two additional SNPs in ureD affecting amino acid positions 38 and 205, in both cases determining whether the encoded amino acid is leucine or proline. Phylogenetic analysis based on Ure protein sequences from a variety of urease-encoding bacteria demonstrates that the proline at position 38 is highly conserved among Gram-negative bacteria. Experiments reveal that the L38P substitution enhances urease enzyme activity; however, the L205P substitution does not. Multilocus sequence typing analysis for a variety of Shiga toxin-producing E. coli isolates combined with the ureD sequence reveals that except for a subset of the O157:H7 strains, neither the in vitro urease-positive phenotype nor the ureD sequence is phylogenetically restricted.

  9. Confirmation of a novel siadenovirus species detected in raptors: partial sequence and phylogenetic analysis.

    PubMed

    Kovács, Endre R; Benko, Mária

    2009-03-01

    Partial genome characterisation of a novel adenovirus, found recently in organ samples of multiple species of dead birds of prey, was carried out by sequence analysis of PCR-amplified DNA fragments. The virus, named as raptor adenovirus 1 (RAdV-1), has originally been detected by a nested PCR method with consensus primers targeting the adenoviral DNA polymerase gene. Phylogenetic analysis with the deduced amino acid sequence of the small PCR product has implied a new siadenovirus type present in the samples. Since virus isolation attempts remained unsuccessful, further characterisation of this putative novel siadenovirus was carried out with the use of PCR on the infected organ samples. The DNA sequence of the central genome part of RAdV-1, encompassing nine full (pTP, 52K, pIIIa, III, pVII, pX, pVI, hexon, protease) and two partial (DNA polymerase and DBP) genes and exceeding 12 kb pairs in size, was determined. Phylogenetic tree reconstructions, based on several genes, unambiguously confirmed the preliminary classification of RAdV-1 as a new species within the genus Siadenovirus. Further study of RAdV-1 is of interest since it represents a rare adenovirus genus of yet undetermined host origin.

  10. Identification and phylogenetic analysis of novel cytochrome P450 1A genes from ungulate species.

    PubMed

    Darwish, Wageh Sobhy; Kawai, Yusuke; Ikenaka, Yoshinori; Yamamoto, Hideaki; Muroya, Tarou; Ishizuka, Mayumi

    2010-09-01

    As part of an ongoing effort to understand the biological response of wild and domestic ungulates to different environmental pollutants such as dioxin-like compounds, cDNAs encoding for CYP1A1 and CYP1A2 were cloned and characterized. Four novel CYP1A cDNA fragments from the livers of four wild ungulates (elephant, hippopotamus, tapir and deer) were identified. Three fragments from hippopotamus, tapir and deer were classified as CYP1A2, and the other fragment from elephant was designated as CYP1A1/2. The deduced amino acid sequences of these fragment CYP1As showed identities ranging from 76 to 97% with other animal CYP1As. The phylogenetic analysis of these fragments showed that both elephant and hippopotamus CYP1As made separate branches, while tapir and deer CYP1As were located beside that of horse and cattle respectively in the phylogenetic tree. Analysis of dN/dS ratio among the identified CYP1As indicated that odd toed ungulate CYP1A2s were exposed to different selection pressure.

  11. Identification, phylogenetic evolutionary analysis of GDQY orf virus isolated from Qingyuan City, Guangdong Province, southern China.

    PubMed

    Duan, Chaohui; Liao, Meiying; Wang, Han; Luo, Xiaohong; Shao, Jing; Xu, Ying; Li, Wei; Hao, Wenbo; Luo, Shuhong

    2015-01-25

    Infection with the orf virus (ORFV) leads to contagious ecthyma, also called contagious pustular dermatitis, which usually affects sheep, goats and other small ruminants. It has a great distribution throughout the world and has also been reported to infect humans. Though many strains have been isolated from differing parts of mainland China, rarely has any strain been reported from the southern provinces of China. We studied a case of orf virus infection that occurred at Qingyuan City, Guangdong Province in southern China. An orf virus strain, GDQY, was successfully isolated and identified through cell culture techniques and transmission electron microscopy. Complete genes of ORFV011, ORFV059, ORFV106 and ORFV107 were amplified for the sequence analysis based on their nucleotide or amino acid level. In order to discuss the genetic variation, precise sequences were used to compare to other reference strains isolated from different districts or countries. Phylogenetic trees based on those strains were built up and evolutionary distances were calculated based on the alignment of their complete sequences. The typical structure of the orf virus was observed in cell-culture suspensions inoculated with GDQY, and the full-length of four genes was amplified and sequenced. Phylogenetic analysis indicated that GDQY is homologous to FJ-DS and CQ/WZ on ORFV011 nucleotides. ORFV059 may be more variable than ORFV011 based on the comparison between GDQY and other isolates. Genetic studies of ORFV106 and 107 are reported for the first time in the presented study.

  12. Amino acid analysis

    NASA Technical Reports Server (NTRS)

    Winitz, M.; Graff, J. (Inventor)

    1974-01-01

    The process and apparatus for qualitative and quantitative analysis of the amino acid content of a biological sample are presented. The sample is deposited on a cation exchange resin and then is washed with suitable solvents. The amino acids and various cations and organic material with a basic function remain on the resin. The resin is eluted with an acid eluant, and the eluate containing the amino acids is transferred to a reaction vessel where the eluant is removed. Final analysis of the purified acylated amino acid esters is accomplished by gas-liquid chromatographic techniques.

  13. Phylogenetic analysis of the N8 neuraminidase gene of influenza A viruses.

    PubMed

    Saito, T; Kawaoka, Y; Webster, R G

    1993-04-01

    Phylogenetic analysis of the N8 neuraminidase (NA) genes from 18 influenza A viruses, representing equine and avian hosts in different geographic locations, revealed three major lineages: (i) currently circulating equine 2 viruses; (ii) avian viruses isolated in the Eurasian region, including A/Equine/Jilin/1/89, a recent avian-like N8 isolate found in horses in China; and (iii) avian viruses isolated in North America. Comparison of mutation rates indicated that avian N8 genes have evolved more slowly than their equine counterparts. That is, in both avian lineages, 72% of the nucleotide changes were silent in the terminal branches of the phylogenetic tree, whereas in equine 2 viruses, 59% of the nucleotide changes were silent. This suggests greater selective pressure on the NA gene from the mammalian immune system, leading to progressive evolution. Alternatively, the slower mutation rate for avian N8 genes could reflect a selective advantage gained from a longer, continuous span of evolution. The shape of the phylogenetic tree, the evolutionary rate, and the calculated date of origin for the N8 equine 2 virus lineage were comparable to findings for the equine 2 virus hemagglutinin (HA) gene (Bean et al., J. Virol. 66, 1129-1138, 1992). This suggests that both viral membrane glycoproteins of equine 2 viruses have evolved together and have been subjected to similar levels of selective pressure. Several amino acid residues were found to differ among the three host-specific lineages, but they may not be involved in host restriction of the NA, as they are shared by EQ/Jilin/1/89 and viruses of avian origin. The present findings complement detailed structural information on the N2 and N9 subtypes and should prove valuable in understanding future X-ray diffraction studies of N8 crystals.

  14. Analysis of phylogenetic and functional diverge in plant nine-cis epoxycarotenoid dioxygenase gene family.

    PubMed

    Priya, R; Siva, Ramamoorthy

    2015-07-01

    During different environmental stress conditions, plant growth is regulated by the hormone abscisic acid (an apocarotenoid). In the biosynthesis of abscisic acid, the oxidative cleavage of cis-epoxycarotenoid catalyzed by 9-cis-epoxycarotenoid dioxygenase (NCED) is the crucial step. The NCED genes were isolated in numerous plant species and those genes were phylogenetically investigated to understand the evolution of NCED genes in various plant lineages comprising lycophyte, gymnosperm, dicot and monocot. A total of 93 genes were obtained from 48 plant species to statistically estimate their sequence conservation and functional divergence. Selaginella moellendorffii appeared to be evolutionarily distinct from those of the angiosperms, insisting the substantial influence of natural selection pressure on NCED genes. Further, using exon-intron structure analysis, the gene structures of NCED were found to be conserved across some species. In addition, the substitution rate ratio of non-synonymous (Ka) versus synonymous (Ks) mutations using the Bayesian inference approach, depicted the critical amino acid residues for functional divergence. A significant functional divergence was found between some subgroups through the co-efficient of type-I functional divergence. Our results suggest that the evolution of NCED genes occurred by duplication, diversification and exon intron loss events. The site-specific profile and functional diverge analysis revealed NCED genes might facilitate the tissue-specific functional divergence in NCED sub-families, that could combat different environmental stress conditions aiding plant survival.

  15. Phylogenetic distribution of phenotypic traits in Bacillus thuringiensis determined by multilocus sequence analysis.

    PubMed

    Blackburn, Michael B; Martin, Phyllis A W; Kuhar, Daniel; Farrar, Robert R; Gundersen-Rindal, Dawn E

    2013-01-01

    Diverse isolates from a world-wide collection of Bacillus thuringiensis were classified based on phenotypic profiles resulting from six biochemical tests; production of amylase (T), lecithinase (L), urease (U), acid from sucrose (S) and salicin (A), and the hydrolysis of esculin (E). Eighty two isolates representing the 15 most common phenotypic profiles were subjected to phylogenetic analysis by multilocus sequence typing; these were found to be distributed among 19 sequence types, 8 of which were novel. Approximately 70% of the isolates belonged to sequence types corresponding to the classical B. thuringiensis varieties kurstaki (20 isolates), finitimus (15 isolates), morrisoni (11 isolates) and israelensis (11 isolates). Generally, there was little apparent correlation between phenotypic traits and phylogenetic position, and phenotypic variation was often substantial within a sequence type. Isolates of the sequence type corresponding to kurstaki displayed the greatest apparent phenotypic variation with 6 of the 15 phenotypic profiles represented. Despite the phenotypic variation often observed within a given sequence type, certain phenotypes appeared highly correlated with particular sequence types. Isolates with the phenotypic profiles TLUAE and LSAE were found to be exclusively associated with sequence types associated with varieties kurstaki and finitimus, respectively, and 7 of 8 TS isolates were found to be associated with the morrisoni sequence type. Our results suggest that the B. thuringiensis varieties israelensis and kurstaki represent the most abundant varieties of Bt in soil.

  16. Genotyping and phylogenetic analysis of Acanthamoeba isolates associated with keratitis.

    PubMed

    Risler, Arnaud; Coupat-Goutaland, Bénédicte; Pélandakis, Michel

    2013-11-01

    We examined a partial SSU-rDNA sequence from 20 Acanthamoeba isolates associated with keratitis infections. The phylogenetic tree inferred from this partial sequence allowed to assign isolates to genotypes. Among the 20 isolates examined, 16 were found to be of the T4 genotype, 2 were T3, 1 was a T5, and 1 was a T2, confirming the predominance of T4 in infections. However, the study highlighted other genotypes more rarely associated with infections, particularly the T2 genotype. Our study is the second one to detect that this genotype is associated with keratitis. Additionally, the phylogenetic analyses showed five main emerging clusters, T4/T3/T11, T2/T6, T10/T12/T14, T13/T16, and T7/T8/T9/T17, regularly obtained whichever method was used. A similar branching pattern was found when the full rDNA sequence was investigated.

  17. Phylogenetic analysis of mammalian maximal oxygen consumption during exercise.

    PubMed

    Dlugosz, Elizabeth M; Chappell, Mark A; Meek, Thomas H; Szafranska, Paulina A; Zub, Karol; Konarzewski, Marek; Jones, James H; Bicudo, J Eduardo P W; Nespolo, Roberto F; Careau, Vincent; Garland, Theodore

    2013-12-15

    We compiled published values of mammalian maximum oxygen consumption during exercise ( ) and supplemented these data with new measurements of for the largest rodent (capybara), 20 species of smaller-bodied rodents, two species of weasels and one small marsupial. Many of the new data were obtained with running-wheel respirometers instead of the treadmill systems used in most previous measurements of mammalian . We used both conventional and phylogenetically informed allometric regression models to analyze of 77 'species' (including subspecies or separate populations within species) in relation to body size, phylogeny, diet and measurement method. Both body mass and allometrically mass-corrected showed highly significant phylogenetic signals (i.e. related species tended to resemble each other). The Akaike information criterion corrected for sample size was used to compare 27 candidate models predicting (all of which included body mass). In addition to mass, the two best-fitting models (cumulative Akaike weight=0.93) included dummy variables coding for three species previously shown to have high (pronghorn, horse and a bat), and incorporated a transformation of the phylogenetic branch lengths under an Ornstein-Uhlenbeck model of residual variation (thus indicating phylogenetic signal in the residuals). We found no statistical difference between wheel- and treadmill-elicited values, and diet had no predictive ability for . Averaged across all models, the allometric scaling exponent was 0.839, with 95% confidence limits of 0.795 and 0.883, which does not provide support for a scaling exponent of 0.67, 0.75 or unity.

  18. Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea

    PubMed Central

    Carapelli, Antonio; Liò, Pietro; Nardi, Francesco; van der Wath, Elizabeth; Frati, Francesco

    2007-01-01

    Background The phylogeny of Arthropoda is still a matter of harsh debate among systematists, and significant disagreement exists between morphological and molecular studies. In particular, while the taxon joining hexapods and crustaceans (the Pancrustacea) is now widely accepted among zoologists, the relationships among its basal lineages, and particularly the supposed reciprocal paraphyly of Crustacea and Hexapoda, continues to represent a challenge. Several genes, as well as different molecular markers, have been used to tackle this problem in molecular phylogenetic studies, with the mitochondrial DNA being one of the molecules of choice. In this study, we have assembled the largest data set available so far for Pancrustacea, consisting of 100 complete (or almost complete) sequences of mitochondrial genomes. After removal of unalignable sequence regions and highly rearranged genomes, we used nucleotide and inferred amino acid sequences of the 13 protein coding genes to reconstruct the phylogenetic relationships among major lineages of Pancrustacea. The analysis was performed with Bayesian inference, and for the amino acid sequences a new, Pancrustacea-specific, matrix of amino acid replacement was developed and used in this study. Results Two largely congruent trees were obtained from the analysis of nucleotide and amino acid datasets. In particular, the best tree obtained based on the new matrix of amino acid replacement (MtPan) was preferred over those obtained using previously available matrices (MtArt and MtRev) because of its higher likelihood score. The most remarkable result is the reciprocal paraphyly of Hexapoda and Crustacea, with some lineages of crustaceans (namely the Malacostraca, Cephalocarida and, possibly, the Branchiopoda) being more closely related to the Insecta s.s. (Ectognatha) than two orders of basal hexapods, Collembola and Diplura. Our results confirm that the mitochondrial genome, unlike analyses based on morphological data or nuclear

  19. Gene structure and amino acid sequence of Latimeria chalumnae (coelacanth) myelin DM20: phylogenetic relation of the fish.

    PubMed

    Tohyama, Y; Kasama-Yoshida, H; Sakuma, M; Kobayashi, Y; Cao, Y; Hasegawa, M; Kojima, H; Tamai, Y; Tanokura, M; Kurihara, T

    1999-07-01

    The structure of Latimeria chalumnae (coelacanth) proteolipid protein/DM20 gene excluding exon 1 was determined, and the amino acid sequence of Latimeria DM20 corresponding to exons 2-7 was deduced. The nucleotide sequence of exon 3 suggests that only DM20 isoform is expressed in Latimeria. The structure of proteolipid protein/DM20 gene is well preserved among human, dog, mouse, and Latimeria. Southern blot analysis indicates that Latimeria DM20 gene is a single-copy gene. When the amino acid sequences of DM20 were compared among various species, Latimeria was more similar to tetrapods than other fishes including lungfish, confirming the previous finding by immunoreactivity (Waehneldt and Malotka 1989 J. Neurochem. 52:1941-1943). However, when phylogenetic trees were constructed from the DM20 sequences, lungfish was clearly the closest to tetrapods. Latimeria was situated outside of lungfish by the maximum likelihood method. The apparent similarity of Latimeria DM20 to tetrapod proteolipid protein/DM20 is explained by the slow amino acid substitution rate of Latimeria DM20.

  20. Phylogenetic Analysis of an Anaerobic, Trichlorobenzene-Transforming Microbial Consortium

    PubMed Central

    von Wintzingerode, Friedrich; Selent, Burkhard; Hegemann, Werner; Göbel, Ulf B.

    1999-01-01

    A culture-independent phylogenetic survey for an anaerobic trichlorobenzene-transforming microbial community was carried out. Small-subunit rRNA genes were PCR amplified from community DNA by using primers specific for Bacteria or Euryarchaeota and were subsequently cloned. Application of a new hybridization-based screening approach revealed 51 bacterial clone families, one of which was closely related to dechlorinating Dehalobacter species. Several clone sequences clustered to rDNA sequences obtained from a molecular study of an anaerobic aquifer contaminated with hydrocarbons and chlorinated solvents (Dojka et al., Appl. Env. Microbiol. 64:3869–3877, 1998). PMID:9872791

  1. Sequence and phylogenetic analysis of the gp200 protein of Ehrlichia canis from dogs in Taiwan.

    PubMed

    Huang, Chia-Chia; Hsieh, Yu-Chen; Tsang, Chau-Loong; Chung, Yang-Tsung

    2010-12-01

    Ehrlichia (E.) canis is a Gram-negative obligate intracellular bacterium responsible for canine monocytic ehrlichiosis. Currently, the genetic diversity of E. canis strains worldwide is poorly defined. In the present study, sequence analysis of the nearly full-length 16S rDNA (1,620 bp) and the complete coding region (4,269 bp) of the gp200 gene, which encodes the largest major immunoreactive protein in E. canis, from 17 Taiwanese samples was conducted. The resultant 16S rDNA sequences were found to be identical to each other and have very high homology (99.4~100%) with previously reported E. canis sequences. Additionally, phylogenetic analysis of gp200 demonstrated that the E. canis Taiwanese genotype was genetically distinct from other reported isolates obtained from the United States, Brazil, and Israel, and that it formed a separate clade. Remarkable variations unique to the Taiwanese genotype were found throughout the deduced amino acid sequence of gp200, including 15 substitutions occurring in two of five known species-specific epitopes. The gp200 amino acid sequences of the Taiwanese genotype bore 94.4~94.6 identities with those of the isolates from the United States and Brazil, and 93.7% homology with that of the Israeli isolate. Taken together, these results suggest that the Taiwanese genotype represents a novel strain of E. canis that has not yet been characterized.

  2. The new vertebrate CYP1C family: cloning of new subfamily members and phylogenetic analysis.

    PubMed

    Godard, Celine A J; Goldstone, Jared V; Said, Maya R; Dickerson, Richard L; Woodin, Bruce R; Stegeman, John J

    2005-06-17

    Two novel CYP1 genes from teleost fish constituting a new subfamily have been cloned. These paralogous sequences are designated CYP1C1 and CYP1C2. Both genes were initially obtained from untreated scup Stenotomus chrysops tissues by RT-PCR and RACE. Scup CYP1C1 and CYP1C2 code for 524 and 525 amino acids, respectively, and share 80-81% identity at the nucleotide and amino acid levels. Orthologues of CYP1C1 and CYP1C2 were identified in genome databases for other fish species, and both CYP1B1 and CYP1C1 were cloned from zebrafish (Danio rerio). Phylogenetic analysis shows that CYP1Cs and CYP1Bs constitute a sister clade to the CYP1As. Analysis of sequence domains likely to have functional significance suggests that the two CYP1Cs in scup may have catalytic functions and/or substrate specificity that differ from each other and from those of mammalian CYP1Bs or CYP1As. RT-PCR results indicate that CYP1C1 and CYP1C2 are variously expressed in several scup organs.

  3. Interferon-gamma of the giant panda (Ailuropoda melanoleuca): complementary DNA cloning, expression, and phylogenetic analysis.

    PubMed

    Tao, Yaqiong; Zeng, Bo; Xu, Liu; Yue, Bisong; Yang, Dong; Zou, Fangdong

    2010-01-01

    Interferon-gamma (IFN-gamma) is the only member of type II IFN and is vital in the regulation of immune and inflammatory responses. Herein we report the cloning, expression, and sequence analysis of IFN-gamma from the giant panda (Ailuropoda melanoleuca). The open reading frame of this gene is 501 base pair in length and encodes a polypeptide consisting of 166 amino acids. All conserved N-linked glycosylation sites and cysteine residues among carnivores were found in the predicted amino acid sequence of the giant panda. Recombinant giant panda IFN-gamma with a V5 epitope and polyhistidine tag was expressed in HEK293 host cells and confirmed by Western blotting. Phylogenetic analysis of mammalian IFN-gamma-coding sequences indicated that the giant panda IFN-gamma was closest to that of carnivores, then to ungulates and dolphin, and shared a distant relationship with mouse and human. These results represent a first step into the study of IFN-gamma in giant panda.

  4. Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages.

    PubMed

    Lee, Sean; Hasegawa, Toshikazu

    2011-12-22

    Languages, like genes, evolve by a process of descent with modification. This striking similarity between biological and linguistic evolution allows us to apply phylogenetic methods to explore how languages, as well as the people who speak them, are related to one another through evolutionary history. Language phylogenies constructed with lexical data have so far revealed population expansions of Austronesian, Indo-European and Bantu speakers. However, how robustly a phylogenetic approach can chart the history of language evolution and what language phylogenies reveal about human prehistory must be investigated more thoroughly on a global scale. Here we report a phylogeny of 59 Japonic languages and dialects. We used this phylogeny to estimate time depth of its root and compared it with the time suggested by an agricultural expansion scenario for Japanese origin. In agreement with the scenario, our results indicate that Japonic languages descended from a common ancestor approximately 2182 years ago. Together with archaeological and biological evidence, our results suggest that the first farmers of Japan had a profound impact on the origins of both people and languages. On a broader level, our results are consistent with a theory that agricultural expansion is the principal factor for shaping global linguistic diversity.

  5. Evolution of climatic niche specialization: a phylogenetic analysis in amphibians.

    PubMed

    Bonetti, Maria Fernanda; Wiens, John J

    2014-11-22

    The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change.

  6. The PNarec method for detection of ancient recombinations through phylogenetic network analysis.

    PubMed

    Saitou, Naruya; Kitano, Takashi

    2013-02-01

    Recombinations are known to disrupt bifurcating tree structure of gene genealogies. Although recently occurred recombinations are easily detectable by using conventional methods, recombinations may have occurred at any time. We devised a new method for detecting ancient recombinations through phylogenetic network analysis, and detected five ancient recombinations in gibbon ABO blood group genes [Kitano et al., 2009. Mol. Phylogenet. Evol., 51, 465-471]. We present applications of this method, now named as "PNarec", to various virus sequences as well as HLA genes.

  7. Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe.

    PubMed

    Pontarp, Mikael; Canbäck, Björn; Tunlid, Anders; Lundberg, Per

    2012-07-01

    The phylogenetic structure and community composition were analysed in an existing data set of marine bacterioplankton communities to elucidate the evolutionary and ecological processes dictating the assembly. The communities were sampled from coastal waters at nine locations distributed worldwide and were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes. The analyses show that the local communities are phylogenetically different from each other and that a majority of them are phylogenetically clustered, i.e. the species (operational taxonomic units) were more related to each other than expected by chance. Accordingly, the local communities were assembled non-randomly from the global pool of available bacterioplankton. Further, the phylogenetic structures of the communities were related to the water temperature at the locations. In agreement with similar studies, including both macroorganisms and bacteria, these results suggest that marine bacterial communities are structured by “habitat filtering”, i.e. through non-random colonization and invasion determined by environmental characteristics. Different bacterial types seem to have different ecological niches that dictate their survival in different habitats. Other eco-evolutionary processes that may contribute to the observed phylogenetic patterns are discussed. The results also imply a mapping between phenotype and phylogenetic relatedness which facilitates the use of community phylogenetic structure analysis to infer ecological and evolutionary assembly processes.

  8. Phylogenetic analysis of bovine astrovirus in Korean cattle.

    PubMed

    Oem, Jae-Ku; An, Dong-Jun

    2014-04-01

    Bovine astrovirus (BAstV) belongs to a genetically divergent lineage within the genus Mamastrovirus. The present study showed that BAstV was associated with the gastroenteric tracts of cattle in nine positive fecal samples from 115 cattle, whereas no positive samples were found in the brain tissues of 14 downer cattle. Interestingly, the positive diarrheal samples were obtained mainly from calves aged 14 days-3 months. Bayesian inference tree analysis of the partial ORF1ab and capsid (ORF2) gene sequences of BAstVs identified four divergent groups. Eleven BAstVs, four porcine astroviruses, and two deer astroviruses (DAstVs; CcAstV-1 and -2) belonged to group 1; group 2 contained two BAstVs (BAstK08-51 and BAstK10-96) with another two in group 3 (BAstK08-2 and BAstK08-53); and group 4 comprised the BAstV-NeuroS1 strain derived from a cattle brain tissue sample and an ovine astrovirus. The same divergent groups were obtained when the pairwise alignments were produced using both amino acid and nucleotide sequences. The Korean BAstVs isolated from infected cattle had a nationwide distribution and they belonged to groups 1, 2, and 3.

  9. Molecular and phylogenetic analysis of the HPV 16 E4 gene in cervical lesions from women in Greece.

    PubMed

    Tsakogiannis, D; Ruether, I G A; Kyriakopoulou, Z; Pliaka, V; Skordas, V; Gartzonika, C; Levidiotou-Stefanou, S; Markoulatos, P

    2012-09-01

    The HPV16 E1(∧)E4 protein is thought to contribute to the release of newly formed viral particles from infected epithelia. In order to investigate amino acid mutations in the HPV16 E1(∧)E4 protein, the complete E4 ORF was amplified by PCR in 27 HPV16-positive cervical samples, and the amplicons were cloned. Fifteen nucleic acid variations were identified in the E4 ORF, including seven silent nucleic acid mutations. In addition, nine amino acid mutations (A7V, A7P, L16I, D45E, L59I, L59T, Q66P, S72F, H75Q) were detected in the E1(∧)E4 protein, and these were associated with the severity of cervical malignancy. A maximum-likelihood phylogenetic tree was constructed based on the E4 ORF, and nucleotide sequence analysis of the E4, E6 and E7 genes from the same samples was conducted in order to determine the phylogenetic origin of the cloned sequences from the amplified HPV16 E4. Based on the nucleotide sequence and phylogenetic analysis it was revealed that even though E4 ORF constitutes a small polymorphic portion of the viral genome (288 bp), it could provide valuable information about the origins of the HPV16 genome. In addition, molecular evolutionary analysis of the E4 coding region revealed that neutral selection is dominant in the overlapping region of the E4 and E2 ORFs.

  10. wolfPAC: building a high-performance distributed computing network for phylogenetic analysis using 'obsolete' computational resources.

    PubMed

    Reeves, Patrick A; Friedman, Philip H; Richards, Christopher M

    2005-01-01

    wolfPAC is an AppleScript-based software package that facilitates the use of numerous, remotely located Macintosh computers to perform computationally-intensive phylogenetic analyses using the popular application PAUP* (Phylogenetic Analysis Using Parsimony). It has been designed to utilise readily available, inexpensive processors and to encourage sharing of computational resources within the worldwide phylogenetics community.

  11. Evolutionary ecology of specialization: insights from phylogenetic analysis

    PubMed Central

    Vamosi, Jana C.; Armbruster, W. Scott; Renner, Susanne S.

    2014-01-01

    In this Special feature, we assemble studies that illustrate phylogenetic approaches to studying salient questions regarding the effect of specialization on lineage diversification. The studies use an array of techniques involving a wide-ranging collection of biological systems (plants, butterflies, fish and amphibians are all represented). Their results reveal that macroevolutionary examination of specialization provides insight into the patterns of trade-offs in specialized systems; in particular, the genetic mechanisms of trade-offs appear to extend to very different aspects of life history in different groups. In turn, because a species may be a specialist from one perspective and a generalist in others, these trade-offs influence whether we perceive specialization to have effects on the evolutionary success of a lineage when we examine specialization only along a single axis. Finally, how geographical range influences speciation and extinction of specialist lineages remains a question offering much potential for further insight. PMID:25274367

  12. Assigning protein functions by comparative genome analysis protein phylogenetic profiles

    DOEpatents

    Pellegrini, Matteo; Marcotte, Edward M.; Thompson, Michael J.; Eisenberg, David; Grothe, Robert; Yeates, Todd O.

    2003-05-13

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  13. Phylogenetic analysis and development of probes for differentiating methylotrophic bacteria.

    PubMed Central

    Brusseau, G A; Bulygina, E S; Hanson, R S

    1994-01-01

    Fifteen small-subunit rRNAs from methylotrophic bacteria have been sequenced. Comparisons of these sequences with 22 previously published sequences further defined the phylogenetic relationships among these bacteria and illustrated the agreement between phylogeny and physiological characteristics of the bacteria. Phylogenetic trees were constructed with 16S rRNA sequences from methylotrophic bacteria and representative organisms from subdivisions within the class Proteobacteria on the basis of sequence similarities by using a weighted least-mean-square difference method. The methylotrophs have been separated into coherent clusters in which bacteria shared physiological characteristics. The clusters distinguished bacteria which used either the ribulose monophosphate or serine pathway for carbon assimilation. In addition, methanotrophs and methylotrophs which do not utilize methane were found to form distinct clusters within these groups. Five new deoxyoligonucleotide probes were designed, synthesized, labelled with digoxigenin-11-ddUTP, and tested for the ability to hybridize to RNA extracted from the bacteria represented in the unique clusters and for the ability to detect RNAs purified from soils enriched for methanotrophs by exposure to a methane-air atmosphere for one month. The 16S rRNA purified from soil hybridized to the probe which was complementary to sequences present in 16S rRNA from serine pathway methanotrophs and hybridized to a lesser extent with a probe complementary to sequences in 16S rRNAs of ribulose monophosphate pathway methanotrophs. The nonradioactive detection system used performed reliably at amounts of RNA from pure cultures as small as 10 ng. Images PMID:7510941

  14. Molecular phylogenetic analysis of Fasciola flukes from eastern India.

    PubMed

    Hayashi, Kei; Ichikawa-Seki, Madoka; Mohanta, Uday Kumar; Singh, T Shantikumar; Shoriki, Takuya; Sugiyama, Hiromu; Itagaki, Tadashi

    2015-10-01

    Fasciola flukes from eastern India were characterized on the basis of spermatogenesis status and nuclear ITS1. Both Fasciola gigantica and aspermic Fasciola flukes were detected in Imphal, Kohima, and Gantoku districts. The sequences of mitochondrial nad1 were analyzed to infer their phylogenetical relationship with neighboring countries. The haplotypes of aspermic Fasciola flukes were identical or showed a single nucleotide substitution compared to those from populations in the neighboring countries, corroborating the previous reports that categorized them in the same lineage. However, the prevalence of aspermic Fasciola flukes in eastern India was lower than those in the neighboring countries, suggesting that they have not dispersed throughout eastern India. In contrast, F. gigantica was predominant and well diversified, and the species was thought to be distributed in the area for a longer time than the aspermic Fasciola flukes. Fasciola gigantica populations from eastern India were categorized into two distinct haplogroups A and B. The level of their genetic diversity suggests that populations belonging to haplogroup A have dispersed from the west side of the Indian subcontinent to eastern India with the artificial movement of domestic cattle, Bos indicus, whereas populations belonging to haplogroup B might have spread from Myanmar to eastern India with domestic buffaloes, Bubalus bubalis.

  15. Molecular characterization and phylogenetic analysis of Fasciola hepatica from Peru.

    PubMed

    Ichikawa-Seki, Madoka; Ortiz, Pedro; Cabrera, Maria; Hobán, Cristian; Itagaki, Tadashi

    2016-06-01

    The causative agent of fasciolosis in South America is thought to be Fasciola hepatica. In this study, Fasciola flukes from Peru were analyzed to investigate their genetic structure and phylogenetic relationships with those from other countries. Fasciola flukes were collected from the three definitive host species: cattle, sheep, and pigs. They were identified as F. hepatica because mature sperms were observed in their seminal vesicles, and also they displayed Fh type, which has an identical fragment pattern to F. hepatica in the nuclear internal transcribed spacer 1. Eight haplotypes were obtained from the mitochondrial NADH dehydrogenase subunit 1 (nad1) sequences of Peruvian F. hepatica; however, no special difference in genetic structure was observed between the three host species. Its extremely low genetic diversity suggests that the Peruvian population was introduced from other regions. Nad1 haplotypes identical to those of Peruvian F. hepatica were detected in China, Uruguay, Italy, Iran, and Australia. Our results indicate that F. hepatica rapidly expanded its range due to human migration. Future studies are required to elucidate dispersal route of F. hepatica from Europe, its probable origin, to other areas, including Peru.

  16. Phylogenetic Analysis of Canine Parvovirus VP2 Gene in China.

    PubMed

    Yi, L; Tong, M; Cheng, Y; Song, W; Cheng, S

    2016-04-01

    In this study, a total of 37 samples (58.0%) were found through PCR assay to be positive for canine parvovirus (CPV) of 66 suspected faecal samples of dogs collected from various cities throughout China. Eight CPV isolates could be obtained in the CRFK cell line. The sequencing of the VP2 gene of CPV identified the predominant CPV strain as CPV-2a (Ser297Ala), with two CPV-2b (Ser297Ala). Sequence comparison revealed homologies of 99.3-99.9%, 99.9% and 99.3-99.7% within the CPV 2a isolates, within the CPV 2b isolates and between the CPV 2a and 2b isolates, respectively. In addition, several non-synonymous and synonymous mutations were also recorded. The phylogenetic tree revealed that most of the CPV strains from different areas in China were located in the formation of a large branch, which were grouped together along with the KU143-09 strain from Thailand and followed the same evolution. In this study, we provide an updated molecular characterization of CPV 2 circulation in China.

  17. Genomic Organization, Phylogenetic and Expression Analysis of the B-BOX Gene Family in Tomato.

    PubMed

    Chu, Zhuannan; Wang, Xin; Li, Ying; Yu, Huiyang; Li, Jinhua; Lu, Yongen; Li, Hanxia; Ouyang, Bo

    2016-01-01

    The B-BOX (BBX) proteins encode a class of zinc-finger transcription factors possessing one or two B-BOX domains and in some cases an additional CCT (CO, CO-like and TOC1) motif, which play important roles in regulating plant growth, development and stress response. Nevertheless, no systematic study of BBX genes has undertaken in tomato (Solanum lycopersicum). Here we present the results of a genome-wide analysis of the 29 BBX genes in this important vegetable species. Their structures, conserved domains, phylogenetic relationships, subcellular localizations, and promoter cis-regulatory elements were analyzed; their tissue expression profiles and expression patterns under various hormones and stress treatments were also investigated in detail. Tomato BBX genes can be divided into five subfamilies, and twelve of them were found to be segmentally duplicated. Real-time quantitative PCR analysis showed that most BBX genes exhibited different temporal and spatial expression patterns. The expression of most BBX genes can be induced by drought, polyethylene glycol-6000 or heat stress. Some BBX genes were induced strongly by phytohormones such as abscisic acid, gibberellic acid, or ethephon. The majority of tomato BBX proteins was predicted to be located in nuclei, and the transient expression assay using Arabidopsis mesophyll protoplasts demonstrated that all the seven BBX members tested (SlBBX5, 7, 15, 17, 20, 22, and 24) were localized in nucleus. Our analysis of tomato BBX genes on the genome scale would provide valuable information for future functional characterization of specific genes in this family.

  18. Genomic Organization, Phylogenetic and Expression Analysis of the B-BOX Gene Family in Tomato

    PubMed Central

    Chu, Zhuannan; Wang, Xin; Li, Ying; Yu, Huiyang; Li, Jinhua; Lu, Yongen; Li, Hanxia; Ouyang, Bo

    2016-01-01

    The B-BOX (BBX) proteins encode a class of zinc-finger transcription factors possessing one or two B-BOX domains and in some cases an additional CCT (CO, CO-like and TOC1) motif, which play important roles in regulating plant growth, development and stress response. Nevertheless, no systematic study of BBX genes has undertaken in tomato (Solanum lycopersicum). Here we present the results of a genome-wide analysis of the 29 BBX genes in this important vegetable species. Their structures, conserved domains, phylogenetic relationships, subcellular localizations, and promoter cis-regulatory elements were analyzed; their tissue expression profiles and expression patterns under various hormones and stress treatments were also investigated in detail. Tomato BBX genes can be divided into five subfamilies, and twelve of them were found to be segmentally duplicated. Real-time quantitative PCR analysis showed that most BBX genes exhibited different temporal and spatial expression patterns. The expression of most BBX genes can be induced by drought, polyethylene glycol-6000 or heat stress. Some BBX genes were induced strongly by phytohormones such as abscisic acid, gibberellic acid, or ethephon. The majority of tomato BBX proteins was predicted to be located in nuclei, and the transient expression assay using Arabidopsis mesophyll protoplasts demonstrated that all the seven BBX members tested (SlBBX5, 7, 15, 17, 20, 22, and 24) were localized in nucleus. Our analysis of tomato BBX genes on the genome scale would provide valuable information for future functional characterization of specific genes in this family. PMID:27807440

  19. [Isolation, phylogenetic analysis and developmental expression parttern of AmphiRab23b in amphioxus].

    PubMed

    Li, Jian-Wei; Lin, Yu-Shuang; Chen, Dong-Yan; Zhang, Hong-Wei

    2009-12-01

    The hedgehog (Hh) pathway plays an important role during the embryonic development and is related to the progression of cancers. Rab23 is a crucial functional molecule in Hh pathway. However, there is no report about amphioxus Rab23 up to now except the annotations of two isoforms in the genome of Florida lancelet (Branchiostoma floridae). Here a 2062 bp full-length cDNA sequence of the Rab23, AmphiRab23b, was isolated from Chinese amphioxus (Branchiostoma belcheri), which included the UTRs and an open reading frame of 714 bp, encoding a protein of 237 amino acids. Phylogenetic analysis suggested that AmphiRab23b falled outside the vertebrate clade. But sequence analysis indicated that this putative AmphiRab23b protein contained a specific Rab23_lke domain, which implied that Rab23 gene was functional conservative during evolution. And its developmental expression pattern showed that AmphiRab23b was expressed in the differentiating neural plate and alimentary canal, as the same as the expression pattern of the homologous vertebrate genes, which suggested that AmphiRab23b may function in the development of nervous system and alimentary canal.

  20. The long and winding road of molecular data in phylogenetic analysis.

    PubMed

    Suárez-Díaz, Edna

    2014-01-01

    The use of molecules and reactions as evidence, markers and/or traits for evolutionary processes has a history more than a century long. Molecules have been used in studies of intra-specific variation and studies of similarity among species that do not necessarily result in the analysis of phylogenetic relations. Promoters of the use of molecular data have sustained the need for quantification as the main argument to make use of them. Moreover, quantification has allowed intensive statistical analysis, as a condition and a product of increasing automation. All of these analyses are subject to the methodological anxiety characteristic of a community in search of objectivity (Suárez-Díaz and Anaya-Munoz, Stud Hist Philos Biol Biomed Sci 39:451–458, 2008). It is in this context that scientists compared and evaluated protein and nucleic acid sequence data with other types of molecular data – including immunological, electrophoretic and hybridization data. This paper argues that by looking at longterm historical processes, such as the use of molecular evidence in evolutionary biology, we gain valuable insights into the history of science. In that sense, it accompanies a growing concern among historians for big-pictures of science that incorporate the fruitful historical research on local cases of the last decades.

  1. Molecular phylogenetic analysis of the Papionina using concatenation and species tree methods.

    PubMed

    Guevara, Elaine E; Steiper, Michael E

    2014-01-01

    The Papionina is a geographically widespread subtribe of African cercopithecid monkeys whose evolutionary history is of particular interest to anthropologists. The phylogenetic relationships among arboreal mangabeys (Lophocebus), baboons (Papio), and geladas (Theropithecus) remain unresolved. Molecular phylogenetic analyses have revealed marked gene tree incongruence for these taxa, and several recent concatenated phylogenetic analyses of multilocus datasets have supported different phylogenetic hypotheses. To address this issue, we investigated the phylogeny of the Lophocebus + Papio + Theropithecus group using concatenation methods, as well as alternative methods that incorporate gene tree heterogeneity to estimate a 'species tree.' Our compiled DNA sequence dataset was ∼56 kb pairs long and included 57 independent partitions. All analyses of concatenated alignments strongly supported a Lophocebus + Papio clade and a basal position for Theropithecus. The Bayesian concordance analysis supported the same phylogeny. A coalescent-based Bayesian method resulted in a very poorly resolved species tree. The topological agreement between concatenation and the Bayesian concordance analysis offers considerable support for a Lophocebus + Papio clade as the dominant relationship across the genome. However, the results of the Bayesian concordance analysis indicate that almost half the genome has an alternative history. As such, our results offer a well-supported phylogenetic hypothesis for the Papio/Lophocebus/Theropithecus trichotomy, while at the same time providing evidence for a complex evolutionary history that likely includes hybridization among lineages.

  2. A genomic schism in birds revealed by phylogenetic analysis of DNA strings.

    PubMed

    Edwards, Scott V; Fertil, Bernard; Giron, Alain; Deschavanne, Patrick J

    2002-08-01

    The molecular systematics of vertebrates has been based entirely on alignments of primary structures of macromolecules; however, higher order features of DNA sequences not used in traditional studies also contain valuable phylogenetic information. Recent molecular data sets conflict over the phylogenetic placement of flightless birds (ratites - paleognaths), but placement of this clade critically influences interpretation of character change in birds. To help resolve this issue, we applied a new bioinformatics approach to the largest molecular data set currently available. We distilled nearly one megabase (1 million base pairs) of heterogeneous avian genomic DNA from 20 birds and an alligator into genomic signatures, defined as the complete set of frequencies of short sequence motifs (strings), thereby providing a way to directly compare higher order features of nonhomologous DNA sequences. Phylogenetic analysis and principal component analysis of the signatures strongly support the traditional hypothesis of basal ratites and monophyly of the nonratite birds (neognaths) and imply that ratite genomes are linguistically primitive within birds, despite their base compositional similarity to neognath genomes. Our analyses show further that the phylogenetic signal of genomic signatures are strongest among deep splits within vertebrates. Despite clear problems with phylogenetic analysis of genomic signatures, our study raises intriguing issues about the biological and genomic differences that fundamentally differentiate paleognaths and neognaths.

  3. Phylogenetic and phylogeographic analysis of Iberian lynx populations.

    PubMed

    Johnson, W E; Godoy, J A; Palomares, F; Delibes, M; Fernandes, M; Revilla, E; O'Brien, S J

    2004-01-01

    The Iberian lynx (Lynx pardinus), one of the world's most endangered cat species, is vulnerable due to habitat loss, increased fragmentation of populations, and precipitous demographic reductions. An understanding of Iberian lynx evolutionary history is necessary to develop rational management plans for the species. Our objectives were to assess Iberian lynx genetic diversity at three evolutionary timescales. First we analyzed mitochondrial DNA (mtDNA) sequence variation to position the Iberian lynx relative to other species of the genus LYNX: We then assessed the pattern of mtDNA variation of isolated populations across the Iberian Peninsula. Finally we estimated levels of gene flow between two of the most important remaining lynx populations (Doñana National Park and the Sierra Morena Mountains) and characterized the extent of microsatellite locus variation in these populations. Phylogenetic analyses of 1613 bp of mtDNA sequence variation supports the hypothesis that the Iberian lynx, Eurasian lynx, and Canadian lynx diverged within a short time period around 1.53-1.68 million years ago, and that the Iberian lynx and Eurasian lynx are sister taxa. Relative to most other felid species, genetic variation in mtDNA genes and nuclear microsatellites were reduced in Iberian lynx, suggesting that they experienced a fairly severe demographic bottleneck. In addition, the effects of more recent reductions in gene flow and population size are being manifested in local patterns of molecular genetic variation. These data, combined with recent studies modeling the viability of Iberian lynx populations, should provide greater urgency for the development and implementation of rational in situ and ex situ conservation plans.

  4. Genotyping and phylogenetic analysis of Pneumocystis jirovecii isolates from India.

    PubMed

    Gupta, Rashmi; Mirdha, Bijay Ranjan; Guleria, Randeep; Agarwal, Sanjay Kumar; Samantaray, Jyotish Chandra; Kumar, Lalit; Kabra, Sushil Kumar; Luthra, Kalpana; Sreenivas, Vishnubhatla

    2010-08-01

    Pneumocystis jirovecii is the cause of Pneumocystis pneumonia (PCP) in immuno-compromised individuals. The aim of this study was to describe the genotypes/haplotypes of P. jirovecii in immuno-compromised individuals with positive polymerase chain reaction (PCR) result for PCP. The typing was based on sequence polymorphism at internal transcribed spacer (ITS) regions of rRNA operon. Phylogenetic relationship between Indian and global haplotypes was also studied. Between January 2005 to October 2008, 43 patients were found to be positive for Pneumocystis using PCR targeting mitochondrial large subunit rRNA (mt LSU rRNA) and ITS region. Genotyping of all the positive samples was performed at the ITS locus by direct sequencing. Nine ITS1 alleles (all previously known) and 11 ITS2 alleles (nine previously defined and two new) were observed. A total of 19 ITS haplotypes, including five novel haplotypes (DEL1r, Edel2, Hr, Adel3 and SYD1a), were observed. The most prevalent type was SYD1g (16.3%), followed by types Ea (11.6%), Ec (9.3%), Eg (6.9%), DEL1r (6.9%), Ne (6.9%) and Ai (6.9%). To detect mixed infection, 30% of the positive isolates were cloned and 4-5 clones were sequenced from each specimen. Cloning and sequencing identified two more haplotypes in addition to the 19 types. Mixed infection was identified in 3 of the 13 cloned samples (23.1%). Upon construction of a haplotype network of 21 haplotypes, type Eg was identified as the most probable ancestral type. The present study is the first study that describes the haplotypes of P. jirovecii based on the ITS gene from India. The study suggests a high diversity of P. jirovecii haplotypes in the population.

  5. Detection of feline calicivirus (FCV) from vaccinated cats and phylogenetic analysis of its capsid genes.

    PubMed

    Ohe, K; Sakai, S; Sunaga, F; Murakami, M; Kiuchi, A; Fukuyama, M; Furuhata, K; Hara, M; Soma, T; Ishikawa, Y; Taneno, A

    2006-04-01

    We analysed genogroups of four feline calcivirus (FCV) isolates (FCV-S, H10, Ao198-1 and ML89) obtained from cats that experienced FCV infection after having been vaccinated against FCV. New PCR primer sets (8F/8R, Ao-S/Ao-A, cp-S/cp-A) were also designed, since the conventional Seal primer failed to amplify the target sequences in two samples. The genogroups of the four isolates as well as eight global and 17 domestic strains were determined by phylogenetic analysis of their amino acid sequences. One out of the four strains (25%) isolated in this study, H10, was grouped into genogroup I, along with the vaccine strains F9 and FCV-255. The other three isolates (75%) belonged to genogroup II. Thus, there were more isolates in genogroup II than in genogroup I. However, the antibody values of the four isolates against cat anti-F9 antisera were significantly decreased. There may be no relationship between the neutralizing antibody titre and genogroup. Amino acid sequence alignment of the four isolates showed that only a single amino acid in region C, which is involved in neutralization epitopes, was different in ML89 strain from that of F9. The other three strains, H10, Ao198-1 and FCV-B, shared the same amino acid sequence with F9. Alignment of amino acids for linear epitopes in the F9 strain, which are located at regions D and E, showed variations in 5' hypervariable region (HVR) of E, whereas D and conE had only synonymous substitutions i.e. no change in the amino acid sequence. This mutation in 5' HVR of region E suggested a vaccine breakdown, as the region is known to be essential for antigenicity. The genogroup II FCV is likely to be the cause of the FCV infection in this study, while the vaccine strains belong to genogroup I. Thus, the existing vaccine may need reevaluation for its effectiveness.

  6. Phylogenetic analysis of human immunodeficiency virus type 2 isolated from Cuban individuals.

    PubMed

    Machado, Liuber Y; Díaz, Héctor M; Noa, Enrique; Martín, Dayamí; Blanco, Madeline; Díaz, Dervel F; Sánchez, Yordank R; Nibot, Carmen; Sánchez, Lourdes; Dubed, Marta

    2014-08-01

    The presence of infection by human immunodeficiency virus type 2 (HIV-2) in Cuba has been previously documented. However, genetic information on the strains that circulate in the Cuban people is still unknown. The present work constitutes the first study concerning the phylogenetic relationship of HIV-2 Cuban isolates conducted on 13 Cuban patients who were diagnosed with HIV-2. The env sequences were analyzed for the construction of a phylogenetic tree with reference sequences of HIV-2. Phylogenetic analysis of the env gene showed that all the Cuban sequences clustered in group A of HIV-2. The analysis indicated several independent introductions of HIV-2 into Cuba. The results of the study will reinforce the program on the epidemiological surveillance of the infection in Cuba and make possible further molecular evolutionary studies.

  7. Phylogenetic analysis of Dengue virus 1 isolated from South Minas Gerais, Brazil.

    PubMed

    Drumond, Betania Paiva; Fagundes, Luiz Gustavo da Silva; Rocha, Raissa Prado; Fumagalli, Marcilio Jorge; Araki, Carlos Shigueru; Colombo, Tatiana Elisa; Nogueira, Mauricio Lacerda; Castilho, Thiago Elias; da Silveira, Nelson José Freitas; Malaquias, Luiz Cosme Cotta; Coelho, Luiz Felipe Leomil

    2016-01-01

    Dengue is a major worldwide public health problem, especially in the tropical and subtropical regions of the world. Primary infection with a single Dengue virus serotype causes a mild, self-limiting febrile illness called dengue fever. However, a subset of patients who experience secondary infection with a different serotype can progress to a more severe form of the disease, called dengue hemorrhagic fever. The four Dengue virus serotypes (1-4) are antigenically and genetically distinct and each serotype is composed of multiple genotypes. In this study we isolated one Dengue virus 1 serotype, named BR/Alfenas/2012, from a patient with dengue hemorrhagic fever in Alfenas, South Minas Gerais, Brazil and molecular identification was performed based on the analysis of NS5 gene. Swiss mice were infected with this isolate to verify its potential to induce histopathological alterations characteristic of dengue. Liver histopathological analysis of infected animals showed the presence of inflammatory infiltrates, hepatic steatosis, as well as edema, hemorrhage and necrosis focal points. Phylogenetic and evolutionary analyses based on the envelope gene provided evidence that the isolate BR/Alfenas/2012 belongs to genotype V, lineage I and it is probably derived from isolates of Rio de Janeiro, Brazil. The isolate BR/Alfenas/2012 showed two unique amino acids substitutions (SER222THRE and PHE306SER) when compared to other Brazilian isolates from the same genotype/lineage. Molecular models were generated for the envelope protein indicating that the amino acid alteration PHE 306 SER could contribute to a different folding in this region located within the domain III. Further genetic and animal model studies using BR/Alfenas/2012 and other isolates belonging to the same lineage/genotype could help determine the relation of these genetic alterations and dengue hemorrhagic fever in a susceptible population.

  8. Phylogenetic analysis of Dengue virus 1 isolated from South Minas Gerais, Brazil

    PubMed Central

    Drumond, Betania Paiva; da Silva Fagundes, Luiz Gustavo; Rocha, Raissa Prado; Fumagalli, Marcilio Jorge; Araki, Carlos Shigueru; Colombo, Tatiana Elisa; Nogueira, Mauricio Lacerda; Castilho, Thiago Elias; da Silveira, Nelson José Freitas; Malaquias, Luiz Cosme Cotta; Coelho, Luiz Felipe Leomil

    2016-01-01

    Dengue is a major worldwide public health problem, especially in the tropical and subtropical regions of the world. Primary infection with a single Dengue virus serotype causes a mild, self-limiting febrile illness called dengue fever. However, a subset of patients who experience secondary infection with a different serotype can progress to a more severe form of the disease, called dengue hemorrhagic fever. The four Dengue virus serotypes (1–4) are antigenically and genetically distinct and each serotype is composed of multiple genotypes. In this study we isolated one Dengue virus 1 serotype, named BR/Alfenas/2012, from a patient with dengue hemorrhagic fever in Alfenas, South Minas Gerais, Brazil and molecular identification was performed based on the analysis of NS5 gene. Swiss mice were infected with this isolate to verify its potential to induce histopathological alterations characteristic of dengue. Liver histopathological analysis of infected animals showed the presence of inflammatory infiltrates, hepatic steatosis, as well as edema, hemorrhage and necrosis focal points. Phylogenetic and evolutionary analyses based on the envelope gene provided evidence that the isolate BR/Alfenas/2012 belongs to genotype V, lineage I and it is probably derived from isolates of Rio de Janeiro, Brazil. The isolate BR/Alfenas/2012 showed two unique amino acids substitutions (SER222THRE and PHE306SER) when compared to other Brazilian isolates from the same genotype/lineage. Molecular models were generated for the envelope protein indicating that the amino acid alteration PHE 306 SER could contribute to a different folding in this region located within the domain III. Further genetic and animal model studies using BR/Alfenas/2012 and other isolates belonging to the same lineage/genotype could help determine the relation of these genetic alterations and dengue hemorrhagic fever in a susceptible population. PMID:26887252

  9. Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis

    PubMed Central

    Kuramoto, Tae; Nishihara, Hidenori; Watanabe, Maiko; Okada, Norihiro

    2015-01-01

    Despite many studies on avian phylogenetics in recent decades that used morphology, mitochondrial genomes, and/or nuclear genes, the phylogenetic positions of several birds (e.g., storks) remain unsettled. In addition to the aforementioned approaches, analysis of retroposon insertions, which are nearly homoplasy-free phylogenetic markers, has also been used in avian phylogenetics. However, the first step in the analysis of retroposon insertions, that is, isolation of retroposons from genomic libraries, is a costly and time-consuming procedure. Therefore, we developed a high-throughput and cost-effective protocol to collect retroposon insertion information based on next-generation sequencing technology, which we call here the STRONG (Screening of Transposons Obtained by Next Generation Sequencing) method, and applied it to 3 waterbird species, for which we identified 35,470 loci containing chicken repeat 1 retroposons (CR1). Our analysis of the presence/absence of 30 CR1 insertions demonstrated the intra- and interordinal phylogenetic relationships in the waterbird assemblage, namely 1) Loons diverged first among the waterbirds, 2) penguins (Sphenisciformes) and petrels (Procellariiformes) diverged next, and 3) among the remaining families of waterbirds traditionally classified in Ciconiiformes/Pelecaniformes, storks (Ciconiidae) diverged first. Furthermore, our genome-scale, in silico retroposon analysis based on published genome data uncovered a complex divergence history among pelican, heron, and ibis lineages, presumably involving ancient interspecies hybridization between the heron and ibis lineages. Thus, our retroposon-based waterbird phylogeny and the established phylogenetic position of storks will help to understand the evolutionary processes of aquatic adaptation and related morphological convergent evolution. PMID:26527652

  10. Phylogenetic analysis of Wheat dwarf virus isolates from Iran.

    PubMed

    Parizipour, Mohamad Hamed Ghodoum; Schubert, Jörg; Behjatnia, Seyed Ali Akbar; Afsharifar, Alireza; Habekuß, Antje; Wu, Beilei

    2017-04-01

    Wheat dwarf virus (WDV) adversely affects cereal production in Asia, Europe, and North Africa. In this study, sequences of several WDV isolates from Iran which is located in the Fertile Crescent were analyzed. Analysis revealed a new geographic cluster for WDV-Wheat from Iran. Recombination analysis demonstrated the existence of several breakpoints in different regions of the viral genome. Data analysis demonstrated that WDV-Barley has an older history and lower diversity than WDV-Wheat. Sequence analysis identified a rare occasion of a co-infection of wheat with WDV-Wheat and WDV-Barley.

  11. Cloning, sequencing and phylogenetic analysis of the small GTPase gene cdc-42 from Ancylostoma caninum.

    PubMed

    Yang, Yurong; Zheng, Jing; Chen, Jiaxin

    2012-12-01

    CDC-42 is a member of the Rho GTPase subfamily that is involved in many signaling pathways, including mitosis, cell polarity, cell migration and cytoskeleton remodeling. Here, we present the first characterization of a full-length cDNA encoding the small GTPase cdc-42, designated as Accdc-42, isolated from the parasitic nematode Ancylostoma caninum. The encoded protein contains 191 amino acid residues with a predicted molecular weight of 21 kDa and displays a high level of identity with the Rho-family GTPase protein CDC-42. Phylogenetic analysis revealed that Accdc-42 was most closely related to Caenorhabditis briggsae cdc-42. Comparison with selected sequences from the free-living nematode Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, Danio rerio, Mus musculus and human genomes showed that Accdc-42 is highly conserved. AcCDC-42 demonstrates the highest identity to CDC-42 from C. briggsae (94.2%), and it also exhibits 91.6% identity to CDC-42 from C. elegans and 91.1% from Brugia malayi. Additionally, the transcript of Accdc-42 was analyzed during the different developmental stages of the worm. Accdc-42 was expressed in the L1/L2 larvae, L3 larvae and female and male adults of A. caninum.

  12. Phylogenetic analysis and expression patterns of p16 and p19 in Paracentrotus lividus embryos.

    PubMed

    Costa, Caterina; Karakostis, Konstantinos; Zito, Francesca; Matranga, Valeria

    2012-07-01

    P16 and P19 are two small acidic proteins involved in the formation of the biomineralized skeleton of sea urchin embryos and adults. Here, we describe the cloning and the embryonic temporal and spatial expression profiles of p16 and p19 mRNAs, identified for the first time in Paracentrotus lividus. Phylogenetic analysis showed a high degree of similarity of the deduced Pl-P16 and Pl-P19 sequences with the Lytechinus variegatus and Strongylocentrotus purpuratus orthologs. While only a reduced similarity with other phyla, including mammals, was detected, their implication in biomineralized tissues calls for their conservation in evolution. By comparative quantitative PCR and in situ hybridization, we found that Pl-p16 and Pl-p19 expression was restricted to skeletogenic cells throughout embryogenesis, with transcript levels peaking at the late gastrula stage. Dissimilar Pl-p16 and Pl-p19 spatial expression within the primary mesenchyme cell syncytium at the gastrula and pluteus stages suggests the occurrence of a different regulation of gene transcription.

  13. Detection and phylogenetic analysis of an atypical pestivirus, strain IZSPLV_To.

    PubMed

    Peletto, Simone; Zuccon, Fabio; Pitti, Monica; Gobbi, Elena; Marco, Luisa De; Caramelli, Maria; Masoero, Loretta; Acutis, Pier Luigi

    2012-02-01

    Recently, atypical bovine pestiviruses (BVDV-3) have been identified in batches of contaminated foetal calf serum (FCS) and in naturally infected cattle. During routine screening of FCS by conventional panpestivirus PCR assay, one batch showed traces of pestivirus nucleic acids, and the contaminating virus was typed as BVDV-3-like. Phylogenetic analysis based on three genome regions (5'UTR, N(pro) and E2) showed that this strain, named IZSPLV_To, clusters in a separate clade with CH_KaHo/cont, a cell culture contaminant detected in Switzerland. This study is the first report of the detection in Italy of a FCS batch contaminated with BVDV-3 and adds more evidence that atypical pestiviruses represent a serious cause for concern in cell culture laboratories, with potential repercussions on BVD control and vaccine biosafety. Our findings suggest that the BE/B2 primers may be able to detect BVDV-3 in a panpestivirus assay, but testing of a larger number of strains is required.

  14. Chitinase from Paracoccidioides brasiliensis: molecular cloning, structural, phylogenetic, expression and activity analysis.

    PubMed

    Bonfim, Sheyla M R C; Cruz, Aline H S; Jesuino, Rosália S A; Ulhoa, Cirano J; Molinari-Madlum, Eugênia E W I; Soares, Célia M A; Pereira, Maristela

    2006-03-01

    A full-length cDNA encoding a chitinase (Pbcts1) was cloned by screening a cDNA library from the yeast cells of Paracoccidioides brasiliensis. The cDNA consists of 1888 bp and encodes an ORF of 1218 bp corresponding to a protein of 45 kDa with 406 amino acid residues. The deduced PbCTS1 is composed of two signature family 18 catalytic domains and seems to belong to fungal/bacterial class. Phylogenetic analysis of PbCTS1 and other chitinases suggests the existence of paralogs of several chitinases to be grouped based on specialized functions, which may reflect the multiple and diverse roles played by fungi chitinases. Glycosyl hydrolase activity assays demonstrated that P. brasiliensis is able to produce and secrete these enzymes mainly during transition from yeast to mycelium. The fungus should be able to use chitin as a carbon source. The presence of an endocytic signal in the deduced protein suggests that it could be secreted by a vesicular nonclassical export pathway. The Pbcts1 expression in mycelium, yeast, during differentiation from mycelium to yeast and in yeast cells obtained from infected mice suggests the relevance of this molecule in P. brasiliensis electing PbCTS1 as an attractive drug target.

  15. Functional phylogenetic analysis of LGI proteins identifies an interaction motif crucial for myelination.

    PubMed

    Kegel, Linde; Jaegle, Martine; Driegen, Siska; Aunin, Eerik; Leslie, Kris; Fukata, Yuko; Watanabe, Masahiko; Fukata, Masaki; Meijer, Dies

    2014-04-01

    The cellular interactions that drive the formation and maintenance of the insulating myelin sheath around axons are only partially understood. Leucine-rich glioma-inactivated (LGI) proteins play important roles in nervous system development and mutations in their genes have been associated with epilepsy and amyelination. Their function involves interactions with ADAM22 and ADAM23 cell surface receptors, possibly in apposing membranes, thus attenuating cellular interactions. LGI4-ADAM22 interactions are required for axonal sorting and myelination in the developing peripheral nervous system (PNS). Functional analysis revealed that, despite their high homology and affinity for ADAM22, LGI proteins are functionally distinct. To dissect the key residues in LGI proteins required for coordinating axonal sorting and myelination in the developing PNS, we adopted a phylogenetic and computational approach and demonstrate that the mechanism of action of LGI4 depends on a cluster of three amino acids on the outer surface of the LGI4 protein, thus providing a structural basis for the mechanistic differences in LGI protein function in nervous system development and evolution.

  16. Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data.

    PubMed

    McMurdie, Paul J; Holmes, Susan

    2012-01-01

    We present a detailed description of a new Bioconductor package, phyloseq, for integrated data and analysis of taxonomically-clustered phylogenetic sequencing data in conjunction with related data types. The phyloseq package integrates abundance data, phylogenetic information and covariates so that exploratory transformations, plots, and confirmatory testing and diagnostic plots can be carried out seamlessly. The package is built following the S4 object-oriented framework of the R language so that once the data have been input the user can easily transform, plot and analyze the data. We present some examples that highlight the methods and the ease with which we can leverage existing packages.

  17. [Molecular phylogenetic analysis of the genus Abies (Pinaceae) based on the nucleotide sequence of chloroplast DNA].

    PubMed

    Semerikova, S A; Semerikov, V L

    2014-01-01

    A phylogenetic study of firs (Abies Mill.) was conducted using nucleotide sequences of several chloroplast DNA regions with a total length of 5580 bp. The analysis included 37 taxa, which represented the main evolutionary lineages of the genus, and Keteleeria daviana. According to phylogenetic reconstruction the Abies species were subdivided into six main groups, generally corresponding to their geographic distribution. The phylogenetic tree had three basal clades. All of these clades contained American species, and only one of them contained Eurasian species. The divergence time calibrations, based on paleobotanical data and the chloroplast DNA mutation rate estimates in Pinaceae, produced similar results..The age of diversification among the clades of the present-day Abies was estimated as the end of the Oligocene-beginning of Miocene. The age of the separation of Mediterranean firs from the Asian-North American branch corresponds to the Miocene. The age of diversification within the young groups of Mediterranean, Asian, and boreal American firs (A. lasiocarpa, A. balsamea, A. fraseri) was estimated as the Pliocene-Pleistocene. Based on the phylogenetic reconstruction obtained, the most plausible biogeographic scenarios were suggested. It is noted that the existing systematic classification of the genus Abies strongly contradicts with phylogenetic reconstruction and requires revision.

  18. Phylogenetic analysis of bacteria preserved in a permafrost ice wedge for 25,000 years.

    PubMed

    Katayama, Taiki; Tanaka, Michiko; Moriizumi, Jun; Nakamura, Toshio; Brouchkov, Anatoli; Douglas, Thomas A; Fukuda, Masami; Tomita, Fusao; Asano, Kozo

    2007-04-01

    Phylogenetic analysis of bacteria preserved within an ice wedge from the Fox permafrost tunnel was undertaken by cultivation and molecular techniques. The radiocarbon age of the ice wedge was determined. Our results suggest that the bacteria in the ice wedge adapted to the frozen conditions have survived for 25,000 years.

  19. EthoSeq: a tool for phylogenetic analysis and data mining in behavioral sequences.

    PubMed

    Japyassú, Hilton F; Alberts, Carlos C; Izar, Patrícia; Sato, Takechi

    2006-11-01

    This article introduces the software program called EthoSeq, which is designed to extract probabilistic behavioral sequences (tree-generated sequences, or TGSs) from observational data and to prepare a TGS-species matrix for phylogenetic analysis. The program uses Graph Theory algorithms to automatically detect behavioral patterns within the observational sessions. It includes filtering tools to adjust the search procedure to user-specified statistical needs. Preliminary analyses of data sets, such as grooming sequences in birds and foraging tactics in spiders, uncover a large number of TGSs which together yield single phylogenetic trees. An example of the use of the program is our analysis of felid grooming sequences, in which we have obtained 1,386 felid grooming TGSs for seven species, resulting in a single phylogeny. These results show that behavior is definitely useful in phylogenetic analysis. EthoSeq simplifies and automates such analyses, uncovers much of the hidden patterns of long behavioral sequences, and prepares this data for further analysis with standard phylogenetic programs. We hope it will encourage many empirical studies on the evolution of behavior.

  20. Aujeszky's disease in red fox (Vulpes vulpes): phylogenetic analysis unravels an unexpected epidemiologic link.

    PubMed

    Caruso, Claudio; Dondo, Alessandro; Cerutti, Francesco; Masoero, Loretta; Rosamilia, Alfonso; Zoppi, Simona; D'Errico, Valeria; Grattarola, Carla; Acutis, Pier Luigi; Peletto, Simone

    2014-07-01

    We describe Aujeszky's disease in a female of red fox (Vulpes vulpes). Although wild boar (Sus scrofa) would be the expected source of infection, phylogenetic analysis suggested a domestic rather than a wild source of virus, underscoring the importance of biosecurity measures in pig farms to prevent contact with wild animals.

  1. Phylogenetic analysis of of Sarcocystis nesbitti (Coccidia: Sarcocystidae) suggests a snake as its probable definitive host

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sarcocystis nesbitti was first described by Mandour in 1969 from rhesus monkey muscle. Its definitive host remains unknown. 18SrRNA gene of Sarcocystis nesbitti was amplified, sequenced, and subjected to phylogenetic analysis. Among those congeners available for comparison, it shares closest affinit...

  2. Phylogenetic analysis of the genus Microbacterium based on 16S rRNA gene sequences.

    PubMed

    Takeuchi, M; Yokota, A

    1994-11-15

    16S rRNA gene (rDNA) studies of the six species of the genus Microbacterium, M. lacticum, M. laevaniformans, M. dextranolyticum, M. imperiale, M. arborescens and M. aurum, were performed and the primary structures were compared with those of 29 representative actinobacteria and related organisms. Phylogenetic analysis indicated that six species of the genus Microbacterium and representative four species of the genus Aureobacterium appear to be phylogenetically coherent as was suggested by Rainey et al., although the peptidoglycan types of these two genera are different (peptidoglycan type B1 or B2). Thus, the phylogenetical analyses revealed that members of actinobacteria with group B-peptidoglycan do not cluster according to their peptidoglycan types, but form compact cluster different from actinobacteria or actinomycetes with group A-peptidoglycan.

  3. Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis

    PubMed Central

    Gibbs, S; Collard, M; Wood, B

    2002-01-01

    This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence. PMID:11833653

  4. Genetic and phylogenetic analysis of South Korean sacbrood virus isolates from infected honey bees (Apis cerana).

    PubMed

    Choe, Se-Eun; Nguyen, Thuy Thi-Dieu; Hyun, Bang-Hun; Noh, Jin-Hyeong; Lee, Hee-Soo; Lee, Chang-Hee; Kang, Seung-Won

    2012-05-25

    Sacbrood virus (SBV) is one of the most destructive honey bee viruses. The virus causes failure to pupate and death in both larvae and adult bees. Genetic analysis of SBV infected honey bees (Apis cerana) from five different provinces was carried out based on three nucleotide sequences; one partial structural protein coding sequence and two non-structural protein coding sequences. Sequences amplified by three specific primer pairs were aligned and compared with reference sequences deposited in the GenBank database. Sequence alignments revealed a low level of sequence variation among Korean isolates (≥ 98.6% nucleotide identity), regardless of the genome regions studied or the geographic origins of the strains. Multiple sequence comparisons indicated that Korean SBV isolates are genetically closely related to Chinese and other Asian strains. Interestingly, the Korean SBV isolates showed a number of unique nucleotides and amino acids that had not been observed in other published strains. Korean and other Asian isolates from the host A. cerana and the UK, European and Japanese strains from the host Apis mellifera showed differences in nucleotide and deduced amino acid identities. This suggests that host-specificity exists among SBV strains isolated from different species. Phylogenetic relatedness between compared sequences was analyzed by MEGA 4.1 software using the neighbor-joining (NJ) method with a boot-strap value of 1000 replicates. Obtained topologies were in agreement with previous studies, in which a distinct group of SBV was formed by UK and European genotypes and another group was comprised of Asian genotypes including strains that originated from China, Japan (japonica), India and Nepal. However, phylogeny based on a partial protein structural coding sequence grouped all Korean SBV isolates identified in A. cerana as a separate cluster. Our findings suggest that further study, including Korean SBV isolated from A. mellifera, is needed.

  5. Molecular characterization of glycoprotein genes and phylogenetic analysis of two swine paramyxoviruses isolated from United States.

    PubMed

    Qiao, Dan; Janke, Bruce H; Elankumaran, Subbiah

    2009-08-01

    Two swine paramyxoviruses (SPMV)-(81-19252 (Texas-81) and 92-7783 (ISU-92)-were isolated from encephalitic pigs in the United States in 1981 and 1992. Antigenic, morphologic, and biological characteristics of these two viruses were essentially similar to members of the family Paramyxoviridae. Antigenic analysis by indirect fluorescent antibody, immunoblot, and one-way cross-neutralization tests placed these viruses along with bovine parainfluenza 3 (BPIV3) viruses. Purified virions were 50-300 nm in size and morphologically indistinguishable from other paramyxoviruses. These two viruses hemagglutinated red blood cells and had neuraminidase activity. The gene junctions of fusion (F) and hemagglutinin (HN) glycoprotein genes of these viruses contained highly conserved transcription start and stop signal sequences and trinucleotide intergenic regions similar to other Paramyxoviridae. The F gene of ISU-92 was longer than Texas-81 due to insertion of a 24-nucleotide "U"-rich 3' untranslated region. Structure-based sequence alignment of glycoproteins of these two SPMVs indicated that they are essentially similar in structure and function to parainfluenzaviruses. The Texas-81 strain was closely related to BPIV3 Shipping Fever (SF) strain at nucleotide and amino acid level, while the ISU-92 strain was more closely related to BPIV3 910N strain. The envelope glycoproteins of ISU-92 had only approximately 92 and approximately 96% identity at nucleotide and amino acid levels with BPIV3-SF strain, respectively. The high sequence identities to BPIV3 indicated cross-species infection in pigs. Phylogenetic analyses based on both F protein and HN protein suggested the classification of these viruses into the subfamily Paramyxovirinae, genus Respirovirus, and genotype A of BPIV3.

  6. Structural and phylogenetic analysis of the MHC class I-like Fc receptor gene

    SciTech Connect

    Kandil, Eman; Ishibashi, Teruo; Kasahara, Masanori

    1995-06-01

    The intestinal epithelium of neonatal mice and rats expresses an Fc receptor that mediates selective uptake of IgG in mothers`milk. This receptor (FcRn), which helps newborn animals to acquire passive immunity, is an MHC class I-like heterodimer made up of a heavy chain and {beta}{sub 2}-microglobulin. In the present study, we determined the genomic structure of a mouse gene (FcRn) encoding the heavy of FcRn. The overall exon-intron organization of the Fcrn gene was similar to that of the Fcrn gene, thus providing structural evidence that Fcrn os a bona fide class I gene. The 5{prime}-flanking region of the Fcrn gene contained the binding motifs for two cytokine-inducible transcription factors, NF-IL6 and NF1. However, regulatory elements found in MHC class I genes (enhancer A, enhancer B, and the IFN response element) were absent. Phylogenetic tree analysis suggested that, like the MICA, AZGP1, and CD1 genes, the Fcrn gene diverged form MHC class I genes after the emergence of amphibians but before the split of placental and marsupial mammals. Consistent with this result, Southern blot analysis with a mouse Fcrn cDNA probe detected cross-hybridizing bands in various mammalian species and chickens. Sequence analysis of the Fcrn gene isolated from eight mouse strains showed that the membrane-distal domain of FcRn has at least three amino acid variants. The fact that Fcrn is a single copy gene indicates that it is expressed in both the neonatal intestine and the fetal yolk sac. 74 refs., 7 figs., 2 tabs.

  7. Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.

    PubMed

    Wen, Dingqiao; Yu, Yun; Hahn, Matthew W; Nakhleh, Luay

    2016-06-01

    The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.

  8. Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis.

    PubMed

    Faith, Daniel P

    2008-12-01

    New species conservation strategies, including the EDGE of Existence (EDGE) program, have expanded threatened species assessments by integrating information about species' phylogenetic distinctiveness. Distinctiveness has been measured through simple scores that assign shared credit among species for evolutionary heritage represented by the deeper phylogenetic branches. A species with a high score combined with a high extinction probability receives high priority for conservation efforts. Simple hypothetical scenarios for phylogenetic trees and extinction probabilities demonstrate how such scoring approaches can provide inefficient priorities for conservation. An existing probabilistic framework derived from the phylogenetic diversity measure (PD) properly captures the idea of shared responsibility for the persistence of evolutionary history. It avoids static scores, takes into account the status of close relatives through their extinction probabilities, and allows for the necessary updating of priorities in light of changes in species threat status. A hypothetical phylogenetic tree illustrates how changes in extinction probabilities of one or more species translate into changes in expected PD. The probabilistic PD framework provided a range of strategies that moved beyond expected PD to better consider worst-case PD losses. In another example, risk aversion gave higher priority to a conservation program that provided a smaller, but less risky, gain in expected PD. The EDGE program could continue to promote a list of top species conservation priorities through application of probabilistic PD and simple estimates of current extinction probability. The list might be a dynamic one, with all the priority scores updated as extinction probabilities change. Results of recent studies suggest that estimation of extinction probabilities derived from the red list criteria linked to changes in species range sizes may provide estimated probabilities for many different species

  9. [Phylogenetic analysis of methanogenic corn stalk degrading microbial communities].

    PubMed

    Qiao, Jiang-Tao; Guo, Rong-Bo; Yuan, Xian-Zheng; Shi, Xiao-Shuang; Xu, Xiao-Hui; Fan, Xiao-Lei; Qiu, Yan-Ling

    2013-04-01

    Methanogenic corn stalk degrading enrichment cultures were constructed using corn stalk as the sole carbon source and eight types of environmental samples as inocula. All the cultures could degrade corn stalk within 30-50 days and the total solids (TS) removal rates were in the range of 30%-40%. In six out of eight cultures, the cumulative methane yields per gram TS were 62.1-118.4 mL x g(-1), with acetate, propionate and butyrate as the major volatile fatty acids (100-500 mg x L(-1)), and the final pH were 6.5-6.7. In the other two cultures, the cumulative methane yields per gram TS were 8.5-9.7 mL xg(-1), while the concentrations of acetate were high (1200 mg x L(-1)), and the final pH were low (5.6-5.9). The bacterial and archaeal structures in eight enrichments were investigated with a 16S rRNA genes-based clone library method. Clones belonging to the bacterial phyla Firmicutes, Bacteroidetes, Synergistetes and Thermotogae were observed in abundance within the bacterial clone libraries, which accounted for 37.8%, 34.3%, 11.6% and 6.4% of the total number of bacterial clones, respectively. Within the domain Archaea, clones affiliated with the classes Methanomicrobia and Methanobacteria were found to be abundant in the archaeal clone libraries, which accounted for 61.1% and 38.9% of the total number of archaeal clones, respectively.

  10. Phylogenetic analysis of vertebrate lactate dehydrogenase (LDH) multigene families.

    PubMed

    Li, Yi-Ju; Tsoi, Stephen C-M; Mannen, Hideyuka; Shoei-lung Li, Steven

    2002-05-01

    In this paper we analyzed 49 lactate dehydrogenase (LDH) sequences, mostly from vertebrates. The amino acid sequence differences were found to be larger for a human-killifish pair than a human-lamprey pair. This indicates that some protein sequence convergence may occur and reduce the sequence differences in distantly related species. We also examined transitions and transversions separately for several species pairs and found that the transitions tend to be saturated in the distantly related species pair, while transversions are increasing. We conclude that transversions maintain a conservative rate through the evolutionary time. Kimura's two-parameter model for multiple-hit correction on transversions only was used to derive a distance measure and then construct a neighbor-joining (NJ) tree. Three findings were revealed from the NJ tree: (i) the branching order of the tree is consistent with the common branch pattern of major vertebrates; (ii) Ldh-A and Ldh-B genes were duplicated near the origin of vertebrates; and (iii) Ldh-C and Ldh-A in mammals were produced by an independent gene duplication in early mammalian history. Furthermore, a relative rate test showed that mammalian Ldh-C evolved more rapidly than mammalian Ldh-A. Under a two-rate model, this duplication event was calibrated to be approximately 247 million years ago (mya), dating back to the Triassic period. Other gene duplication events were also discovered in Xenopus, the first duplication occurring approximately 60-70 mya in both Ldh-A and Ldh-B, followed by another recent gene duplication event, approximately 20 mya, in Ldh-B.

  11. Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimal Information about a Phylogenetic Analysis (MIAPA)

    PubMed Central

    LEEBENS-MACK, JIM; VISION, TODD; BRENNER, ERIC; BOWERS, JOHN E.; CANNON, STEVEN; CLEMENT, MARK J.; CUNNINGHAM, CLIFFORD W.; dePAMPHILIS, CLAUDE; deSALLE, ROB; DOYLE, JEFF J.; EISEN, JONATHAN A.; GU, XUN; HARSHMAN, JOHN; JANSEN, ROBERT K.; KELLOGG, ELIZABETH A.; KOONIN, EUGENE V.; MISHLER, BRENT D.; PHILIPPE, HERVÉ; PIRES, J. CHRIS; QIU, YIN-LONG; RHEE, SEUNG Y.; SJÖLANDER, KIMMEN; SOLTIS, DOUGLAS E.; SOLTIS, PAMELA S.; STEVENSON, DENNIS W.; WALL, KERR; WARNOW, TANDY; ZMASEK, CHRISTIAN

    2011-01-01

    In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors. PMID:16901231

  12. Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis.

    PubMed

    Kushwaha, Hariom; Gupta, Shubhra; Singh, Vinay Kumar; Rastogi, Smita; Yadav, Dinesh

    2011-11-01

    The Dof (DNA binding with One Finger) family represents a classic zinc-finger transcription factors involved with multifarious roles exclusively in plants. There exists great diversity in terms of number of Dof genes observed in different crops. In current study, a total of 28 putative Dof genes have been predicted in silico from the recently available whole genome shotgun sequence of Sorghum bicolor (L.) Moench (with assigned accession numbers TPA:BK006983-BK007006 and TPA:BK007079-BK007082). The predicted SbDof genes are distributed on nine out of ten chromosomes of sorghum and most of these genes lack introns based on canonical intron/exon structure. Phylogenetic analysis of 28 SbDof proteins resulted in four subgroups constituting six clusters. The comparative phylogenetic analysis of these Dof proteins along with 30 rice and 36 Arabidopsis Dof proteins revealed six major groups similar to what has been observed earlier for rice and Arabidopsis. Motif analysis revealed the presence of conserved 50-52 amino acids Dof domain uniformly distributed across all the 28 Dof proteins of sorghum. The in silico cis-regulatory elements analysis of these SbDof genes suggested its diverse functions associated with light responsiveness, endosperm specific gene expression, hormone responsiveness, meristem specific expression and stress responsiveness.

  13. A phylogenetic analysis of the myxobacteria: basis for their classification

    NASA Technical Reports Server (NTRS)

    Shimkets, L.; Woese, C. R.

    1992-01-01

    The primary sequence and secondary structural features of the 16S rRNA were compared for 12 different myxobacteria representing all the known cultivated genera. Analysis of these data show the myxobacteria to form a monophyletic grouping consisting of three distinct families, which lies within the delta subdivision of the purple bacterial phylum. The composition of the families is consistent with differences in cell and spore morphology, cell behavior, and pigment and secondary metabolite production but is not correlated with the morphological complexity of the fruiting bodies. The Nannocystis exedens lineage has evolved at an unusually rapid pace and its rRNA shows numerous primary and secondary structural idiosyncrasies.

  14. Phylogenetic sequence analysis, recombinant expression, and tissue distribution of a channel catfish estrogen receptor beta

    USGS Publications Warehouse

    Xia, Zhenfang; Gale, William L.; Chang, Xiaotian; Langenau, David; Patino, Reynaldo; Maule, Alec G.; Densmore, Llewellyn D.

    2000-01-01

    An estrogen receptor β (ERβ) cDNA fragment was amplified by RT-PCR of total RNAextracted from liver and ovary of immature channel catfish. This cDNA fragment was used to screen an ovarian cDNA library made from an immature female fish. A clone was obtained that contained an open reading frame encoding a 575-amino-acid protein with a deduced molecular weight of 63.9 kDa. Maximum parsimony and Neighbor Joining analyses were used to generate a phylogenetic classification of channel catfish ERβ on the basis of 25 full-length teleost and tetrapod ER sequences. The consensus tree obtained indicated the existence of two major vertebrate ER subtypes, α and β. Within each subtype, and in accordance with established phylogenetic relationships, teleost and tetrapod ER were monophyletic confirming the results of a previous analysis (Z. Xiaet al., 1999, Gen. Comp. Endocrinol. 113, 360–368). Extracts of COS-7 cells transfectedwith channel catfish ERβ cDNA bound estrogen with high affinity (Kd = 0.21 nM) and specificity. The affinity of channel catfish ERβ for estrogen was higher than previously reported for channel catfish ERα. As determined by qualitative RT-PCR, the tissue distributions of ERα and ERβ were similar but not identical. Both ER subtypes were present in ovary and testis. ERα was found in all other tissues examined from juvenile and mature fish of both sexes. ERβ was also found in most tissues except, in most cases, whole blood and head kidney. Interestingly, the pattern of expression of ER subtypes in head kidney always corresponded to the pattern in whole blood. In conclusion, we isolated a channel catfish ERβ with ligand-binding affinity and tissue expression patterns different from ERα. Also, we confirmed the validity of our previously proposed general classification scheme for vertebrate ER into α and β subtypes and within each subtype, into teleost and tetrapod clades.

  15. Hepatitis E Virus Circulation in Italy: Phylogenetic and Evolutionary Analysis

    PubMed Central

    Montesano, Carla; Giovanetti, Marta; Ciotti, Marco; Cella, Eleonora; Lo Presti, Alessandra; Grifoni, Alba; Zehender, Gianguglielmo; Angeletti, Silvia; Ciccozzi, Massimo

    2016-01-01

    Background Hepatitis E virus (HEV), a major cause of acute viral hepatitis in developing countries, has been classified into four main genotypes and a number of subtypes. New genotypes have been recently identified in various mammals, including HEV genotype 3, which has a worldwide distribution. It is widespread among pigs in developed countries. Objectives This study investigated the genetic diversity of HEV among humans and swine in Italy. The date of origin and the demographic history of the HEV were also estimated. Materials and Methods A total of 327 HEV sequences of swine and humans from Italy were downloaded from the national centre for biotechnology information. Three different data sets were constructed. The first and the second data set were used to confirm the genotype of the sequences analyzed. The third data set was used to estimate the mean evolutionary rate and to determine the time-scaled phylogeny and demographic history. Results The Bayesian maximum clade credibility tree and the time of the most common recent ancestor estimates showed that the root of the tree dated back to the year 1907 (95% HPD: 1811 - 1975). Two main clades were found, divided into two subclades. Skyline plot analysis, performed separately for human and swine sequences, demonstrated the presence of a bottleneck only in the skyline plot from the swine sequences. Selective pressure analysis revealed only negatively selected sites. Conclusions This study provides support for the hypothesis that humans are probably infected after contact with swine sources. The findings emphasize the importance of checking the country of origin of swine and of improving sanitary control measures from the veterinary standpoint to prevent the spread of HEV infection in Italy. PMID:27226798

  16. Molecular analysis of phylogenetic relationships among Myrmecophytic macaranga species (Euphorbiaceae).

    PubMed

    Blattner, F R; Weising, K; Bänfer, G; Maschwitz, U; Fiala, B

    2001-06-01

    Many species of the paleotropical pioneer tree genus Macaranga Thou. (Euphorbiaceae) live in association with ants. Various types of mutualistic interactions exist, ranging from the attraction of unspecific ant visitors to obligate myrmecophytism. In the latter, nesting space and food bodies are exchanged for protection by highly specific ant partners (mainly species of the myrmicine genus Crematogaster). As a first step toward elucidating the coevolution of ant-plant interactions in the Macaranga-Crematogaster system, we have initiated a molecular investigation of the plant partners' phylogeny. Nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were analyzed for 73 accessions from 47 Macaranga species, representing 17 sections or informally described species groups. Three accessions from the putative sister taxon Mallotus Lour, were included as outgroups. Cladograms of the ITS data revealed Macaranga to be nested within Mallotus. ITS sequences are highly similar within section Pachystemon s.str., suggesting a relatively recent and rapid radiation of obligate myrmecophytes within this section. Forty-three accessions, mainly of ant-inhabited species, were additionally investigated by random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) techniques. Phenetic analysis of RAPD and MP-PCR banding profiles generally confirmed the ITS results. Best resolutions for individual clades were obtained when ITS and RAPD/MP-PCR data were combined into a single matrix and analyzed phenetically. The combined analysis suggests multiple (four) rather than a single evolutionary origin of myrmecophytism, at least one reversal from obligate myrmecophytism to nonmyrmecophytism, and one loss of mutualistic specifity.

  17. Phylogenetic Analysis of Human Immunodeficiency Virus Type 2 Group B

    PubMed Central

    Cella, Eleonora; Lo Presti, Alessandra; Giovanetti, Marta; Veo, Carla; Lai, Alessia; Dicuonzo, Giordano; Angeletti, Silvia; Ciotti, Marco; Zehender, Gianguglielmo; Ciccozzi, Massimo

    2016-01-01

    Context: Human immunodeficiency virus type 2 (HIV-2) infections are mainly restricted to West Africa; however, in the recent years, the prevalence of HIV-2 is a growing concern in some European countries and the Southwestern region of India. Despite the presence of different HIV-2 groups, only A and B Groups have established human-to-human transmission chains. Aims: This work aimed to evaluate the phylogeographic inference of HIV-2 Group B worldwide to estimate their data of origin and the population dynamics. Materials and Methods: The evolutionary rates, the demographic history for HIV-2 Group B dataset, and the phylogeographic analysis were estimated using a Bayesian approach. The viral gene flow analysis was used to count viral gene out/in flow among different locations. Results: The root of the Bayesian maximum clade credibility tree of HIV-2 Group B dated back to 1957. The demographic history of HIV-2 Group B showed that the epidemic remained constant up to 1970 when started an exponential growth. From 1985 to early 2000s, the epidemic reached a plateau, and then it was characterized by two bottlenecks and a new plateau at the end of 2000s. Phylogeographic reconstruction showed that the most probable location for the root of the tree was Ghana. Regarding the viral gene flow of HIV-2 Group B, the only observed viral gene flow was from Africa to France, Belgium, and Luxembourg. Conclusions: The study gives insights into the origin, history, and phylogeography of HIV-2 Group B epidemic. The growing number of infections of HIV-2 worldwide indicates the need for strengthening surveillance. PMID:27621561

  18. Composition and phylogenetic analysis of vitellogenin coding sequences in the Indonesian coelacanth Latimeria menadoensis.

    PubMed

    Canapa, Adriana; Olmo, Ettore; Forconi, Mariko; Pallavicini, Alberto; Makapedua, Monica Daisy; Biscotti, Maria Assunta; Barucca, Marco

    2012-07-01

    The coelacanth Latimeria menadoensis, a living fossil, occupies a key phylogenetic position to explore the changes that have affected the genomes of the aquatic vertebrates that colonized dry land. This is the first study to isolate and analyze L. menadoensis mRNA. Three different vitellogenin transcripts were identified and their inferred amino acid sequences compared to those of other known vertebrates. The phylogenetic data suggest that the evolutionary history of this gene family in coelacanths was characterized by a different duplication event than those which occurred in teleosts, amniotes, and amphibia. Comparison of the three sequences highlighted differences in functional sites. Moreover, despite the presence of conserved sites compared with the other oviparous vertebrates, some sites were seen to have changed, others to be similar only to those of teleosts, and others still to resemble only to those of tetrapods.

  19. Phylogenetic Analysis of Brassica rapa MATH-Domain Proteins

    PubMed Central

    Zhao, Liming; Huang, Yong; Hu, Yan; He, Xiaoli; Shen, Wenhui; Liu, Chunlin; Ruan, Ying

    2013-01-01

    The MATH (meprin and TRAF-C homology) domain is a fold of seven anti-parallel β-helices involved in protein-protein interaction. Here, we report the identification and characterization of 90 MATH-domain proteins from the Brassica rapa genome. By sequence analysis together with MATH-domain proteins from other species, the B. rapa MATH-domain proteins can be grouped into 6 classes. Class-I protein has one or several MATH domains without any other recognizable domain; Class-II protein contains a MATH domain together with a conserved BTB (Broad Complex, Tramtrack, and Bric-a-Brac ) domain; Class-III protein belongs to the MATH/Filament domain family; Class-IV protein contains a MATH domain frequently combined with some other domains; Class-V protein has a relative long sequence but contains only one MATH domain; Class-VI protein is characterized by the presence of Peptidase and UBQ (Ubiquitinylation) domains together with one MATH domain. As part of our study regarding seed development of B. rapa, six genes are screened by SSH (Suppression Subtractive Hybridization) and their expression levels are analyzed in combination with seed developmental stages, and expression patterns suggested that Bra001786, Bra03578 and Bra036572 may be seed development specific genes, while Bra001787, Bra020541 and Bra040904 may be involved in seed and flower organ development. This study provides the first characterization of the MATH domain proteins in B. rapa PMID:24179444

  20. Phylogenetic analysis and homology modelling of Paracentrotus lividus nectin.

    PubMed

    Costa, Caterina; Cavalcante, Carmela; Zito, Francesca; Yokota, Yukio; Matranga, Valeria

    2010-11-01

    The extracellular matrix protein Pl-nectin, a 210-kDa homodimer originally purified from sea urchin eggs, plays a crucial role in cell adhesion and embryonic morphogenesis. The compiled cDNA sequence, obtained by RT-PCR primer walking and 3' RACE, identified a 984aa product containing a 23aa signal peptide and including all six internal peptides identified by protein microsequencing. The protein is a new member of the galactose-binding protein superfamily as it consists of six 151-156aa-long tandemly repeated domains (D1-D6), homologous to the discoidin-like domains, also known as F5/8-type C domains. Based on homology modelling, we present a three-dimensional structure (3D) for D5, identified as the prototype domain. The molecular modelling of the assembled Pl-nectin homodimer accounts for a Pl-nectin quaternary structure composed of two 105-kDa C-shaped monomers linked by a S-S bridge. The presence of an LDT motif between the first and the second exposed loops of the D2 domain suggests the binding of Pl-nectin to an integrin receptor. Altogether, the in silico analysis described here is consistent with previous biochemical reports and offers a basis for predictions to be experimentally tested.

  1. Investigation of glycan evolution based on a comprehensive analysis of glycosyltransferases using phylogenetic profiling

    PubMed Central

    Tomono, Takayoshi; Kojima, Hisao; Fukuchi, Satoshi; Tohsato, Yukako; Ito, Masahiro

    2015-01-01

    Glycans play important roles in such cell-cell interactions as signaling and adhesion, including processes involved in pathogenic infections, cancers, and neurological diseases. Glycans are biosynthesized by multiple glycosyltransferases (GTs), which function sequentially. Excluding mucin-type O-glycosylation, the non-reducing terminus of glycans is biosynthesized in the Golgi apparatus after the reducing terminus is biosynthesized in the ER. In the present study, we performed genome-wide analyses of human GTs by investigating the degree of conservation of homologues in other organisms, as well as by elucidating the phylogenetic relationship between cephalochordates and urochordates, which has long been controversial in deuterostome phylogeny. We analyzed 173 human GTs and functionally linked glycan synthesis enzymes by phylogenetic profiling and clustering, compiled orthologous genes from the genomes of other organisms, and converted them into a binary sequence based on the presence (1) or absence (0) of orthologous genes in the genomes. Our results suggest that the non-reducing terminus of glycans is biosynthesized by newly evolved GTs. According to our analysis, the phylogenetic profiles of GTs resemble the phylogenetic tree of life, where deuterostomes, metazoans, and eukaryotes are resolved into separate branches. Lineage-specific GTs appear to play essential roles in the divergence of these particular lineages. We suggest that urochordates lose several genes that are conserved among metazoans, such as those expressing sialyltransferases, and that the Golgi apparatus acquires the ability to synthesize glycans after the ER acquires this function. PMID:27493855

  2. The complete mitochondrial genome of Microtus fortis calamorum (Arvicolinae, Rodentia) and its phylogenetic analysis.

    PubMed

    Jiang, Xianhuan; Gao, Jun; Ni, Liju; Hu, Jianhua; Li, Kai; Sun, Fengping; Xie, Jianyun; Bo, Xiong; Gao, Chen; Xiao, Junhua; Zhou, Yuxun

    2012-05-01

    Microtus fortis is a special resource of rodent in China. It is a promising experimental animal model for the study on the mechanism of Schistosome japonicum resistance. The first complete mitochondrial genome sequence for Microtus fortis calamorum, a subspecies of M. fortis (Arvicolinae, Rodentia), was reported in this study. The mitochondrial genome sequence of M. f. calamorum (Genbank: JF261175) showed a typical vertebrate pattern with 13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs and one major noncoding region (CR region).The extended termination associated sequences (ETAS-1 and ETAS-2) and conserved sequence block 1 (CSB-1) were found in the CR region. The putative origin of replication for the light strand (O(L)) of M. f. calamorum was 35bp long and showed high conservation in stem and adjacent sequences, but the difference existed in the loop region among three species of genus Microtus. In order to investigate the phylogenetic position of M. f. calamorum, the phylogenetic trees (Maximum likelihood and Bayesian methods) were constructed based on 12 protein-coding genes (except for ND6 gene) on H strand from 16 rodent species. M. f. calamorum was classified into genus Microtus, Arvcicolinae for the highly phylogenetic relationship with Microtus kikuchii (Taiwan vole). Further phylogenetic analysis results based on the cytochrome b gene ranged from M. f. calamorum to one of the subspecies of M. fortis, which formed a sister group of Microtus middendorfii in the genus Microtus.

  3. Phylogenetic Analysis of Petunia sensu Jussieu (Solanaceae) using Chloroplast DNA RFLP

    PubMed Central

    ANDO, TOSHIO; KOKUBUN, HISASHI; WATANABE, HITOSHI; TANAKA, NORIO; YUKAWA, TOMOHISA; HASHIMOTO, GORO; MARCHESI, EDUARDO; SUÁREZ, ENRIQUE; BASUALDO, ISABEL L.

    2005-01-01

    • Background and Aims The phylogenetic relationships of Petunia sensu Jussieu (Petunia sensu Wijsman plus Calibrachoa) are unclear. This study aimed to resolve this uncertainty using molecular evidence. • Methods Phylogenetic trees of 52 taxa of Petunia sensu Jussieu were constructed using restriction fragment length polymorphism (RFLP) of chloroplast DNA digested with 19 restriction enzymes and hybridized with 12 cloned Nicotiana chloroplast DNA fragments as probes. • Key Results In all, 89 phylogenetically informative RFLPs were detected and one 50 % majority consensus tree was obtained, using the maximum parsimony method, and one distance matrix tree, using the neighbour joining method. Petunia sensu Wijsman and Calibrachoa were monophyletic sister clades in both trees. Calibrachoa parviflora and C. pygmaea, previously thought to differ from the other species in terms of their cross-compatibility, seed morphology, and nuclear DNA content, formed a basal clade that was sister to the remainder of Calibrachoa. Several clades found in the phylogenetic trees corresponded to their distribution ranges, suggesting that recent speciation in the genus Petunia sensu Jussieu occurred independently in several different regions. • Conclusions The separation of Petunia sensu Wijsman and Calibrachoa was supported by chloroplast DNA analysis. Two groups in the Calibrachoa were also recognized with a high degree of confidence. PMID:15944177

  4. Molecular phylogenetic analysis of Indonesia Solanaceae based on DNA sequences of internal transcribed spacer region

    NASA Astrophysics Data System (ADS)

    Hidayat, Topik; Priyandoko, Didik; Islami, Dina Karina; Wardiny, Putri Yunitha

    2016-02-01

    Solanaceae is one of largest family in Angiosperm group with highly diverse in morphological character. In Indonesia, this group of plant is very popular due to its usefulness as food, ornamental and medicinal plants. However, investigation on phylogenetic relationship among the member of this family in Indonesia remains less attention. The purpose of this study was to evaluate the phylogenetics relationship of the family especially distributed in Indonesia. DNA sequences of Internal Transcribed Spacer (ITS) region of 19 species of Solanaceae and three species of outgroup, which belongs to family Convolvulaceae, Apocynaceae, and Plantaginaceae, were isolated, amplified, and sequenced. Phylogenetic tree analysis based on parsimony method was conducted with using data derived from the ITS-1, 5.8S, and ITS-2, separately, and the combination of all. Results indicated that the phylogenetic tree derived from the combined data established better pattern of relationship than separate data. Thus, three major groups were revealed. Group 1 consists of tribe Datureae, Cestreae, and Petunieae, whereas group 2 is member of tribe Physaleae. Group 3 belongs to tribe Solaneae. The use of the ITS region as a molecular markers, in general, support the global Solanaceae relationship that has been previously reported.

  5. Phylogenetic Analysis of Selected Menthol-Producing Species Belonging to the Lamiaceae Family.

    PubMed

    Mirzaei, Motahareh; Mirzaei, Hamed; Sahebkar, Amirhossein; Bagherian, Ali; Masoud Khoi, Mohammad Jaber; Reza Mirzaei, Hamid; Salehi, Rasoul; Reza Jaafari, Mahmoud; Kazemi Oskuee, Reza

    2015-01-01

    Menthol is an organic compound with diverse medicinal and commercial applications, and is made either synthetically or through extraction from mint oils. The aim of the present study was to investigate menthol levels in selected menthol-producing species belonging to the Lamiaceae family, and to determine phylogenetic relationships of menthol dehydrogenase gene sequence among these species. Three genus of Lamiaceae, namely Mentha, Salvia, and Micromeria, were selected for phytochemical and phylogenetic analyses. After identification of each species based on menthol dehydrogenase gene in NCBI, BLAST software was used for the sequence alignment. MEGA4 software was used to draw phylogenetic tree for various species. Phytochemical analysis revealed that the highest and lowest amounts of both essential oil and menthol belonged to Mentha spicata and Micromeria hyssopifolia, respectively. The species Mentha spicata and Mentha piperita, which were assigned to one cluster in the dendrogram, contained the highest amounts of essential oil and menthol while Micromeria species, which was in the distinct cluster and placed in the farther evolutionary distance, contained the lowest amount of essential oil and menthol. Phylogenetic and phytochemistry analyses showed that essential oil and menthol contents of menthol-producing species are associated with menthol dehydrogenase gene sequence.

  6. Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core

    NASA Technical Reports Server (NTRS)

    Sheridan, Peter P.; Miteva, Vanya I.; Brenchley, Jean E.

    2003-01-01

    The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at -9 degrees C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at -2 degrees C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years.

  7. Phylogenetic Analysis of Anaerobic Psychrophilic Enrichment Cultures Obtained from a Greenland Glacier Ice Core

    PubMed Central

    Sheridan, Peter P.; Miteva, Vanya I.; Brenchley, Jean E.

    2003-01-01

    The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at −9°C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 × 107 cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at −2°C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years. PMID:12676695

  8. Phylogenetic analysis of Austrian canine distemper virus strains from clinical samples from dogs and wild carnivores.

    PubMed

    Benetka, V; Leschnik, M; Affenzeller, N; Möstl, K

    2011-04-09

    Austrian field cases of canine distemper (14 dogs, one badger [Meles meles] and one stone marten [Martes foina]) from 2002 to 2007 were investigated and the case histories were summarised briefly. Phylogenetic analysis of fusion (F) and haemagglutinin (H) gene sequences revealed different canine distemper virus (CDV) lineages circulating in Austria. The majority of CDV strains detected from 2002 to 2004 were well embedded in the European lineage. One Austrian canine sample detected in 2003, with a high similarity to Hungarian sequences from 2005 to 2006, could be assigned to the Arctic group (phocine distemper virus type 2-like). The two canine sequences from 2007 formed a clearly distinct group flanked by sequences detected previously in China and the USA on an intermediate position between the European wildlife and the Asia-1 cluster. The Austrian wildlife strains (2006 and 2007) could be assigned to the European wildlife group and were most closely related to, yet clearly different from, the 2007 canine samples. To elucidate the epidemiological role of Austrian wildlife in the transmission of the disease to dogs and vice versa, H protein residues related to receptor and host specificity (residues 530 and 549) were analysed. All samples showed the amino acids expected for their host of origin, with the exception of a canine sequence from 2007, which had an intermediate position between wildlife and canine viral strains. In the period investigated, canine strains circulating in Austria could be assigned to four different lineages reflecting both a high diversity and probably different origins of virus introduction to Austria in different years.

  9. Variability of P1 protein of zucchini yellow mosaic virus for strain differentiation and phylogenetic analysis with other potyviruses.

    PubMed

    Lee, K C; Wong, S M

    1998-01-01

    The complete nucleotide sequence of a Singapore isolate of zucchini yellow mosaic potyvirus (ZYMV-S) was determined from viral cDNA clones. The complete genome is 9603 nucleotides in length excluding the poly (A) tail. Computer analysis of the sequence revealed a single large open reading frame (ORF) that presumably encodes a polyprotein of 3082 amino acids with a calculated molecular weight of 350 kDa. Analysis of the helper component (HC) protein showed that the highly conserved motif K-I-T-C which is involved in aphid transmission appeared as K-L-S-C. There is also a change of D-A-G to G-A-G triplet near the N-terminal of the coat protein (CP). Amino acid sequence identity comparison of ZYMV-S gene products with the California and Reunion Island isolates of ZYMV revealed a minimum range of 65-75% to a maximum range of 95-98%. Comparison with other distinct potyviruses showed a low degree of identity from 19-74%. The 5' untranslated region (UTR) of ZYMV-S showed 67% and 72% identity when compared with the California and Reunion Island isolates, respectively. The sequence variability in the 5' UTR of ZYMV can be exploited for strain differentiation and phylogenetic analysis. ZYMV-S shared 94% and 82% identity in the 3' UTR as compared to the California and Reunion Island isolates, respectively. The P1 protein of ZYMV-S shared moderate sequence variability among ZYMV isolates but high sequence variability among all potyviruses. In addition, phylogenetic analysis using the P1 protein indicated that highly variable proteins in the viral genome could also be employed in the study of potyvirus taxonomy and used for strain differentiation.

  10. Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic.

    PubMed

    Storfer, Andrew; Alfaro, Michael E; Ridenhour, Benjamin J; Jancovich, James K; Mech, Stephen G; Parris, Matthew J; Collins, James P

    2007-11-01

    Distinguishing whether pathogens are novel or endemic is critical for controlling emerging infectious diseases, an increasing threat to wildlife and human health. To test the endemic vs. novel pathogen hypothesis, we present a unique analysis of intraspecific host-pathogen phylogenetic concordance of tiger salamanders and an emerging Ranavirus throughout Western North America. There is significant non-concordance of host and virus gene trees, suggesting pathogen novelty. However, non-concordance has likely resulted from virus introductions by human movement of infected salamanders. When human-associated viral introductions are excluded, host and virus gene trees are identical, strongly supporting coevolution and endemism. A laboratory experiment showed an introduced virus strain is significantly more virulent than endemic strains, likely due to artificial selection for high virulence. Thus, our analysis of intraspecific phylogenetic concordance revealed that human introduction of viruses is the mechanism underlying tree non-concordance and possibly disease emergence via artificial selection.

  11. Phylogenetic analysis of Porphyromonas species isolated from the oral cavity of Australian marsupials.

    PubMed

    Mikkelsen, Deirdre; Milinovich, Gabriel J; Burrell, Paul C; Huynh, Sharnan C; Pettett, Lyndall M; Blackall, Linda L; Trott, Darren J; Bird, Philip S

    2008-09-01

    Porphyromonas species are frequently isolated from the oral cavity and are associated with periodontal disease in both animals and humans. Black, pigmented Porphyromonas spp. isolated from the gingival margins of selected wild and captive Australian marsupials with varying degrees of periodontal disease (brushtail possums, koalas and macropods) were compared phylogenetically to Porphyromonas strains from non-marsupials (bear, wolf, coyote, cats and dogs) and Porphyromonas gingivalis strains from humans using 16S rRNA gene sequence analysis. The results of the phylogenetic analysis identified three distinct groups of strains. A monophyletic P. gingivalis group (Group 1) contained only strains isolated from humans and a Porphyromonas gulae group (Group 2) was divided into three distinct subclades, each containing both marsupial and non-marsupial strains. Group 3, which contained only marsupial strains, including all six strains isolated from captive koalas, was genetically distinct from P. gulae and may constitute a new Porphyromonas species.

  12. K-mer natural vector and its application to the phylogenetic analysis of genetic sequences

    PubMed Central

    Wen, Jia; Chan, Raymond H.; Yau, Shek-Chung; He, Rong L.; Yau, Stephen S. T.

    2014-01-01

    Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency. PMID:24858075

  13. Biological pattern and transcriptomic exploration and phylogenetic analysis in the odd floral architecture tree: Helwingia willd

    PubMed Central

    2014-01-01

    Background Odd traits in few of plant species usually implicate potential biology significances in plant evolutions. The genus Helwingia Willd, a dioecious medical shrub in Aquifoliales order, has an odd floral architecture-epiphyllous inflorescence. The potential significances and possible evolutionary origin of this specie are not well understood due to poorly available data of biological and genetic studies. In addition, the advent of genomics-based technologies has widely revolutionized plant species with unknown genomic information. Results Morphological and biological pattern were detailed via anatomical and pollination analyses. An RNA sequencing based transcriptomic analysis were undertaken and a high-resolution phylogenetic analysis was conducted based on single-copy genes in more than 80 species of seed plants, including H. japonica. It is verified that a potential fusion of rachis to the leaf midvein facilitates insect pollination. RNA sequencing yielded a total of 111450 unigenes; half of them had significant similarity with proteins in the public database, and 20281 unigenes were mapped to 119 pathways. Deduced from the phylogenetic analysis based on single-copy genes, the group of Helwingia is closer with Euasterids II and rather than Euasterids, congruent with previous reports using plastid sequences. Conclusions The odd flower architecture make H. Willd adapt to insect pollination by hosting those insects larger than the flower in size via leave, which has little common character that other insect pollination plants hold. Further the present transcriptome greatly riches genomics information of Helwingia species and nucleus genes based phylogenetic analysis also greatly improve the resolution and robustness of phylogenetic reconstruction in H. japonica. PMID:24969969

  14. Genotyping and Phylogenetic Analysis of Giardia duodenalis Isolates from Turkish Children

    PubMed Central

    Tamer, Gulden Sonmez; Kasap, Murat; Er, Doganhan Kadir

    2015-01-01

    Background Giardiasis is caused by the intestinal protozoan parasite Giardia duodenalis (synonyms: G. lamblia, G. intestinalis), which is one of the most frequent parasites that infect Turkish children. However, molecular characterization of G. duodenalis in Turkey is relatively scarce. The present work aimed at genotyping G. duodenalis isolates from Turkey using molecular techniques. Material/Methods In the present study, 145 fecal samples from children were collected to search for the presence of Giardia by microscopy and PCR screening. PCR generated a 384 bp fragment for β-giardin. The PCR products were sequenced and the sequences were subjected to phylogenetic analysis by using PHYLIP. Results Based on the phylogenetic analysis of the sequences, assemblage A, B, and mixed subtypes were determined. Of 22 isolates, 11 were identified as assemblage A (50%), 7 were assemblage B (31.8%), and 4 were assemblage AB (18.2%). Association between G. duodenalis assemblages and the epidemiological data was analyzed. No correlation was found between symptoms and infection with specific assemblages (P>0.05), but we found statistically significant association between age and the assemblage AB (P=0.001). Conclusions The association between G. duodenalis and the epidemiologic data were analyzed. Since assemblage A is the more prevalent subgroup compared with assemblage B, this subgroup might be responsible for common Giardia infections in Turkey. This is the first study that included a detailed phylogenetic analysis of Giardia strains from Turkey. PMID:25689970

  15. Distribution and genetic analysis of TTV and TTMV major phylogenetic groups in French blood donors.

    PubMed

    Biagini, Philippe; Gallian, Pierre; Cantaloube, Jean-François; Attoui, Houssam; de Micco, Philippe; de Lamballerie, Xavier

    2006-02-01

    TTV and TTMV (recently assigned to the floating genus Anellovirus) infect human populations (including healthy individuals) at high prevalence (>80%). They display notably high levels of genetic diversity, but very little is known regarding the distribution of Anellovirus genetic groups in human populations. We analyzed the distribution of the major genetic groups of TTV and TTMV in healthy voluntary blood donors using group-independent and group-specific PCR amplifications systems, combined with sequence determination and phylogenetic analysis. Analysis of Anellovirus groups revealed a non-random pattern of group distribution with a predominant prevalence of TTV phylogenetic groups 1, 3, and 5, and of TTMV group 1. Multiple co-infections were observed. In addition, TTMV sequences exhibiting a high genetic divergence with reference sequences were identified. This study provided the first picture of the genetic distribution of the major phylogenetic groups of members of the genus Anellovirus in a cohort of French voluntary blood donors. Obtaining such data from a reference population comprising healthy individuals was an essential step that will allow the subsequent comparative analysis of cohorts including patients with well-characterized diseases, in order to identify any possible relationship between Anellovirus infection and human diseases.

  16. A revision and phylogenetic analysis of the spider genus Oxysoma Nicolet (Araneae: Anyphaenidae, Amaurobioidinae).

    PubMed

    Aisen, Santiago; Ramírez, Martín J

    2015-08-06

    We review the spider genus Oxysoma Nicolet, with most of its species endemic from the southern temperate forests in Chile and Argentina, and present a phylogenetic analysis including seven species, of which three are newly described in this study (O. macrocuspis new species, O. kuni new species, and O. losruiles new species, all from Chile), together with other 107 representatives of Anyphaenidae. New geographical records and distribution maps are provided for all species, with illustrations and reviewed diagnoses for the genus and the four previously known species (O. punctatum Nicolet, O. saccatum (Tullgren), O. longiventre (Nicolet) and O. itambezinho Ramírez). The phylogenetic analysis using cladistic methods is based on 264 previously defined characters plus one character that arises from this study. The three new species are closely related with Oxysoma longiventre, and this four species compose what we define as the Oxysoma longiventre species group. The phylogenetic analysis did not retrieve the monophyly of Oxysoma, which should be reevaluated in the future, together with the genus Tasata.

  17. Comparative analysis of mitochondrial genomes in Diplura (hexapoda, arthropoda): taxon sampling is crucial for phylogenetic inferences.

    PubMed

    Chen, Wan-Jun; Koch, Markus; Mallatt, Jon M; Luan, Yun-Xia

    2014-01-01

    Two-pronged bristletails (Diplura) are traditionally classified into three major superfamilies: Campodeoidea, Projapygoidea, and Japygoidea. The interrelationships of these three superfamilies and the monophyly of Diplura have been much debated. Few previous studies included Projapygoidea in their phylogenetic considerations, and its position within Diplura still is a puzzle from both morphological and molecular points of view. Until now, no mitochondrial genome has been sequenced for any projapygoid species. To fill in this gap, we determined and annotated the complete mitochondrial genome of Octostigma sinensis (Octostigmatidae, Projapygoidea), and of three more dipluran species, one each from the Campodeidae, Parajapygidae, and Japygidae. All four newly sequenced dipluran mtDNAs encode the same set of genes in the same gene order as shared by most crustaceans and hexapods. Secondary structure truncations have occurred in trnR, trnC, trnS1, and trnS2, and the reduction of transfer RNA D-arms was found to be taxonomically correlated, with Campodeoidea having experienced the most reduction. Partitioned phylogenetic analyses, based on both amino acids and nucleotides of the protein-coding genes plus the ribosomal RNA genes, retrieve significant support for a monophyletic Diplura within Pancrustacea, with Projapygoidea more closely related to Campodeoidea than to Japygoidea. Another key finding is that monophyly of Diplura cannot be recovered unless Projapygoidea is included in the phylogenetic analyses; this explains the dipluran polyphyly found by past mitogenomic studies. Including Projapygoidea increased the sampling density within Diplura and probably helped by breaking up a long-branch-attraction artifact. This finding provides an example of how proper sampling is significant for phylogenetic inference.

  18. Overview of chitin metabolism enzymes in Manduca sexta: Identification, domain organization, phylogenetic analysis and gene expression.

    PubMed

    Tetreau, Guillaume; Cao, Xiaolong; Chen, Yun-Ru; Muthukrishnan, Subbaratnam; Jiang, Haobo; Blissard, Gary W; Kanost, Michael R; Wang, Ping

    2015-07-01

    Chitin is one of the most abundant biomaterials in nature. The biosynthesis and degradation of chitin in insects are complex and dynamically regulated to cope with insect growth and development. Chitin metabolism in insects is known to involve numerous enzymes, including chitin synthases (synthesis of chitin), chitin deacetylases (modification of chitin by deacetylation) and chitinases (degradation of chitin by hydrolysis). In this study, we conducted a genome-wide search and analysis of genes encoding these chitin metabolism enzymes in Manduca sexta. Our analysis confirmed that only two chitin synthases are present in M. sexta as in most other arthropods. Eleven chitin deacetylases (encoded by nine genes) were identified, with at least one representative in each of the five phylogenetic groups that have been described for chitin deacetylases to date. Eleven genes encoding for family 18 chitinases (GH18) were found in the M. sexta genome. Based on the presence of conserved sequence motifs in the catalytic sequences and phylogenetic relationships, two of the M. sexta chitinases did not cluster with any of the current eight phylogenetic groups of chitinases: two new groups were created (groups IX and X) and their characteristics are described. The result of the analysis of the Lepidoptera-specific chitinase-h (group h) is consistent with its proposed bacterial origin. By analyzing chitinases from fourteen species that belong to seven different phylogenetic groups, we reveal that the chitinase genes appear to have evolved sequentially in the arthropod lineage to achieve the current high level of diversity observed in M. sexta. Based on the sequence conservation of the catalytic domains and on their developmental stage- and tissue-specific expression, we propose putative functions for each group in each category of enzymes.

  19. Phylogenetic and Diversity Analysis of Dactylis glomerata Subspecies Using SSR and IT-ISJ Markers.

    PubMed

    Yan, Defei; Zhao, Xinxin; Cheng, Yajuan; Ma, Xiao; Huang, Linkai; Zhang, Xinquan

    2016-10-31

    The genus Dactylis, an important forage crop, has a wide geographical distribution in temperate regions. While this genus is thought to include a single species, Dactylis glomerata, this species encompasses many subspecies whose relationships have not been fully characterized. In this study, the genetic diversity and phylogenetic relationships of nine representative Dactylis subspecies were examined using SSR and IT-ISJ markers. In total, 21 pairs of SSR primers and 15 pairs of IT-ISJ primers were used to amplify 295 polymorphic bands with polymorphic rates of 100%. The average polymorphic information contents (PICs) of SSR and IT-ISJ markers were 0.909 and 0.780, respectively. The combined data of the two markers indicated a high level of genetic diversity among the nine D. glomerata subspecies, with a Nei's gene diversity index value of 0.283 and Shannon's diversity of 0.448. Preliminarily phylogenetic analysis results revealed that the 20 accessions could be divided into three groups (A, B, C). Furthermore, they could be divided into five clusters, which is similar to the structure analysis with K = 5. Phylogenetic placement in these three groups may be related to the distribution ranges and the climate types of the subspecies in each group. Group A contained eight accessions of four subspecies, originating from the west Mediterranean, while Group B contained seven accessions of three subspecies, originating from the east Mediterranean.

  20. The complete mitochondrial genome of Pallisentis celatus (Acanthocephala) with phylogenetic analysis of acanthocephalans and rotifers.

    PubMed

    Pan, Ting Shuang; Nie, Pin

    2013-07-01

    Acanthocephalans are a small group of obligate endoparasites. They and rotifers are recently placed in a group called Syndermata. However, phylogenetic relationships within classes of acanthocephalans, and between them and rotifers, have not been well resolved, possibly due to the lack of molecular data suitable for such analysis. In this study, the mitochondrial (mt) genome was sequenced from Pallisentis celatus (Van Cleave, 1928), an acanthocephalan in the class Eoacanthocephala, an intestinal parasite of rice-field eel, Monopterus albus (Zuiew, 1793), in China. The complete mt genome sequence of P. celatus is 13 855 bp long, containing 36 genes including 12 protein-coding genes, 22 transfer RNAs (tRNAs) and 2 ribosomal RNAs (rRNAs) as reported for other acanthocephalan species. All genes are encoded on the same strand and in the same direction. Phylogenetic analysis indicated that acanthocephalans are closely related with a clade containing bdelloids, which then correlates with the clade containing monogononts. The class Eoacanthocephala, containing P. celatus and Paratenuisentis ambiguus (Van Cleave, 1921) was closely related to the Palaeacanthocephala. It is thus indicated that acanthocephalans may be just clustered among groups of rotifers. However, the resolving of phylogenetic relationship among all classes of acanthocephalans and between them and rotifers may require further sampling and more molecular data.

  1. Molecular cloning, phylogenetic analysis and heat shock response of Babesia gibsoni heat shock protein 90

    PubMed Central

    YAMASAKI, Masahiro; TSUBOI, Yoshihiro; TANIYAMA, Yusuke; UCHIDA, Naohiro; SATO, Reeko; NAKAMURA, Kensuke; OHTA, Hiroshi; TAKIGUCHI, Mitsuyoshi

    2016-01-01

    The Babesia gibsoni heat shock protein 90 (BgHSP90) gene was cloned and sequenced. The length of the gene was 2,610 bp with two introns. This gene was amplified from cDNA corresponding to full length coding sequence (CDS) with an open reading frame of 2,148 bp. A phylogenetic analysis of the CDS of HSP90 gene showed that B. gibsoni was most closely related to B. bovis and Babesia sp. BQ1/Lintan and lies within a phylogenetic cluster of protozoa. Moreover, mRNA transcription profile for BgHSP90 exposed to high temperature were examined by quantitative real-time reverse transcription-polymerase chain reaction. BgHSP90 levels were elevated when the parasites were incubated at 43°C for 1 hr. PMID:27149891

  2. [Molecular-phylogenetic analysis of cyclopoids (Copepoda: Cyclopoida) from Lake Baikal and its water catchment basin].

    PubMed

    Maĭor, T Iu; Sheveleva, N G; Sukhanova, L V; Timoshkin, O A; Kiril'chik, S V

    2010-11-01

    Baikalian cyclopoids represent one of the richest endemic faunas of freshwater cyclopoid copepods. The genus Diacyclops Kiefer, 1927 is the most numerous by species number in the lake. In this work, molecular-phylogenetic analysis of 14 species and 1 sub-species from Lake Baikal and its water catchment basin is performed. The regions of mitochondrial cytochrom-oxydase I (COI) and of nuclear small-subunit 18S rRNA were used as evolution markers. In the obtained set of nucleotide sequences of COT gene, an effect of synonymous substitution saturation is revealed. Baikalian representatives of the genus Diacyclops form at phylogenetic schemes by two markers a monophyletic griup, it suggest their origin from a common ancestral form. Preliminary estimate of the age of this group is 20-25 My.

  3. Phylogenetic analysis and evolutionary origins of DNA polymerase X-family members

    PubMed Central

    Bienstock, Rachelle J.; Beard, William A.; Wilson, Samuel H.

    2014-01-01

    Mammalian DNA polymerase (pol) β is the founding member of a large group of DNA polymerases now termed the X-family. DNA polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. Accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the X-family of DNA polymerases. The bacterial X-family DNA polymerases, Saccharomyces cerevisiae pol IV, and four mammalian X-family polymerases appear to be directly related. These enzymes originated from an ancient common ancestor characterized in two Bacillus species. Understanding distinct functions for each of the X-family polymerases, evolving from a common bacterial ancestor is of significant interest in light of the specialized roles of these enzymes in DNA metabolism. PMID:25112931

  4. Full-genome sequencing and phylogenetic analysis of four neurovirulent Mexican isolates of porcine rubulavirus.

    PubMed

    Garcia-Barrera, Ali A; Del Valle, Alberto; Montaño-Hirose, Juan A; Barrón, Blanca Lilia; Salinas-Trujano, Juana; Torres-Flores, Jesus

    2017-02-09

    We report the complete genome sequences of four neurovirulent isolates of porcine rubulavirus (PorPV) from 2015 and one historical PorPV isolate from 1984 obtained by next-generation sequencing. A phylogenetic tree constructed using the individual sequences of the complete HN genes of the 2015 isolates and other historical sequences deposited in the GenBank database revealed that several recent neurovirulent isolates of PorPV (2008-2015) cluster together in a separate clade. Phylogenetic analysis of the complete genome sequences revealed that the neurovirulent strains of PorPV that circulated in Mexico during 2015 are genetically different from the PorPV strains that circulated during the 1980s.

  5. Molecular characterization and phylogenetic analysis of full-genome HBV subgenotype D3 sequences from Serbia.

    PubMed

    Stanojević, Boban; Osiowy, Carla; Schaefer, Stephan; Bojović, Ksenija; Blagojević, Jelena; Nešić, Milica; Yamashita, Shunichi; Stamenković, Gorana

    2011-08-01

    Hepatitis B virus (HBV) is classified into 8 genotypes with distinct geographical distribution. Genotype D (HBV/D) has the widest distribution area and is comprised of 7 subgenotypes. Subgenotypes D1, D2 and D3 appear worldwide, while D4-D7 have a more restricted distribution. Within the Mediterranean area, HBV/D and subgenotype D3 are the most prevalent. The purpose of this study was to characterize the full genome of Serbian HBV/D3 isolates by comparison and phylogenetic analysis with HBV/D3 sequences (66 samples) found in GeneBank/DDBJ databases from different parts of the world. Isolates were obtained from three patients diagnosed with chronic hepatitis B (HBsAg+). All three isolates have two very rare nucleotide substitutions, A929T and T150A, which indicate the same ancestor. Phylogenetic analysis of HBV/D3 genome sequences throughout the world follows an ethno-geographical origin of isolates with rare exceptions, which could be explained by human travelling and migration. The geographically close but ethnically different Serbian and Italian isolates clustered in the same subnode, and on a common branch with strains from Northern Canada. To test the apparently close HBV phylogenetic relationship between completely separated patients from Serbia and Northern Canada we analyzed in depth a 440 bp region of the HBsAg from Canadian (n=73) and Serbian (n=70) isolates. The constructed parsimony tree revealed that strains from Serbia and Northern Canada fell along the same branch which indicates independent evolution within regions of each country. Considering that HBsAg sequence has limited variability for phylogenetic analyses, our hypothesis needs further confirmation with more HBV complete genome sequences.

  6. Phylogenetic analysis of proteins involved in the stringent response in plant cells.

    PubMed

    Ito, Doshun; Ihara, Yuta; Nishihara, Hidenori; Masuda, Shinji

    2017-03-16

    The nucleotide (p)ppGpp is a second messenger that controls the stringent response in bacteria. The stringent response modifies expression of a large number of genes and metabolic processes and allows bacteria to survive under fluctuating environmental conditions. Recent genome sequencing analyses have revealed that genes responsible for the stringent response are also found in plants. These include (p)ppGpp synthases and hydrolases, RelA/SpoT homologs (RSHs), and the pppGpp-specific phosphatase GppA/Ppx. However, phylogenetic relationship between enzymes involved in bacterial and plant stringent responses is as yet generally unclear. Here, we investigated the origin and evolution of genes involved in the stringent response in plants. Phylogenetic analysis and primary structures of RSH homologs from different plant phyla (including Embryophyta, Charophyta, Chlorophyta, Rhodophyta and Glaucophyta) indicate that RSH gene families were introduced into plant cells by at least two independent lateral gene transfers from the bacterial Deinococcus-Thermus phylum and an unidentified bacterial phylum; alternatively, they were introduced into a proto-plant cell by a lateral gene transfer from the endosymbiotic cyanobacterium followed by gene loss of an ancestral RSH gene in the cyanobacterial linage. Phylogenetic analysis of gppA/ppx families indicated that plant gppA/ppx homologs form an individual cluster in the phylogenetic tree, and show a sister relationship with some bacterial gppA/ppx homologs. Although RSHs contain a plastidial transit peptide at the N terminus, GppA/Ppx homologs do not, suggesting that plant GppA/Ppx homologs function in the cytosol. These results reveal that a proto-plant cell obtained genes for the stringent response by lateral gene transfer events from different bacterial phyla and have utilized them to control metabolism in plastids and the cytosol.

  7. Origin and evolution of a new exon of 14-3-3ξ in bees and phylogenetic analysis.

    PubMed

    Zhan, Leilei; Jiang, Chao

    2013-04-01

    Mutually exclusive splicing, one type of alternative splicing, involves selection of alternatively spliced exons arranged in tandem and creates protein products with substitution of one segment of the amino acid sequence for another. Previous studies revealed that exon 5 of 14-3-3ξ from Apis mellifera (western honeybee) had three mutually exclusive exons, while orthologous exon of Nasonia vitripennis (parasitic wasp) had only two, suggesting that cases of exon gain or loss might have happened during the evolution of hymenopteran species. In the current study, we annotated and analyzed the 14-3-3ξ genes from 20 hymenopteran species successfully, and the results of phylogenetic analysis revealed the presence of a new mutually exclusive exon in corbiculate bees. In addition, we found that duplication via staggered homologous recombination was responsible for the origin of the new exon.

  8. Cloning and characterization of an actin gene of Chlamys farreri and the phylogenetic analysis of mollusk actins

    NASA Astrophysics Data System (ADS)

    Ma, Hongming; Mai, Kangsen; Liufu, Zhiguo; Xu, Wei

    2007-07-01

    An actingene (CfACTI) was cloned by using RT-PCR, 3’ and 5’RACE from hemocytes of the sea scallop Chlamys farreri. The full length of the transcript is 1 535 bp, which contains a long 3’ un-translated region of 436bp and 59bp of a 5’ un-translated sequence. The open reading frame encodes a polypeptide of 376 amino acids. Sequence comparisons indicated that CfACTI is more closely related to vertebrate cytoplasmic actins than muscle types. Phylogenetic analysis showed that molluscan actins could be generally divided into two categories: muscle and cytoplasmic, although both are similar to vertebrate cytoplasmic actins. It was also inferred that different isotypes existed in muscle or cytoplasma in mollusks. The genomic sequence of CfACTI was cloned and sequenced. Only one intron was detected: it was located between codons 42 and 43 and different from vertebrate actin genes.

  9. Analysis of Comparative Sequence and Genomic Data to Verify Phylogenetic Relationship and Explore a New Subfamily of Bacterial Lipases

    PubMed Central

    Salleh, Abu Bakar; Basri, Mahiran

    2016-01-01

    Thermostable and organic solvent-tolerant enzymes have significant potential in a wide range of synthetic reactions in industry due to their inherent stability at high temperatures and their ability to endure harsh organic solvents. In this study, a novel gene encoding a true lipase was isolated by construction of a genomic DNA library of thermophilic Aneurinibacillus thermoaerophilus strain HZ into Escherichia coli plasmid vector. Sequence analysis revealed that HZ lipase had 62% identity to putative lipase from Bacillus pseudomycoides. The closely characterized lipases to the HZ lipase gene are from thermostable Bacillus and Geobacillus lipases belonging to the subfamily I.5 with ≤ 57% identity. The amino acid sequence analysis of HZ lipase determined a conserved pentapeptide containing the active serine, GHSMG and a Ca2+-binding motif, GCYGSD in the enzyme. Protein structure modeling showed that HZ lipase consisted of an α/β hydrolase fold and a lid domain. Protein sequence alignment, conserved regions analysis, clustal distance matrix and amino acid composition illustrated differences between HZ lipase and other thermostable lipases. Phylogenetic analysis revealed that this lipase represented a new subfamily of family I of bacterial true lipases, classified as family I.9. The HZ lipase was expressed under promoter Plac using IPTG and was characterized. The recombinant enzyme showed optimal activity at 65°C and retained ≥ 97% activity after incubation at 50°C for 1h. The HZ lipase was stable in various polar and non-polar organic solvents. PMID:26934700

  10. Molecular surveillance and phylogenetic analysis of Old World arenaviruses in Zambia.

    PubMed

    Ishii, Akihiro; Thomas, Yuka; Moonga, Ladslav; Nakamura, Ichiro; Ohnuma, Aiko; Hang'ombe, Bernard M; Takada, Ayato; Mweene, Aaron S; Sawa, Hirofumi

    2012-10-01

    In order to survey arenaviruses in the Republic of Zambia, we captured 335 rodents from three cities between 2010 and 2011. Eighteen Luna virus (LUNV) and one lymphocytic choriomeningitis virus (LCMV)-related virus RNAs were detected by one-step RT-PCR from Mastomys natalensis and Mus minutoides, respectively. Four LUNV strains and one LCMV-related virus were isolated, and the whole genome nucleotide sequence was determined by pyrosequencing. Phylogenetic analyses revealed that the LUNV clade consists of two branches that are distinguished by geographical location and that the LCMV-related virus belongs to the LCMV clade, but diverges from the typical LCMVs. Comparison of nucleoprotein amino acid sequences indicated that the LCMV-related virus could be designated a novel arenavirus, which was tentatively named as the Lunk virus. Amino acid sequences of the GP, NP, Z and L proteins showed poor similarity among the three Zambian arenavirus strains, i.e. Luna, Lunk and Lujo virus.

  11. Phylogenetic and recombination analysis of rice black-streaked dwarf virus segment 9 in China.

    PubMed

    Zhou, Yu; Weng, Jian-Feng; Chen, Yan-Ping; Liu, Chang-Lin; Han, Xiao-Hua; Hao, Zhuan-Fang; Li, Ming-Shun; Yong, Hong-Jun; Zhang, De-Gui; Zhang, Shi-Huang; Li, Xin-Hai

    2015-04-01

    Rice black-streaked dwarf virus (RBSDV) is an economically important virus that causes maize rough dwarf disease and rice black-streaked dwarf disease in East Asia. To study RBSDV variation and recombination, we examined the segment 9 (S9) sequences of 49 RBSDV isolates from maize and rice in China. Three S9 recombinants were detected in Baoding, Jinan, and Jining, China. Phylogenetic analysis showed that Chinese RBSDV isolates could be classified into two groups based on their S9 sequences, regardless of host or geographical origin. Further analysis suggested that S9 has undergone negative and purifying selection.

  12. Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis

    PubMed Central

    Kim, Byoung-Jun; Kim, Bo-Ram; Lee, So-Young; Kim, Ga-Na; Kook, Yoon-Hoh; Kim, Bum-Joon

    2016-01-01

    Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950T and Mycobacterium yongonense DSM 45126T. Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126T than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum. PMID:27031100

  13. Phylogenetic analysis of Escherichia coli isolated from broilers with colibacillosis based on gyrA gene sequences.

    PubMed

    Shamsi, Hamid; Mardani, Karim; Ownagh, Abdolghaffar

    2017-01-01

    Escherichia coli isolates from chickens with colibacillosis were assigned to phylogenetic groups based on multiplex polymerase chain reaction (PCR) and antibacterial resistance of E. coli belonging to these groups was examined. Furthermore, the gyrA gene of isolates was sequenced and a phylogenetic tree was generated. A total of 84 E. coli isolates were grouped using multiplex PCR of TSPE4.C2, chuA, yjaA, and gadA molecular markers. Four phylogenetic groups were identified with strains divided as follows: 16 in group A (19.05%), 17 in group B1 (20.24%), 23 in group B2 (27.38%), and 28 in group D (33.33%). Escherichia coli isolates belonging to phylogenetic groups B2 and D were resistant to Soltrim and Flumequine unlike the majority of E. coli isolates that belonged to groups A and B1, and which were susceptible to these antibiotics. The phylogenetic results based on gyrA gene sequences from multiplex PCR revealed that E. coli phylogenetic grouping was in accordance with the clusters obtained in the phylogenetic tree. In conclusion, the comparative sequence analysis of gyrA sequences provides a firm framework for an accurate classification of E. coli and related taxa and may constitute a pertinent phylogenetic marker for E. coli.

  14. Diversification of land plants: insights from a family-level phylogenetic analysis

    PubMed Central

    2011-01-01

    Background Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic. Results We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate. Conclusions This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario. PMID:22103931

  15. Isolation and phylogenetic analysis of novel γ-gliadin genes in genus Dasypyrum.

    PubMed

    Li, G R; Liu, C; Yang, E N; Yang, Z J

    2013-03-13

    As the most ancient member of the wheat gluten family, the γ-gliadin genes are suitable for phylogenetic analysis among wheat and related species. Species in the grass genus Dasypyrum have been widely used for wheat cross breeding. However, the genomic relationships among Dasypyrum species have been little studied. We isolated 22 novel γ-gliadin gene sequences, among which 10 are putatively functional. The open reading frame lengths of these sequences range from 642 to 933 bp, and these putative proteins consist of five domains. Phylogenetic analyses showed that all Dasypyrum γ-gliadin gene sequences clustered in a large group; D. villosum and tetraploid D. breviaristatum γ-gliadin gene sequences clustered in a subgroup, while diploid D. breviaristatum γ-gliadin gene sequences clustered at the edge of the subgroup. All of the Dasypyrum γ-gliadin gene sequences were absent in three major T cell-stimulatory epitopes binding to HLA-DQ2/8 in celiac disease patients. Based on the phylogenetic analyses, we suggest that D. villosum and tetraploid D. breviaristatum evolved in parallel from a diploid ancestor D. breviaristatum.

  16. Phylogenetic analysis of the Trypanosoma genus based on the heat-shock protein 70 gene.

    PubMed

    Fraga, Jorge; Fernández-Calienes, Aymé; Montalvo, Ana Margarita; Maes, Ilse; Deborggraeve, Stijn; Büscher, Philippe; Dujardin, Jean-Claude; Van der Auwera, Gert

    2016-09-01

    Trypanosome evolution was so far essentially studied on the basis of phylogenetic analyses of small subunit ribosomal RNA (SSU-rRNA) and glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) genes. We used for the first time the 70kDa heat-shock protein gene (hsp70) to investigate the phylogenetic relationships among 11 Trypanosoma species on the basis of 1380 nucleotides from 76 sequences corresponding to 65 strains. We also constructed a phylogeny based on combined datasets of SSU-rDNA, gGAPDH and hsp70 sequences. The obtained clusters can be correlated with the sections and subgenus classifications of mammal-infecting trypanosomes except for Trypanosoma theileri and Trypanosoma rangeli. Our analysis supports the classification of Trypanosoma species into clades rather than in sections and subgenera, some of which being polyphyletic. Nine clades were recognized: Trypanosoma carassi, Trypanosoma congolense, Trypanosoma cruzi, Trypanosoma grayi, Trypanosoma lewisi, T. rangeli, T. theileri, Trypanosoma vivax and Trypanozoon. These results are consistent with existing knowledge of the genus' phylogeny. Within the T. cruzi clade, three groups of T. cruzi discrete typing units could be clearly distinguished, corresponding to TcI, TcIII, and TcII+V+VI, while support for TcIV was lacking. Phylogenetic analyses based on hsp70 demonstrated that this molecular marker can be applied for discriminating most of the Trypanosoma species and clades.

  17. Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa.

    PubMed

    Rajhi, Mouna; Ghedira, Kais; Chouikha, Anissa; Djebbi, Ahlem; Cheikh, Imed; Ben Yahia, Ahlem; Sadraoui, Amel; Hammami, Walid; Azouz, Msaddek; Ben Mami, Nabil; Triki, Henda

    2016-01-01

    HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization.

  18. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

    PubMed Central

    Broughton, Richard E.; Betancur-R., Ricardo; Li, Chenhong; Arratia, Gloria; Ortí, Guillermo

    2013-01-01

    Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on a broad taxonomic sample of 61 actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to teleosts; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group. PMID:23788273

  19. The Green Clade grows: A phylogenetic analysis of Aplastodiscus (Anura; Hylidae).

    PubMed

    Berneck, Bianca V M; Haddad, Célio F B; Lyra, Mariana L; Cruz, Carlos A G; Faivovich, Julián

    2016-04-01

    Green tree frogs of the genus Aplastodiscus occur in the Atlantic Forest and Cerrado biomes of South America. The genus comprises 15 medium-sized species placed in three species groups diagnosed mainly by cloacal morphology. A phylogenetic analysis was conducted to: (1) test the monophyly of these species groups; (2) explore the phylogenetic relationships among putative species; and (3) investigate species boundaries. The dataset included eight mitochondrial and nuclear gene fragments for up to 6642 bp per specimen. The results strongly support the monophyly of Aplastodiscus and of the A. albofrenatus and A. perviridis groups. Aplastodiscus sibilatus is the sister taxon of all other species of Aplastodiscus, making the A. albosignatus Group non-monophyletic as currently defined. At least six unnamed species are recognized for Aplastodiscus, increasing the diversity of the genus by 40%. A fourth species group, the A. sibilatus Group is recognized. Aplastodiscus musicus is transferred from the A. albofrenatus Group to the A. albosignatus Group, and A. callipygius is considered a junior synonym of A. albosignatus. Characters related to external cloacal morphology reveal an interesting evolutionary pattern of parallelisms and reversions, suggesting an undocumented level of complexity. We analyze, in light of our phylogenetic results, the evolution of reproductive biology and chromosome morphology in Aplastodiscus.

  20. Dynamic functional characterization and phylogenetic changes due to Long Chain Fatty Acids pulses in biogas reactors

    PubMed Central

    Kougias, Panagiotis G.; Treu, Laura; Campanaro, Stefano; Zhu, Xinyu; Angelidaki, Irini

    2016-01-01

    The process stability of biogas plants is often deteriorated by the accumulation of Long Chain Fatty Acids (LCFA). The microbial community shifts due to LCFA disturbances have been poorly understood as the molecular techniques used were not able to identify the genome characteristics of uncultured microorganisms, and additionally, the presence of limited number of reference genomes in public databases prevented the comprehension of specific functional roles characterizing these microorganisms. The present study is the first research which deciphers by means of high throughput shotgun sequencing the dynamics of the microbial community during an inhibitory shock load induced by single pulses of unsaturated LCFA at two different concentrations (i.e. 2 g/L-reactor and 3 g/L-reactor). The metagenomic analysis showed that only the microbes associated with LCFA degradation could encode proteins related to “chemotaxis” and “flagellar assembly”, which promoted the ability to move towards the LCFA sources so as to degrade them. Moreover, the syntrophic interactions found between Syntrophomonas sp. together with Methanosarcina sp. were possibly assigned to the menaquinone-electron transfer. Finally, it was proven that a previously exposed to LCFA inoculum is more efficient in the degradation process of LCFA due to the specialization of the microbial consortium. PMID:27353502

  1. Phylogenetic diversity of the Bacillus pumilus group and the marine ecotype revealed by multilocus sequence analysis.

    PubMed

    Liu, Yang; Lai, Qiliang; Dong, Chunming; Sun, Fengqin; Wang, Liping; Li, Guangyu; Shao, Zongze

    2013-01-01

    Bacteria closely related to Bacillus pumilus cannot be distinguished from such other species as B. safensis, B. stratosphericus, B. altitudinis and B. aerophilus simply by 16S rRNA gene sequence. In this report, 76 marine strains were subjected to phylogenetic analysis based on 7 housekeeping genes to understand the phylogeny and biogeography in comparison with other origins. A phylogenetic tree based on the 7 housekeeping genes concatenated in the order of gyrB-rpoB-pycA-pyrE-mutL-aroE-trpB was constructed and compared with trees based on the single genes. All these trees exhibited a similar topology structure with small variations. Our 79 strains were divided into 6 groups from A to F; Group A was the largest and contained 49 strains close to B. altitudinis. Additional two large groups were presented by B. safensis and B. pumilus respectively. Among the housekeeping genes, gyrB and pyrE showed comparatively better resolution power and may serve as molecular markers to distinguish these closely related strains. Furthermore, a recombinant phylogenetic tree based on the gyrB gene and containing 73 terrestrial and our isolates was constructed to detect the relationship between marine and other sources. The tree clearly showed that the bacteria of marine origin were clustered together in all the large groups. In contrast, the cluster belonging to B. safensis was mainly composed of bacteria of terrestrial origin. Interestingly, nearly all the marine isolates were at the top of the tree, indicating the possibility of the recent divergence of this bacterial group in marine environments. We conclude that B. altitudinis bacteria are the most widely spread of the B. pumilus group in marine environments. In summary, this report provides the first evidence regarding the systematic evolution of this bacterial group, and knowledge of their phylogenetic diversity will help in the understanding of their ecological role and distribution in marine environments.

  2. Molecular Phylogenetic Analysis of Infidum similis, Including Morphological Data and Estimation of its Genome Size.

    PubMed

    Martínez-Salazar, Elizabeth A; Rosas-Valdez, Rogelio; Gregory, T Ryan; Violante-González, Juan

    2016-08-01

    :   Infidum similis Travassos, 1916 (Dicrocoeliidae: Leipertrematinae) was found in the gall bladder of Leptophis diplotropis Günther, 1872 from El Podrido, Acapulco, Guerrero, Mexico. A phylogenetic analysis based on partial sequences of the 28S ribosomal RNA using maximum likelihood (ML) and Bayesian inference (BI) analyses was carried out to assess its phylogenetic position within suborder Xiphidiata, alongside members of the superfamilies Gorgoderoidea and Plagiorchoidea. The phylogenetic trees showed that the genus is most-closely related to the Plagiorchoidea rather than to the Gorgoderoidea, in keeping with previous taxonomic designations. Phylogenies obtained from ML and BI analysis of the 28S rDNA gene revealed a well supported clade in which Choledocystus hepaticus (Lutz, 1928) Sullivan, 1977 is sister to I. similis. On the other hand, a tree obtained using a partial sequence of the cytochrome c oxidase subunit 1 (cox1) mtDNA gene (ML and BI analysis), with species supposed to be closely related to I. similis according to 28S, does not support this relatedness. Based on the independence of Infidum from the subfamily Leipertrematinae Yamaguti, 1958 , our results clearly demonstrated that the genus corresponds to a different family and with species closely related to C. hepaticus within Plagiorchoidea. New data are presented about the tegumental surface of I. similis by scanning electron microscopy as well as the estimation of its haploid genome size using Feulgen Image Analysis Densitometry of sperm nuclei as part of the characterization of this species. This is the first genome size estimated for a member of Plagiorchiida, and these data will provide a new source of knowledge on helminth diversity and evolutionary studies. This constitutes the first host record, and new geographical distribution, for this species in Mexico.

  3. Complete nucleotide sequence of the Coturnix chinensis (blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species.

    PubMed

    Nishibori, M; Tsudzuki, M; Hayashi, T; Yamamoto, Y; Yasue, H

    2002-01-01

    Coturnix chinensis (blue-breasted quail) has been classically grouped in Galliformes Phasianidae Coturnix, based on morphologic features and biochemical evidence. Since the blue-breasted quail has the smallest body size among the species of Galliformes, in addition to a short generation time and an excellent reproductive performance, it is a possible model fowl for breeding and physiological studies of the Coturnix japonica (Japanese quail) and Gallus gallus domesticus (chicken), which are classified in the same family as blue-breasted quail. However, since its phylogenetic position in the family Phasianidae has not been determined conclusively, the sequence of the entire blue-breasted quail mitochondria (mt) genome was obtained to provide genetic information for phylogenetic analysis in the present study. The blue-breasted quail mtDNA was found to be a circular DNA of 16,687 base pairs (bp) with the same genomic structure as the mtDNAs of Japanese quail and chicken, though it is smaller than Japanese quail and chicken mtDNAs by 10 bp and 88 bp, respectively. The sequence identity of all mitochondrial genes, including those for 12S and 16S ribosomal RNAs, between blue-breasted quail and Japanese quail ranged from 84.5% to 93.5%; between blue-breasted quail and chicken, sequence identity ranged from 78.0% to 89.6%. In order to obtain information on the phylogenetic position of blue-breasted quail in Galliformes Phasianidae, the 2,184 bp sequence comprising NADH dehydrogenase subunit 2 and cytochrome b genes available for eight species in Galliformes [Japanese quail, chicken, Gallus varius (green junglefowl), Bambusicola thoracica (Chinese bamboo partridge), Pavo cristatus (Indian peafowl), Perdix perdix (gray partridge), Phasianus colchicus (ring-neck pheasant), and Tympanchus phasianellus (sharp-tailed grouse)] together with that of Aythya americana (redhead) were examined using a maximum likelihood (ML) method. The ML analyses on the first/second codon positions

  4. Structural, Functional and Phylogenetic Analysis of Sperm Lysozyme-Like Proteins.

    PubMed

    Kalra, Shalini; Pradeep, Mangottil Ayyappan; Mohanty, Ashok K; Kaushik, Jai K

    2016-01-01

    well as hydrogen bonding network between (NAG)3 and proteins were mostly conserved. LYZL5 in buffalo and other mammalian species contained additional 10-12 amino acid sequence at c-terminal that matched with ankyrin repeat domain-containing protein 27. Phylogenetic analysis indicated LYZL2 to be most ancient among all the LYZL proteins and that the evolution of LYZL proteins occurred through several gene duplications preceding the speciation of mammals from other vertebrates as distant as reptiles and amphibians.

  5. Structural, Functional and Phylogenetic Analysis of Sperm Lysozyme-Like Proteins

    PubMed Central

    Kalra, Shalini; Pradeep, Mangottil Ayyappan; Mohanty, Ashok K.; Kaushik, Jai K.

    2016-01-01

    well as hydrogen bonding network between (NAG)3 and proteins were mostly conserved. LYZL5 in buffalo and other mammalian species contained additional 10–12 amino acid sequence at c-terminal that matched with ankyrin repeat domain-containing protein 27. Phylogenetic analysis indicated LYZL2 to be most ancient among all the LYZL proteins and that the evolution of LYZL proteins occurred through several gene duplications preceding the speciation of mammals from other vertebrates as distant as reptiles and amphibians. PMID:27832206

  6. The amino acid sequences of two alpha chains of hemoglobins from Komodo dragon Varanus komodoensis and phylogenetic relationships of amniotes.

    PubMed

    Fushitani, K; Higashiyama, K; Moriyama, E N; Imai, K; Hosokawa, K

    1996-09-01

    To elucidate phylogenetic relationships among amniotes and the evolution of alpha globins, hemoglobins were analyzed from the Komodo dragon (Komodo monitor lizard) Varanus komodoensis, the world's largest extant lizard, inhabiting Komodo Islands, Indonesia. Four unique globin chains (alpha A, alpha D, beta B, and beta C) were isolated in an equal molar ratio by high performance liquid chromatography from the hemolysate. The amino acid sequences of two alpha chains were determined. The alpha D chain has a glutamine at E7 as does an alpha chain of a snake, Liophis miliaris, but the alpha A chain has a histidine at E7 like the majority of hemoglobins. Phylogenetic analyses of 19 globins including two alpha chains of Komodo dragon and ones from representative amniotes showed the following results: (1) The a chains of squamates (snakes and lizards), which have a glutamine at E7, are clustered with the embryonic alpha globin family, which typically includes the alpha D chain from birds; (2) birds form a sister group with other reptiles but not with mammals; (3) the genes for embryonic and adult types of alpha globins were possibly produced by duplication of the ancestral alpha gene before ancestral amniotes diverged, indicating that each of the present amniotes might carry descendants of the two types of alpha globin genes; (4) squamates first split off from the ancestor of other reptiles and birds.

  7. Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria.

    PubMed

    Ahmad, S; Weisburg, W G; Jensen, R A

    1990-02-01

    A comprehensive phylogenetic tree for virtually the entire assemblage of enteric bacteria is presented. Character states of aromatic amino acid biosynthesis are used as criteria, and the results are compared with partial trees based upon sequencing of 16S rRNA, 5S rRNA, and tryptophan leader peptide. Three major clusters are apparent. Enterocluster 1 possesses a gene fusion (trpG-trpD) encoding anthranilate synthase: anthranilate 5-phosphoribosylpyrophosphate phosphoribosyltransferase of tryptophan biosynthesis. This cluster includes the genera Escherichia, Shigella, Citrobacter, Salmonella, Klebsiella, and Enterobacter. The remaining two clusters lack the trpG-trpD gene fusion, but differ in the presence (enterocluster 2) or absence (enterocluster 3) of the three-step overflow pathway to L-phenylalanine. Enterocluster 2 consists of the genera Serratia and Erwinia. Enterocluster 3 includes the genera Cedecea, Kluyvera, Edwardsiella, Hafnia, Yersinia, Proteus, Providencia, and Morganella. Within these three major clusters, a tentative hierarchy of subcluster ordering is formulated on the basis of all data available. This hierarchical framework is proposed as a general working basis for continued refinement of the phylogenetic relationships of enteric bacteria.

  8. Application of phylogenetic microarray analysis to discriminate sources of fecal pollution.

    PubMed

    Dubinsky, Eric A; Esmaili, Laleh; Hulls, John R; Cao, Yiping; Griffith, John F; Andersen, Gary L

    2012-04-17

    Conventional methods for fecal source tracking typically use single biomarkers to systematically identify or exclude sources. High-throughput DNA sequence analysis can potentially identify all sources of microbial contaminants in a single test by measuring the total diversity of fecal microbial communities. In this study, we used phylogenetic microarray analysis to determine the comprehensive suite of bacteria that define major sources of fecal contamination in coastal California. Fecal wastes were collected from 42 different populations of humans, birds, cows, horses, elk, and pinnipeds. We characterized bacterial community composition using a DNA microarray that probes for 16S rRNA genes of 59,316 different bacterial taxa. Cluster analysis revealed strong differences in community composition among fecal wastes from human, birds, pinnipeds, and grazers. Actinobacteria, Bacilli, and many Gammaproteobacteria taxa discriminated birds from mammalian sources. Diverse families within the Clostridia and Bacteroidetes taxa discriminated human wastes, grazers, and pinnipeds from each other. We found 1058 different bacterial taxa that were unique to either human, grazing mammal, or bird fecal wastes. These OTUs can serve as specific identifier taxa for these sources in environmental waters. Two field tests in marine waters demonstrate the capacity of phylogenetic microarray analysis to track multiple sources with one test.

  9. [Topological Conflicts in Phylogenetic Analysis of Different Regions of the Sable (Martes zibellina L.) Mitochondrial Genome].

    PubMed

    Malyarchuk, B A; Derenko, M V; Denisova, G A; Litvinov, A N

    2015-08-01

    Phylogenetic analysis of different regions of the mitochondrial genome of the sable showed the presence of several topologies of phylogenetic trees, but the most statistically significant topology is A-BC, which was obtained as a result of the analysis of the mitochondrial genome as a whole, as well as of the individual CO1, ND4, and ND5 genes. Analysis of the intergroup divergence of the mtDNA haplotypes (Dxy) indicated that the maximum Dxy values between A and BC groups were accompanied by minimum differences between B and C groups only for six genes showing the A-BC topology (12S rRNA; CO1, CO2, ND4, ND5, and CYTB). It is assumed that the topological conflicts observed in the analysis of individual sable mtDNA genes are associated with the uneven distribution of mutations along the mitochondrial genome and the mitochondrial tree. This may be due to random causes, as well as the nonuniform effect of selection.

  10. Phylogenetic analysis of the Australian rosella parrots (Platycercus) reveals discordance among molecules and plumage.

    PubMed

    Shipham, Ashlee; Schmidt, Daniel J; Joseph, Leo; Hughes, Jane M

    2015-10-01

    Relationships and species limits among the colourful Australian parrots known as rosellas (Platycercus) are contentious because of poorly understood patterns of parapatry, sympatry and hybridization as well as complex patterns of geographical replacement of phenotypic forms. Two subgenera are, however, conventionally recognised: Platycercus comprises the blue-cheeked crimson rosella complex (Crimson Rosella P. elegans and Green Rosella P. caledonicus), and Violania contains the remaining four currently recognised species (Pale-headed Rosella P. adscitus, Eastern Rosella P. eximius, Northern Rosella P. venustus, and Western Rosella P. icterotis). We used phylogenetic analysis of ten loci (one mitochondrial, eight autosomal and one z-linked) and several individuals per nominal species primarily to examine relationships within the subgenera, especially the relationships and species limits within Violania. Of these, P. adscitus and P. eximius have long been considered sister species or conspecific due to a morphology-based hybrid zone and an early phylogenetic analysis of mitochondrial DNA restriction fragment length polymorphisms. The multilocus phylogenetic analysis presented here supports an alternative hypothesis aligning P. adscitus and P. venustus as sister species. Using divergence rates published in other avian studies, we estimated the divergence between P. venustus and P. adscitus at 0.0148-0.6124MYA and that between the P. adscitus/P. venustus ancestor and P. eximius earlier at 0.1617-1.0816MYA, both within the Pleistocene. Discordant topologies among gene and species trees are discussed and proposed to be the result of historical gene flow and/or incomplete lineage sorting (ILS). In particular, we suggest that discordance between mitochondrial and nuclear data may be the result of asymmetrical mitochondrial introgression from P. adscitus into P. eximius. The biogeographical implications of our findings are discussed relative to similarly distributed groups

  11. Isolation and Phylogenetic Analysis of Mucambo Virus (Venezuelan Equine Encephalitis Complex Subtype IIIA) in Trinidad

    PubMed Central

    Auguste, Albert J.; Volk, Sara M.; Arrigo, Nicole C.; Martinez, Raymond; Ramkissoon, Vernie; Adams, A. Paige; Thompson, Nadin N.; Adesiyun, Abiodun A.; Chadee, Dave D.; Foster, Jerome E.; Travassos Da Rosa, Amelia P.A.; Tesh, Robert B.; Weaver, Scott C.; Carrington, Christine V. F.

    2009-01-01

    In the 1950s and 1960s, alphaviruses in the Venezuelan equine encephalitis (VEE) antigenic complex were the most frequently isolated arboviruses in Trinidad. Since then, there has been very little research performed with these viruses. Herein, we report on the isolation, sequencing, and phylogenetic analyses of Mucambo virus (MUCV; VEE complex subtype IIIA), including 6 recently isolated from Culex (Melanoconion) portesi mosquitoes and 11 previously isolated in Trinidad and Brazil. Results show that nucleotide and amino acid identities across the complete structural polyprotein for the MUCV isolates were 96.6 – 100% and 98.7 – 100%, respectively, and the phylogenetic tree inferred for MUCV was highly geographically- and temporally- structured. Bayesian analyses suggest the sampled MUCV lineages have a recent common ancestry of approximately 198 years (with a 95% highest posterior density (HPD) interval of 63 – 448 years) prior to 2007, and an overall rate of evolution of 1.28 × 10−4 substitutions/site/yr. PMID:19631956

  12. Inclusion of cetaceans within the order Artiodactyla based on phylogenetic analysis of pancreatic ribonuclease genes.

    PubMed

    Kleineidam, R G; Pesole, G; Breukelman, H J; Beintema, J J; Kastelein, R A

    1999-03-01

    Mammalian secretory ribonucleases (RNases 1) form a family of extensively studied homologous proteins that were already used for phylogenetic analyses at the protein sequence level previously. In this paper we report the determination of six ribonuclease gene sequences of Artiodactyla and two of Cetacea. These sequences have been used with ruminant homologues in phylogenetic analyses that supported a group including hippopotamus and toothed whales, a group of ruminant pancreatic and brain-type ribonucleases, and a group of tylopod sequences containing the Arabian camel pancreatic ribonuclease gene and Arabian and Bactrian camel and alpaca RNase 1 genes of unknown function. In all analyses the pig was the first diverging artiodactyl. This DNA-based tree is compatible to published trees derived from a number of other genes. The differences to those trees obtained with ribonuclease protein sequences can be explained by the influence of convergence of pancreatic RNases from hippopotamus, camel, and ruminants and by taking into account the information from third codon positions in the DNA-based analyses. The evolution of sequence features of ribonucleases such as the distribution of positively charged amino acids and of potential glycosylation sites is described with regard to increased double-stranded RNA cleavage that is observed in several cetacean and artiodactyl RNases which may have no role in ruminant or ruminant-like digestion.

  13. Phylogenetic analysis of Gansu sheeppox virus isolates based on P32, GPCR, and RPO30 genes.

    PubMed

    Su, H L; Jia, H J; Yin, C; Jing, Z Z; Luo, X N; Chen, Y X

    2015-03-13

    Two outbreaks of sheeppox in sheep have occurred in Gansu Province, China. The P32, GPCR, and RPO30 genes were used as markers for differential diagnosis. We confirmed that the outbreaks were caused by sheeppox virus. Sequence and phylogenetic analysis of the P32, GPCR, and RPO30 genes revealed a close relationship between the 2 isolates and Chinese sheeppox viruses. Because ill sheep were imported from Jingyuan, another county of Gansu Province, our results strongly suggest the importance of veterinary surveillance prior to transportation.

  14. Genotyping and phylogenetic analysis of bovine viral diarrhea virus (BVDV) isolates in Kosovo.

    PubMed

    Goga, Izedin; Berxholi, Kristaq; Hulaj, Beqe; Sylejmani, Driton; Yakobson, Boris; Stram, Yehuda

    2014-01-01

    Three serum samples positive in Antigen ELISA BVDV have been tested to characterise genetic diversity of bovine viral diarrhea virus (BVDV) in Kosovo. Samples were obtained in 2011 from heifers and were amplified by reverse transcription-polymerase chain reaction, sequenced and analysed by computer-assisted phylogenetic analysis. Amplified products and nucleotide sequence showed that all 3 isolates belonged to BVDV 1 genotype and 1b sub genotype. These results enrich the extant knowledge of BVDV and represent the first documented data about Kosovo BVDV isolates.

  15. Analysis of Organic Acids.

    ERIC Educational Resources Information Center

    Griswold, John R.; Rauner, Richard A.

    1990-01-01

    Presented are the procedures and a discussion of the results for an experiment in which students select unknown carboxylic acids, determine their melting points, and investigate their solubility behavior in water and ethanol. A table of selected carboxylic acids is included. (CW)

  16. Detection and phylogenetic analysis of Orf virus from sheep in Brazil: a case report

    PubMed Central

    Abrahão, Jônatas S; Campos, Rafael K; Trindade, Giliane S; Guedes, Maria IM; Lobato, Zélia IP; Mazur, Carlos; Ferreira, Paulo CP; Bonjardim, Cláudio A; Kroon, Erna G

    2009-01-01

    Background Orf virus (ORFV), the prototype of the genus Parapoxvirus (PPV), is the etiological agent of contagious ecthyma, a severe exanthematic dermatitis that afflicts domestic and wild small ruminants. Although South American ORFV outbreaks have occurred and diagnosed there are no South American PPV major membrane glycoprotein B2L gene nucleotide sequences available. Case presentation an outbreak of ovine contagious ecthyma in Midwest Brazil was investigated. The diagnosis was based on clinical examinations and molecular biology techniques. The molecular characterization of the virus was done using PCR amplification, cloning and DNA sequencing of the B2L gene. The phylogenetic analysis demonstrated a high degree of identity with ORFV strains, and the isolate was closest to the ORFV-India 82/04 isolate. Another Brazilian ORFV isolate, NE1, was sequenced for comparative analysis and also showed a high degree of identity with an Asian ORFV strain. Conclusion Distinct ORFV strains are circulating in Brazil. This is the first report on the phylogenetic analysis of an ORFV in South America. PMID:19413907

  17. Fusarium culmorum is a single phylogenetic species based on multilocus sequence analysis.

    PubMed

    Obanor, Friday; Erginbas-Orakci, G; Tunali, B; Nicol, J M; Chakraborty, S

    2010-09-01

    Fusarium culmorum is a major pathogen of wheat and barley causing head blight and crown rot in cooler temperate climates of Australia, Europe, West Asia and North Africa. To better understand its evolutionary history we partially sequenced single copy nuclear genes encoding translation elongation factor 1-α (TEF), reductase (RED) and phosphate permease (PHO) in 100 F. culmorum isolates with 11 isolates of Fusarium crookwellense, Fusarium graminearum and Fusarium pseudograminearum. Phylogenetic analysis of multilocus sequence (MLS) data using Bayesian inference and maximum parsimony analysis showed that F. culmorum from wheat is a single phylogenetic species with no significant linkage disequilibrium and little or no lineage development along geographic origin. Both MLS and TEF and RED gene sequence analysis separated the four Fusarium species used and delineated three to four groups within the F. culmorum clade. But the PHO gene could not completely resolve isolates into their respective species. Fixation index and gene flow suggest significant genetic exchange between the isolates from distant geographic regions. A lack of strong lineage structure despite the geographic separation of the three collections indicates a frequently recombining species and/or widespread distribution of genotypes due to international trade, tourism and long-range dispersal of macroconidia. Moreover, the two mating type genes were present in equal proportion among the F. culmorum collection used in this study, leaving open the possibility of sexual reproduction.

  18. Phylogenetic and evolutionary analysis of influenza A H7N9 virus.

    PubMed

    Babakir-Mina, Muhammed; Dimonte, Slavatore; Lo Presti, Alessandra; Cella, Eleonora; Perno, Carlo Federico; Ciotti, Marco; Ciccozzi, Massimo

    2014-07-01

    Recently, human infections with the novel avian-origin influenza A H7N9 virus have been reported from various provinces in China. Human infections with avian influenza A viruses are rare and may cause a wide spectrum of clinical symptoms. This is the first time that human infection with a low pathogenic avian influenza A virus has been associated with a fatal outcome. Here, a phylogenetic and positive selective pressure analysis of haemagglutin (HA), neuraminidase (NA), and matrix protein (MP) genes of the novel reassortant H7N9 virus was carried out. The analysis showed that both structural genes of this reassortant virus likely originated from Euro-Asiatic birds, while NA was more likely to have originated from South Korean birds. The Bayesian phylogenetic tree of the MP showed a main clade and an outside cluster including four sequences from China. The United States and Guatemala classical H7N9-isolates appeared homogeneous and clustered together, although they are distinct from other classical Euro-Asiatic and novel H7N9 viruses. Selective pressure analysis did not reveal any site under statistically significant positive selective pressure in any of the three genes analyzed. Unknown certain intermediate hosts involved might be implicated, so extensive global surveillance and bird-to-person transmission should be closely considered in the future.

  19. Genome-wide identification and phylogenetic analysis of the SBP-box gene family in melons.

    PubMed

    Ma, Y; Guo, J W; Bade, R; Men, Z H; Hasi, A

    2014-10-27

    The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants, including green algae, moss, silver birch, snapdragon, Arabidopsis, rice, and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in melon. Using the highly conserved sequence of the Arabidopsis thaliana SBP-box domain protein as a probe of information sequence, the genome-wide protein database of melon was explored to obtain 13 SBP-box protein sequences, which were further divided into 4 groups, based on phylogenetic analysis. A further analysis centered on the melon SBP-box genetic family's phylogenetic evolution, sequence similarities, gene structure, and miR156 target sequence was also conducted. Analysis of all the expression patterns of melon SBP-box family genes showed that the SBP-box genes were detected in 7 kinds of tissue, and fruit had the highest expression level. CmSBP11 tends to present its specific expression in melon fruit and root. CmSBP09 expression was the highest in flower. Overall, the molecular evolution and expression pattern of the melon SBP-box gene family, revealed by these results, suggest its function differentiation that followed gene duplication.

  20. Phylogenetic analysis reveals the evolution and diversification of cyclins in eukaryotes.

    PubMed

    Ma, Zhaowu; Wu, Yuliang; Jin, Jialu; Yan, Jun; Kuang, Shuzhen; Zhou, Mi; Zhang, Yuexuan; Guo, An-Yuan

    2013-03-01

    Cyclins are a family of diverse proteins that play fundamental roles in regulating cell cycle progression in Eukaryotes. Cyclins have been identified from protists to higher Eukaryotes, while its evolution remains vague and the findings turn out controversial. Current classification of cyclins is mainly based on their functions, which may not be appropriate for the systematic evolutionary analysis. In this work, we performed comparative and phylogenetic analysis of cyclins to investigate their classification, origin and evolution. Cyclins originated in early Eukaryotes and evolved from protists to plants, fungi and animals. Based on the phylogenetic tree, cyclins can be divided into three major groups designated as the group I, II and III with different functions and features. Group I plays key roles in cell cycle, group II varied in actions are kingdom (plant, fungi and animal) specific, and group III functions in transcription regulation. Our results showed that the dominating cyclins (group I) diverged from protists to plants, fungi and animals, while divergence of the other cyclins (groups II and III) has occurred in protists. We also discussed the evolutionary relationships between cyclins and cyclin-dependent kinases (CDKs) and found that the cyclins have undergone divergence in protists before the divergence of animal CDKs. This reclassification and evolutionary analysis of cyclins might facilitate understanding eukaryotic cell cycle control.

  1. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    PubMed Central

    2011-01-01

    Background The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotrophia/Granulicatella. Results As lactobacilli are known for notorious resistance to probe penetration, probe-specific assay protocols were experimentally developed to provide maximum cell wall permeability, probe accessibility, hybridization stringency, and fluorescence intensity. The new assays were then applied in a pilot study to three biofilm samples harvested from variably demineralized bovine enamel discs that had been carried in situ for 10 days by different volunteers. Best probe penetration and fluorescent labeling of reference strains were obtained after combined lysozyme and achromopeptidase treatment followed by exposure to lipase. Hybridization stringency had to be established strictly for each probe. Thereafter all probes showed the expected specificity with reference strains and labeled the anticipated morphotypes in dental plaques. Applied to in situ grown biofilms the set of probes detected only Lactobacillus fermentum and bacteria of the Lactobacillus casei group. The most cariogenic biofilm contained two orders of magnitude higher L. fermentum cell numbers than the other biofilms. Abiotrophia/Granulicatella and streptococci from the mitis group were found in all samples at high levels, whereas Streptococcus mutans was detected in only one sample in very low numbers. Conclusions Application of these new group- and species-specific FISH probes to oral biofilm-forming lactic acid bacteria will allow a clearer understanding of the supragingival biome, its spatial architecture and of structure-function relationships implicated during plaque homeostasis and caries development. The probes should prove of value far beyond the field of oral microbiology, as many of

  2. The Complete Mitochondrial Genome of Corizus tetraspilus (Hemiptera: Rhopalidae) and Phylogenetic Analysis of Pentatomomorpha

    PubMed Central

    Guo, Zhong-Long; Wang, Juan; Shen, Yu-Ying

    2015-01-01

    Insect mitochondrial genome (mitogenome) are the most extensively used genetic information for molecular evolution, phylogenetics and population genetics. Pentatomomorpha (>14,000 species) is the second largest infraorder of Heteroptera and of great economic importance. To better understand the diversity and phylogeny within Pentatomomorpha, we sequenced and annotated the complete mitogenome of Corizus tetraspilus (Hemiptera: Rhopalidae), an important pest of alfalfa in China. We analyzed the main features of the C. tetraspilus mitogenome, and provided a comparative analysis with four other Coreoidea species. Our results reveal that gene content, gene arrangement, nucleotide composition, codon usage, rRNA structures and sequences of mitochondrial transcription termination factor are conserved in Coreoidea. Comparative analysis shows that different protein-coding genes have been subject to different evolutionary rates correlated with the G+C content. All the transfer RNA genes found in Coreoidea have the typical clover leaf secondary structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm and possesses a unusual anticodon stem (9 bp vs. the normal 5 bp). The control regions (CRs) among Coreoidea are highly variable in size, of which the CR of C. tetraspilus is the smallest (440 bp), making the C. tetraspilus mitogenome the smallest (14,989 bp) within all completely sequenced Coreoidea mitogenomes. No conserved motifs are found in the CRs of Coreoidea. In addition, the A+T content (60.68%) of the CR of C. tetraspilus is much lower than that of the entire mitogenome (74.88%), and is lowest among Coreoidea. Phylogenetic analyses based on mitogenomic data support the monophyly of each superfamily within Pentatomomorpha, and recognize a phylogenetic relationship of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))). PMID:26042898

  3. Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets

    PubMed Central

    2016-01-01

    Aetosauria is an early-diverging clade of pseudosuchians (crocodile-line archosaurs) that had a global distribution and high species diversity as a key component of various Late Triassic terrestrial faunas. It is one of only two Late Triassic clades of large herbivorous archosaurs, and thus served a critical ecological role. Nonetheless, aetosaur phylogenetic relationships are still poorly understood, owing to an overreliance on osteoderm characters, which are often poorly constructed and suspected to be highly homoplastic. A new phylogenetic analysis of the Aetosauria, comprising 27 taxa and 83 characters, includes more than 40 new characters that focus on better sampling the cranial and endoskeletal regions, and represents the most comprenhensive phylogeny of the clade to date. Parsimony analysis recovered three most parsimonious trees; the strict consensus of these trees finds an Aetosauria that is divided into two main clades: Desmatosuchia, which includes the Desmatosuchinae and the Stagonolepidinae, and Aetosaurinae, which includes the Typothoracinae. As defined Desmatosuchinae now contains Neoaetosauroides engaeus and several taxa that were previously referred to the genus Stagonolepis, and a new clade, Desmatosuchini, is erected for taxa more closely related to Desmatosuchus. Overall support for some clades is still weak, and Partitioned Bremer Support (PBS) is applied for the first time to a strictly morphological dataset demonstrating that this weak support is in part because of conflict in the phylogenetic signals of cranial versus postcranial characters. PBS helps identify homoplasy among characters from various body regions, presumably the result of convergent evolution within discrete anatomical modules. It is likely that at least some of this character conflict results from different body regions evolving at different rates, which may have been under different selective pressures. PMID:26819845

  4. Phylogenetic Analysis of Fusarium solani Associated with the Asian Longhorned Beetle, Anoplophora glabripennis

    PubMed Central

    Geib, Scott M.; Scully, Erin D.; Jimenez-Gasco, Maria del Mar; Carlson, John E.; Tien, Ming; Hoover, Kelli

    2012-01-01

    Culture-independent analysis of the gut of a wood-boring insect, Anoplophora glabripennis (Coleoptera: Cerambycidae), revealed a consistent association between members of the fungal Fusarium solani species complex and the larval stage of both colony-derived and wild A. glabripennis populations. Using the translation elongation factor 1-alpha region for culture-independent phylogenetic and operational taxonomic unit (OTU)-based analyses, only two OTUs were detected, suggesting that genetic variance at this locus was low among A. glabripennis-associated isolates. To better survey the genetic variation of F. solani associated with A. glabripennis, and establish its phylogenetic relationship with other members of the F. solani species complex, single spore isolates were created from different populations and multi-locus phylogenetic analysis was performed using a combination of the translation elongation factor alpha-1, internal transcribed spacer, and large subunit rDNA regions. These analyses revealed that colony-derived larvae reared in three different tree species or on artificial diet, as well as larvae from wild populations collected from three additional tree species in New York City and from a single tree species in Worcester, MA, consistently harbored F. solani within their guts. While there is some genetic variation in the F. solani carried between populations, within-population variation is low. We speculate that F. solani is able to fill a broad niche in the A. glabripennis gut, providing it with fungal lignocellulases to allow the larvae to grow and develop on woody tissue. However, it is likely that many F. solani genotypes could potentially fill this niche, so the relationship may not be limited to a single member of the F. solani species complex. While little is known about the role of filamentous fungi and their symbiotic associations with insects, this report suggests that larval A. glabripennis has developed an intimate relationship with F. solani

  5. Phylogenetic Analysis of Fusarium solani Associated with the Asian Longhorned Beetle, Anoplophora glabripennis.

    PubMed

    Geib, Scott M; Scully, Erin D; Jimenez-Gasco, Maria Del Mar; Carlson, John E; Tien, Ming; Hoover, Kelli

    2012-02-10

    Culture-independent analysis of the gut of a wood-boring insect, Anoplophora glabripennis (Coleoptera: Cerambycidae), revealed a consistent association between members of the fungal Fusarium solani species complex and the larval stage of both colony-derived and wild A. glabripennis populations. Using the translation elongation factor 1-alpha region for culture-independent phylogenetic and operational taxonomic unit (OTU)-based analyses, only two OTUs were detected, suggesting that genetic variance at this locus was low among A. glabripennis-associated isolates. To better survey the genetic variation of F. solani associated with A. glabripennis, and establish its phylogenetic relationship with other members of the F. solani species complex, single spore isolates were created from different populations and multi-locus phylogenetic analysis was performed using a combination of the translation elongation factor alpha-1, internal transcribed spacer, and large subunit rDNA regions. These analyses revealed that colony-derived larvae reared in three different tree species or on artificial diet, as well as larvae from wild populations collected from three additional tree species in New York City and from a single tree species in Worcester, MA, consistently harbored F. solani within their guts. While there is some genetic variation in the F. solani carried between populations, within-population variation is low. We speculate that F. solani is able to fill a broad niche in the A. glabripennis gut, providing it with fungal lignocellulases to allow the larvae to grow and develop on woody tissue. However, it is likely that many F. solani genotypes could potentially fill this niche, so the relationship may not be limited to a single member of the F. solani species complex. While little is known about the role of filamentous fungi and their symbiotic associations with insects, this report suggests that larval A. glabripennis has developed an intimate relationship with F. solani

  6. Phylogenetic analysis of vitamin B12-related metabolism in Mycobacterium tuberculosis

    PubMed Central

    Young, Douglas B.; Comas, Iñaki; de Carvalho, Luiz P. S.

    2015-01-01

    Comparison of genome sequences from clinical isolates of Mycobacterium tuberculosis with phylogenetically-related pathogens Mycobacterium marinum, Mycobacterium kansasii, and Mycobacterium leprae reveals diversity amongst genes associated with vitamin B12-related metabolism. Diversity is generated by gene deletion events, differential acquisition of genes by horizontal transfer, and single nucleotide polymorphisms (SNPs) with predicted impact on protein function and transcriptional regulation. Differences in the B12 synthesis pathway, methionine biosynthesis, fatty acid catabolism, and DNA repair and replication are consistent with adaptations to different environmental niches and pathogenic lifestyles. While there is no evidence of further gene acquisition during expansion of the M. tuberculosis complex, the emergence of other forms of genetic diversity provides insights into continuing host-pathogen co-evolution and has the potential to identify novel targets for disease intervention. PMID:25988174

  7. Phylogenetic analysis of field isolates of feline calcivirus (FCV) in Japan by sequencing part of its capsid gene.

    PubMed

    Sato, Y; Ohe, K; Murakami, M; Fukuyama, M; Furuhata, K; Kishikawa, S; Suzuki, Y; Kiuchi, A; Hara, M; Ishikawa, Y; Taneno, A

    2002-04-01

    The molecular epidemiology of the infectious disease caused by feline calcivirus (FCV) in Japan was investigated by analysing the phylogenetic relationship among 21 Japanese field isolates, including the F4 strain, and 30 global isolates. Parts of the capsid gene (B-F) of the isolates were amplified by RT-PCR, and the amino acid sequences were compared with those from the global isolates. Thirty-seven and 14 out of a total of 51 isolates were clustered into two distinct genogroups, I and II respectively, by UPGMA and NJ analysis. Seven of the 21 Japanese isolates (33%) fell into group I together with 30 global isolates, while the other 14 Japanese isolates (67%) belonged to group II. The bootstrap repetition analysis of groups I and II formed by the NJ method gave a value of 99.00%. The 14 latter Japanese isolates were clearly separated from the isolates in group I, and they were different from any previously known FCV, forming a new genogroup, which implies that this lineage has been confined to Japan. Comparing the amino acid sequences shared by groups I and II, the amino acid at position 377 in B region was asparagine (Asn or Asp (NH2)) in group I, while it was lysine (Lys) in all the strains in group II. Similarly, the amino acid at position 539 in the F region was alanine (Ala) or proline (Pro) in group I, while it was valine (Val) in group II; glycine (Gly) at position 557 in group I was serine (Ser) in Group II; and phenylalanine (Phe) or leucine (Leu) at position 566 in genogroup I was tyrosine (Tyr) in group II.

  8. Organic amendments increase phylogenetic diversity of arbuscular mycorrhizal fungi in acid soil contaminated by trace elements.

    PubMed

    Montiel-Rozas, María Del Mar; López-García, Álvaro; Kjøller, Rasmus; Madejón, Engracia; Rosendahl, Søren

    2016-08-01

    In 1998, a toxic mine spill polluted a 55-km(2) area in a basin southward to Doñana National Park (Spain). Subsequent attempts to restore those trace element-contaminated soils have involved physical, chemical, or biological methodologies. In this study, the restoration approach included application of different types and doses of organic amendments: biosolid compost (BC) and leonardite (LEO). Twelve years after the last addition, molecular analyses of arbuscular mycorrhizal (AM) fungal communities associated with target plants (Lamarckia aurea and Chrysanthemum coronarium) as well as analyses of trace element concentrations both in soil and in plants were performed. The results showed an improved soil quality reflected by an increase in soil pH and a decrease in trace element availability as a result of the amendments and dosages. Additionally, the phylogenetic diversity of the AM fungal community increased, reaching the maximum diversity at the highest dose of BC. Trace element concentration was considered the predominant soil factor determining the AM fungal community composition. Thereby, the studied AM fungal community reflects a community adapted to different levels of contamination as a result of the amendments. The study highlights the long-term effect of the amendments in stabilizing the soil system.

  9. Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling.

    PubMed

    Shin, Junha; Lee, Insuk

    2015-01-01

    Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life-Archaea, Bacteria, and Eukaryota-suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co-inheritance analysis

  10. Molecular characterization and phylogenetic analysis of human influenza A viruses isolated in Iran during the 2014-2015 season.

    PubMed

    Moasser, Elham; Behzadian, Farida; Moattari, Afagh; Fotouhi, Fatemeh; Rahimi, Amir; Zaraket, Hassan; Hosseini, Seyed Younes

    2017-03-22

    Influenza A viruses are an important cause of severe infectious diseases in humans and are characterized by their fast evolution rate. Global monitoring of these viruses is critical to detect newly emerging variants during annual epidemics. Here, we sought to genetically characterize influenza A/H1N1pdm09 and A/H3N2 viruses collected in Iran during the 2014-2015 influenza season. A total of 200 nasopharyngeal swabs were collected from patients with influenza-like illnesses. Swabs were screened for influenza A and B using real-time PCR. Furthermore, positive specimens with high virus load underwent virus isolation and genetic characterization of their hemagglutinin (HA) and M genes. Of the 200 specimens, 80 were influenza A-positive, including 44 A/H1N1pdm09 and 36 A/H3N2, while 18 were influenza B-positive. Phylogenetic analysis of the HA genes of the A/H1N1pdm09 viruses revealed the circulation of clade 6C, characterized by amino acid substitutions D97N, V234I and K283E. Analysis of the A/H3N2 viruses showed a genetic drift from the vaccine strain A/Texas/50/2012 with 5 mutations (T128A, R142G, N145S, P198S and S219F) belonging to the antigenic sites A, B, and D of the HA protein. The A/H3N2 viruses belonged to phylogenetic clades 3C.2 and 3C.3. The M gene trees of the Iranian A/H1N1pdm09 and A/H3N2 mirrored the clustering patterns of their corresponding HA trees. Our results reveal co-circulation of several influenza A virus strains in Iran during the 2014-2015 influenza season.

  11. Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics.

    PubMed

    Harrison, Nicola; Harrison, Richard J; Kidner, Catherine A

    2016-01-01

    Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia.

  12. Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics

    PubMed Central

    Harrison, Nicola; Harrison, Richard J.

    2016-01-01

    Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia. PMID:27058864

  13. Molecular phylogenetic and dating analysis of pierid butterfly species using complete mitochondrial genomes.

    PubMed

    Cao, Y; Hao, J S; Sun, X Y; Zheng, B; Yang, Q

    2016-12-02

    Pieridae is a butterfly family whose evolutionary history is poorly understood. Due to the difficulties in identifying morphological synapomorphies within the group and the scarcity of the fossil records, only a few studies on higher phylogeny of Pieridae have been reported to date. In this study, we describe the complete mitochondrial genomes of four pierid butterfly species (Aporia martineti, Aporia hippia, Aporia bieti, and Mesapia peloria), in order to better characterize the pierid butterfly mitogenomes and perform the phylogenetic analyses using all available mitogenomic sequence data (13PCGs, rRNAs, and tRNAs) from the 18 pierid butterfly species comprising the three main subfamilies (Dismorphiinae, Coliadinae and Pierinae). Our analysis shows that the four new mitogenomes share similar features with other known pierid mitogenomes in gene order and organization. Phylogenetic analyses by maximum likelihood and Bayesian inference show that the pierid higher-level relationship is: Dismorphiinae + (Coliadinae + Pierinae), which corroborates the results of some previous molecular and morphological studies. However, we found that the Hebomoia and Anthocharis make a sister group, supporting the traditional tribe Anthocharidini; in addition, the Mesapia peloria was shown to be clustered within the Aporia group, suggesting that the genus Mesapia should be reduced to the taxonomic status of subgenus. Our molecular dating analysis indicates that the family Pieridae began to diverge during the Late Cretaceous about 92 million years ago (mya), while the subfamily Pierinae diverged from the Coliadinae at about 86 mya (Late Cretaceous).

  14. Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2).

    PubMed

    Talens-Perales, David; Górska, Anna; Huson, Daniel H; Polaina, Julio; Marín-Navarro, Julia

    2016-01-01

    In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2). We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module) with two β-sandwich domains (non-catalytic) at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins. Our results led us to propose a model in which evolutionary diversity of GH2 enzymes is driven by the addition of different non-catalytic domains at the C-terminal region. This model accounts for the divergence of β-galactosidases from β-glucuronidases, the diversification of β-galactosidases with different transglycosylation specificities, and the emergence of bicistronic β-galactosidases. This study also allows the identification of groups of functionally uncharacterized protein sequences with potential biotechnological interest.

  15. Phylogenetic analysis and antimicrobial activities of Streptomyces isolates from mangrove sediment.

    PubMed

    Satheeja, Santhi V; Jebakumar, Solomon R D

    2011-02-01

    The phylogeny of members of Streptomyces bacteria isolated from mangrove sediments in the Manakudi estuary near the Arabian Sea, India, was analyzed in the present study. Among the 35 different isolates, five organisms, JS-9, JS-11, JS-12, JS-13 and JS-20, exhibited potent antimicrobial effects against methicillin-resistant Staphylococcus aureus (clinical isolate) and methicillin-susceptible S. aureus MTCC 3160 and Salmonella typhi MTCC 733; all other isolates displayed intermediate antimicrobial effects. RFLP analysis of HaeIII and BstUI double-digested 16S rRNA gene fragments of the isolates were distinguished into 20 distinct RFLP types, with the genetic similarity coefficient varying from 0.57 to 0.97. On average, 17 RFLP markers were observed from approximately 50 to 350 bp size and all the RFLP types showed significant genetic polymorphism by clustering into three major clusters. Phylogenetic analysis showed that the 20-member Streptomyces isolates were divided into three major clusters and they shared 97.2-99.8% sequence identity to the 16S rRNA gene sequences of the Streptomyces taxons of marine origin. The distribution of the isolates revealed that the distinct Streptomyces groups were clustered in the phylogenetic tree and there was a good correlation between the diversity of the antimicrobial phenotype and that of the 16S rRNA gene.

  16. Phylogenetic analysis of rabies virus isolated from canids in North and Northeast Brazil.

    PubMed

    de Souza, Débora Nunes; Carnieli, Pedro; Macedo, Carla Isabel; de Novaes Oliveira, Rafael; de Carvalho Ruthner Batista, Helena Beatriz; Rodrigues, Adriana Candido; Pereira, Patricia Mariano Cruz; Achkar, Samira Maria; Vieira, Luiz Fernando Pereira; Kawai, Juliana Galera Castilho

    2017-01-01

    Cases of canine rabies continue to occur in North and Northeast Brazil, and the number of notifications of rabies cases in wild canids has increased as a result of the expansion of urban areas at the expense of areas with native vegetation. In light of this, we performed molecular characterization of rabies virus isolates from dogs and Cerdocyon thous from various states in North and Northeast Brazil. In all, 102 samples from dogs (n = 56) and Cerdocyon thous (n = 46) collected between 2006 and 2012 were used. The nucleotide sequences obtained for the N gene of rabies virus were analyzed, and phylogenetic analysis revealed the presence of two distinct genetic lineages, one associated with canids and one with bats, and, within the canid cluster, two distinct sublineages circulating among dogs and Cerdocyon thous. In addition, phylogenetic groups associated with geographic region and fourteen cases of interspecific infection were observed among the isolates from canids. Our findings show that analysis of rabies virus lineages isolated from reservoirs such as canids must be constantly evaluated because the mutation rate is high.

  17. Phylogenetic Analysis of Cryptosporidium Parasites Based on the Small-Subunit rRNA Gene Locus

    PubMed Central

    Xiao, Lihua; Escalante, Lillian; Yang, Chunfu; Sulaiman, Irshad; Escalante, Anannias A.; Montali, Richard J.; Fayer, Ronald; Lal, Altaf A.

    1999-01-01

    Biological data support the hypothesis that there are multiple species in the genus Cryptosporidium, but a recent analysis of the available genetic data suggested that there is insufficient evidence for species differentiation. In order to resolve the controversy in the taxonomy of this parasite genus, we characterized the small-subunit rRNA genes of Cryptosporidium parvum, Cryptosporidium baileyi, Cryptosporidium muris, and Cryptosporidium serpentis and performed a phylogenetic analysis of the genus Cryptosporidium. Our study revealed that the genus Cryptosporidium contains the phylogenetically distinct species C. parvum, C. muris, C. baileyi, and C. serpentis, which is consistent with the biological characteristics and host specificity data. The Cryptosporidium species formed two clades, with C. parvum and C. baileyi belonging to one clade and C. muris and C. serpentis belonging to the other clade. Within C. parvum, human genotype isolates and guinea pig isolates (known as Cryptosporidium wrairi) each differed from bovine genotype isolates by the nucleotide sequence in four regions. A C. muris isolate from cattle was also different from parasites isolated from a rock hyrax and a Bactrian camel. Minor differences were also detected between C. serpentis isolates from snakes and lizards. Based on the genetic information, a species- and strain-specific PCR-restriction fragment length polymorphism diagnostic tool was developed. PMID:10103253

  18. Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2)

    PubMed Central

    Talens-Perales, David; Górska, Anna; Huson, Daniel H.; Polaina, Julio

    2016-01-01

    In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2). We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module) with two β-sandwich domains (non-catalytic) at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins. Our results led us to propose a model in which evolutionary diversity of GH2 enzymes is driven by the addition of different non-catalytic domains at the C-terminal region. This model accounts for the divergence of β-galactosidases from β-glucuronidases, the diversification of β-galactosidases with different transglycosylation specificities, and the emergence of bicistronic β-galactosidases. This study also allows the identification of groups of functionally uncharacterized protein sequences with potential biotechnological interest. PMID:27930742

  19. Phylogenetic analysis of the NS5 gene of dengue viruses isolated in Ecuador.

    PubMed

    Regato, Mary; Recarey, Ricardo; Moratorio, Gonzalo; de Mora, Domenica; Garcia-Aguirre, Laura; Gónzalez, Manuel; Mosquera, Carlos; Alava, Aracely; Fajardo, Alvaro; Alvarez, Macarena; D' Andrea, Lucia; Dubra, Ana; Martínez, Mariela; Khan, Baldip; Cristina, Juan

    2008-03-01

    Dengue virus (DENV) is a member of the genus Flavivirus of the family Flaviviridae. DENV causes a wide range of diseases in humans, from the acute febrile illness dengue fever (DF) to life-threatening dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). There is not knowledge of the genetic relations among DENV circulating in Ecuador. Given the emerging behaviour of DENV, a single tube RT-PCR assay using a pair of consensus primers to target the NS5 coding region has been recently validated for rapid detection of flaviviruses. In order to gain insight into the degree of genetic variation of DENV strains isolated in Ecuador, DENV NS5 sequences from 23 patients were obtained by direct sequencing of PCR fragments using the mentioned one step RT-PCR assay. Phylogenetic analysis carried out using the 23 Ecuadorian DENV NS5 sequences, as well as 56 comparable sequences from DENV strains isolated elsewhere, revealed a close genetic relation among Ecuadorian strains and DENV isolates of Caribbean origin. The use of partial NS5 gene sequences may represent a useful alternative for a rapid phylogenetic analysis of DENV outbreaks.

  20. First epidemiological and phylogenetic analysis of Hepatitis B virus infection in migrants from Mali.

    PubMed

    Cella, Eleonora; Ceccarelli, Giancarlo; Vita, Serena; Lai, Alessia; Presti, Alessandra Lo; Blasi, Aletheia; Palco, Maurizio Lo; Guarino, Michele Pier Luca; Zehender, Gianguglielmo; Angeletti, Silvia; Ciccozzi, Massimo

    2017-04-01

    The armed conflict in Mali caused a migration crisis since 2012. Most Malian refugees were in Italy. In Sub-Saharan Africa, the seroprevalence of anti-HBV antibodies is particularly high. Genotype E is the most prevalent throughout a crescent covering area from Angola to Senegal, including Mali. We report 16 HBV positive individual from 136 Malian asylum seekers in order to investigate the genetic diversity of HBV in this population. Sequencing and phylogenetic analysis has been used. The HBV genotype E isolates from Mali did not cluster together but were intermixed, with the other African sequences. Only three supported clade were evidenced and closely related to sequences from Burkina Faso. The estimated evolutionary rate was 9.29 × 10(4) . The root of the tree dated back to February 2008 in (95% HPD: 2006-2011). From this ancestor six main statistically supported clusters (pp > 0.80) were identified. The most recent Clade dated back to May 2015. The BSP showed that the effective number of infections softly increased from 2011 to the 2015. Phylogenetic analysis helped in understanding how two on sixteen individuals, have been infected in Italy, and give an important improvement in prevention campaigns and monitoring of the viral infection in migrants. J. Med. Virol. 89:639-646, 2017. © 2016 Wiley Periodicals, Inc.

  1. Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.

    PubMed

    Lu, Bin; Yang, Weizhao; Dai, Qiang; Fu, Jinzhong

    2013-01-01

    The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a

  2. Phylogenetic analysis of Demodex caprae based on mitochondrial 16S rDNA sequence.

    PubMed

    Zhao, Ya-E; Hu, Li; Ma, Jun-Xian

    2013-11-01

    Demodex caprae infests the hair follicles and sebaceous glands of goats worldwide, which not only seriously impairs goat farming, but also causes a big economic loss. However, there are few reports on the DNA level of D. caprae. To reveal the taxonomic position of D. caprae within the genus Demodex, the present study conducted phylogenetic analysis of D. caprae based on mt16S rDNA sequence data. D. caprae adults and eggs were obtained from a skin nodule of the goat suffering demodicidosis. The mt16S rDNA sequences of individual mite were amplified using specific primers, and then cloned, sequenced, and aligned. The sequence divergence, genetic distance, and transition/transversion rate were computed, and the phylogenetic trees in Demodex were reconstructed. Results revealed the 339-bp partial sequences of six D. caprae isolates were obtained, and the sequence identity was 100% among isolates. The pairwise divergences between D. caprae and Demodex canis or Demodex folliculorum or Demodex brevis were 22.2-24.0%, 24.0-24.9%, and 22.9-23.2%, respectively. The corresponding average genetic distances were 2.840, 2.926, and 2.665, and the average transition/transversion rates were 0.70, 0.55, and 0.54, respectively. The divergences, genetic distances, and transition/transversion rates of D. caprae versus the other three species all reached interspecies level. The five phylogenetic trees all presented that D. caprae clustered with D. brevis first, and then with D. canis, D. folliculorum, and Demodex injai in sequence. In conclusion, D. caprae is an independent species, and it is closer to D. brevis than to D. canis, D. folliculorum, or D. injai.

  3. Characterization and phylogenetic analysis of Bovine viral diarrhea virus in brain tissues from nonambulatory (downer) cattle in Korea.

    PubMed

    Oem, Jae-Ku; Chung, Joon-Yee; Roh, In-Soon; Kim, Hye-Ryoung; Bae, You-Chan; Lee, Kyung-Hyun; Jin, Young-Hwa; Lee, O-Soo

    2010-07-01

    Between August 2008 and May 2009, 386 brain and serum samples from adult cattle (2-7 years old) showing a variety of clinical signs of downer cow syndrome were received by the National Veterinary Research and Quarantine Service. All brain samples were tested for the presence of Bovine viral diarrhea virus (BVDV) by reverse transcription polymerase chain reaction (RT-PCR), immunohistochemistry (IHC), and antigen capture ELISA (Ag-ELISA). The BVDV nucleic acid was detected in 54 of 386 (15.5%) brain samples tested by RT-PCR. Positive results were detected in 14 (3.67%) and 13 (3.4%) of samples tested by IHC and Ag-ELISA, respectively. Both BVDV nucleic acid and antigen were detected in 11 cattle (2.9%) by all 3 diagnostic tests; however, antibodies against BVDV were not detected in these 11 cattle. A molecular classification of the identified viral strains (n = 40) was also carried out. Neighbor-joining phylogenetic analysis revealed that most of the identified viruses belonged to BVDV genotype 1a (n = 10), 1b (n = 16), and 2a (n = 8). The remaining strains were subtypes 1c (n = 1), 1n (n = 4), and 1m (n = 1). Interestingly, most of the BVDV-1b strains (n = 9) identified in brain samples were confirmed by all 3 diagnostic tests. Further studies should be performed to determine why the BVDV-1b strain was found in brain samples that were positive using all 3 diagnostic tests.

  4. Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli.

    PubMed

    Hasanpour, Mojtaba; Najafi, Akram

    2017-03-28

    Uropathogenic Escherichia coli (UPEC) is among major pathogens causing 80-90% of all episodes of urinary tract infections (UTIs). Recently, E. coli strains are divided into eight main phylogenetic groups including A, B1, B2, C, D, E, F, and clade I. This study was aimed to develop a rapid, sensitive, and specific multiplex real time PCR method capable of detecting phylogenetic groups of E. coli strains. This study was carried out on E. coli strains (isolated from the patient with UTI) in which the presence of all seven target genes had been confirmed in our previous phylogenetic study. An EvaGreen-based singleplex and multiplex real-time PCR with melting curve analysis was designed for simultaneous detection and differentiation of these genes. The primers were selected mainly based on the production of amplicons with melting temperatures (Tm) ranging from 82°C to 93°C and temperature difference of more than 1.5°C between each peak.The multiplex real-time PCR assays that have been developed in the present study were successful in detecting the eight main phylogenetic groups. Seven distinct melting peaks were discriminated, with Tm value of 93±0.8 for arpA, 89.2±0.1for chuA, 86.5±0.1 for yjaA, 82.3±0.2 for TspE4C2, 87.8±0.1for trpAgpC, 85.4±0.6 for arpAgpE genes, and 91±0.5 for the internal control. To our knowledge, this study is the first melting curve-based real-time PCR assay developed for simultaneous and discrete detection of these seven target genes. Our findings showed that this assay has the potential to be a rapid, reliable and cost-effective alternative for routine phylotyping of E. coli strains.

  5. Molecular identification and phylogenetic analysis of Lactobacillus and Bifidobacterium spp. isolated from gut of honeybees (Apis mellifera) from West Azerbaijan, Iran

    PubMed Central

    Sharifpour, Mohammad Farouq; Mardani, Karim; Ownagh, Abdulghaffar

    2016-01-01

    Polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) and phylogenetic analysis were used for molecular identification of lactic acid bacteria (LABs) isolated from Apis mellifera. Eighteen honeybee workers were collected from three different apiaries in West Azerbaijan. LABs from the gut of honeybees were isolated and cultured using routine biochemical procedures. Genomic DNA was extracted from LABs and a fragment of 1540 bp in size of 16S rRNA gene was amplified. PCR products were digested using HinfI endonuclease and digested products with different RFLP patterns were subjected to nucleotide sequencing and phylogenetic analysis. The results revealed that Lactobacillus and Bifidobacteria spp. are were the most abundant LABs in honeybee gut. Phylogenetic analysis showed that both Lactobacillus and Bifidobacterium were closely clustered with high similarity percentage with the same bacteria isolated from honeybees’ gut elsewhere. It was concluded that LABs isolated from honeybees had low sequence divergence in comparison with LABs isolated from other sources such as dairy products. PMID:28144419

  6. Molecular identification and phylogenetic analysis of Lactobacillus and Bifidobacterium spp. isolated from gut of honeybees (Apis mellifera) from West Azerbaijan, Iran.

    PubMed

    Sharifpour, Mohammad Farouq; Mardani, Karim; Ownagh, Abdulghaffar

    2016-01-01

    Polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) and phylogenetic analysis were used for molecular identification of lactic acid bacteria (LABs) isolated from Apis mellifera. Eighteen honeybee workers were collected from three different apiaries in West Azerbaijan. LABs from the gut of honeybees were isolated and cultured using routine biochemical procedures. Genomic DNA was extracted from LABs and a fragment of 1540 bp in size of 16S rRNA gene was amplified. PCR products were digested using HinfI endonuclease and digested products with different RFLP patterns were subjected to nucleotide sequencing and phylogenetic analysis. The results revealed that Lactobacillus and Bifidobacteria spp. are were the most abundant LABs in honeybee gut. Phylogenetic analysis showed that both Lactobacillus and Bifidobacterium were closely clustered with high similarity percentage with the same bacteria isolated from honeybees' gut elsewhere. It was concluded that LABs isolated from honeybees had low sequence divergence in comparison with LABs isolated from other sources such as dairy products.

  7. A revision and phylogenetic analysis of Stoiba Spaeth 1909 (Coleoptera, Chrysomelidae)

    PubMed Central

    Shin, Chulwoo; Chaboo, Caroline S.

    2012-01-01

    Abstract Stoiba Spaeth, 1909 is revised with a phylogenetic analysis of 38 adult morphological characters for nine Stoiba species and 11 outgroup species (Mesomphaliini, Ischyrosonychini, and Hemisphaerotini). Four Cuban species of Stoiba were not sampled. Parsimony analysis located the four most parsimonious trees. The strict consensus (CI=0.59, RI=0.78, Steps=83) resolved the monophyly of Stoiba. The monophyly of Stoiba is supported by pale yellow antennae, antennomere VII broader than its length, and rounded basal line of pronotum. An illustrated key to ten species of Stoiba is provided along with a distribution map of 11 species. Stoiba rufa Blake is synonymized with Stoiba swartzii (Thunberg) by a morphological comparison which includes female genitalia. PMID:23129988

  8. Phylogenetic analysis and positive-selection site detecting of vascular endothelial growth factor family in vertebrates.

    PubMed

    He, Wenwu; Tang, Yanyan; Qi, Bin; Lu, Chuansen; Qin, Chao; Wei, Yunfei; Yi, Jiachao; Chen, Mingwu

    2014-02-10

    Vascular endothelial growth factor (VEGF), known to play an important role in vascular homeostasis, vascular integrity and angiogenesis, is little known about the evolutionary relationship of its five members especially the role of gene duplication and natural selection in the evolution of the VEGF family. In this study, seventy-five full-length cDNA sequences from 33 vertebrate species were extracted from the NCBI's GenBank, UniProt protein database and the Ensembl database. By phylogenetic analyses, we investigated the origin, conservation, and evolution of the VEGFs. Five VEGF family members in vertebrates might be formed by gene duplication. The inferred evolutionary transitions that separate members which belong to different gene clusters correlated with changes in functional properties. Selection analysis and protein structure analysis were combined to explain the relationship of the site-specific evolution in the vertebrate VEGF family. Eleven positive selection sites, one transmembrane region and the active sites were detected in this process.

  9. Phylogenetic Analysis of Enterohemorrhagic Escherichia coli O157, Germany, 1987–2008

    PubMed Central

    Jenke, Christian; Harmsen, Dag; Weniger, Thomas; Rothgänger, Jörg; Hyytiä-Trees, Eija; Bielaszewska, Martina; Karch, Helge

    2010-01-01

    Multilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC) O157. We determined the phylogeny of 202 epidemiologically unrelated EHEC O157:H7/H– clinical isolates through 8 MLVA loci obtained in Germany during 1987–2008. Biodiversity in the loci ranged from 0.66 to 0.90. Four of 8 loci showed null alleles and a frequency <44.1%. These loci were distributed among 48.5% of all strains. Overall, 141 MLVA profiles were identified. Phylogenetic analysis assigned 67.3% of the strains to 19 MLVA clusters. Specific MLVA profiles with an evolutionary persistence were identified, particularly within sorbitol-fermenting EHEC O157:H–.These pathogens belonged to the same MLVA cluster. Our findings indicate successful persistence of this clone. PMID:20350374

  10. Phylogenetic analysis of the sharpshooter genus Subrasaca Young, 1977 (Hemiptera, Cicadellidae, Cicadellini).

    PubMed

    da Silva, Roberta Dos Santos; Mejdalani, Gabriel; Cavichioli, Rodney R

    2015-01-01

    The South American sharpshooter genus Subrasaca comprises 14 species. Some species of this genus are quite common in the Brazilian Atlantic Rainforest. In this paper, a phylogenetic analysis of Subrasaca, based on a matrix of 20 terminal taxa and 72 morphological characters of the head, thorax, and male and female genitalia, is presented. The analysis yielded six equally most parsimonious trees (197 steps, CI = 0.6091, RI = 0.5722, and RC = 0.3486). The results suggest that Subrasaca is a monophyletic taxon, although the genus branch is not robust. The clade showing the highest bootstrap and Bremer scores is formed by species with longitudinal dark brown to black stripes on the forewings (Subrasacabimaculata, Subrasacaconstricta, Subrasacacurvovittata, and Subrasacaflavolineata), followed by Subrasacaatronasa + Subrasacaaustera.

  11. Molecular cytogenetic (FISH) and genome analysis of diploid wheatgrasses and their phylogenetic relationship

    PubMed Central

    Gaál, Eszter; Molnár, István; Icsó, Diana; Badaeva, Ekaterina; Molnár-Láng, Márta

    2017-01-01

    This paper reports detailed FISH-based karyotypes for three diploid wheatgrass species Agropyron cristatum (L.) Beauv., Thinopyrum bessarabicum (Savul.&Rayss) A. Löve, Pseudoroegneria spicata (Pursh) A. Löve, the supposed ancestors of hexaploid Thinopyrum intermedium (Host) Barkworth & D.R.Dewey, compiled using DNA repeats and comparative genome analysis based on COS markers. Fluorescence in situ hybridization (FISH) with repetitive DNA probes proved suitable for the identification of individual chromosomes in the diploid JJ, StSt and PP genomes. Of the seven microsatellite markers tested only the (GAA)n trinucleotide sequence was appropriate for use as a single chromosome marker for the P. spicata AS chromosome. Based on COS marker analysis, the phylogenetic relationship between diploid wheatgrasses and the hexaploid bread wheat genomes was established. These findings confirmed that the J and E genomes are in neighbouring clusters. PMID:28278169

  12. Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data

    PubMed Central

    Tanner, Alastair R.; Fleming, James F.; Tarver, James E.; Pisani, Davide

    2017-01-01

    Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods. PMID:28077778

  13. Phylogenetic analysis of Bacillus P450 monooxygenases and evaluation of their activity towards steroids.

    PubMed

    Furuya, Toshiki; Shibata, Daisuke; Kino, Kuniki

    2009-11-01

    Cytochrome P450 (P450) open reading frames (ORFs) identified in genome sequences of Bacillus species are potential resources for new oxidation biocatalysts. Phylogenetic analysis of 29 Bacillus P450 ORFs revealed that the P450s consist of a limited number of P450 families, CYP102, CYP106, CYP107, CYP109, CYP134, CYP152, and CYP197. Previously, we identified the catalytic activities of three P450s of Bacillus subtilis towards steroids by rapid substrate screening using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). Here, we further applied this method to evaluate the activity of Bacillus cereus P450s towards steroids. Five P450 genes were cloned from B. cereus ATCC 10987 based on its genomic sequence and were expressed in Escherichia coli. These P450s were reacted with a mixture of 30 compounds that mainly included steroids, and the reaction mixtures were analyzed using FT-ICR/MS. We found that BCE_2659 (CYP106) catalyzed the monooxygenation of methyltestosterone, progesterone, 11-ketoprogesterone, medroxyprogesterone acetate, and chlormadinone acetate. BCE_2654 (CYP107) monooxygenated testosterone enanthate, and BCE_3250 (CYP109) monooxygenated testosterone and compactin. Based on the phylogenetic relationship and the known substrate specificities including ones identified in this study, we discuss the catalytic potential of Bacillus P450s towards steroids.

  14. Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome Sequencing

    PubMed Central

    Naushad, Sohail; Barkema, Herman W.; Luby, Christopher; Condas, Larissa A. Z.; Nobrega, Diego B.; Carson, Domonique A.; De Buck, Jeroen

    2016-01-01

    Non-aureus staphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA, hsp60, rpoB, sodA, and tuf genes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity. PMID:28066335

  15. Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome Sequencing.

    PubMed

    Naushad, Sohail; Barkema, Herman W; Luby, Christopher; Condas, Larissa A Z; Nobrega, Diego B; Carson, Domonique A; De Buck, Jeroen

    2016-01-01

    Non-aureus staphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA, hsp60, rpoB, sodA, and tuf genes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity.

  16. Phylogenetic analysis indicates that Culicoides dewulfi should not be considered part of the Culicoides obsoletus complex.

    PubMed

    Schwenkenbecher, J M; Mordue, A J; Piertney, S B

    2009-08-01

    Analysis of DNA sequence data has proven invaluable for defining the relationships among taxa, as well as resolving their evolutionary histories. Here, we analyzed DNA sequence variation of one mitochondrial gene (COI) and two nuclear regions (ITSI and II) to clarify the phylogenetic position of Culicoides dewulfi, a midge species widely spread in Europe and a suspected vector for bluetongue virus. Various authors have described C. dewulfi either as part of the Culicoides obsoletus sensu lato complex or as a separate taxonomic group. A maximum likelihood phylogeny, based upon an optimal model of sequence evolution, placed C. dewulfi outwith the C. obsoletus s.l. complex. Shimodaira-Hasegawa test highlighted that this topology was significantly more likely than any topology that placed C. dewulfi anywhere else in the phylogeny. As such, C. dewulfi should not be considered part of the C. obsoletus s.l. complex and instead be treated as a separate group, phylogenetically close to the classical Old World vector C. imicola.

  17. Preliminary phylogenetic analysis of the Andean clade and the placement of new Colombian blueberries (Ericaceae, Vaccinieae).

    PubMed

    Pedraza-Peñalosa, Paola; Salinas, Nelson R; Virnig, Anne Lucy S; Wheeler, Ward C

    2015-01-01

    The blueberry tribe Vaccinieae (Ericaceae) is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fieldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed before being named. This is particularly important, as the monophyly of many of the studied genera have not been confirmed. In order to advance our understanding of the relationships within neotropical Vaccinieae and advice the taxonomy of the new blueberry relatives, here we present the most comprehensive phylogenetic analysis for the Andean clade. Anthopterus, Demosthenesia, and Pellegrinia are among the putative Andean genera recovered as monophyletic, while other eight Andean genera were not. The analyses also showed that genera that have been traditionally widely defined are non-monophyletic and could be further split into more discrete groups. Four newly discovered Colombian Vaccinieae are placed in the monophyletic Satyria s.s. and the Psammisia I clade. Although these new species are endemic to the Colombian Western Cordillera and Chocó biogeographic region and three are not known outside of Las Orquídeas National Park, they do not form sister pairs.

  18. Comparative and phylogenetic analysis of the mitochondrial genomes in basal hymenopterans

    PubMed Central

    Song, Sheng-Nan; Tang, Pu; Wei, Shu-Jun; Chen, Xue-Xin

    2016-01-01

    The Symphyta is traditionally accepted as a paraphyletic group located in a basal position of the order Hymenoptera. Herein, we conducted a comparative analysis of the mitochondrial genomes in the Symphyta by describing two newly sequenced ones, from Trichiosoma anthracinum, representing the first mitochondrial genome in family Cimbicidae, and Asiemphytus rufocephalus, from family Tenthredinidae. The sequenced lengths of these two mitochondrial genomes were 15,392 and 14,864 bp, respectively. Within the sequenced region, trnC and trnY were rearranged to the upstream of trnI-nad2 in T. anthracinum, while in A. rufocephalus all sequenced genes were arranged in the putative insect ancestral gene arrangement. Rearrangement of the tRNA genes is common in the Symphyta. The rearranged genes are mainly from trnL1 and two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY. The mitochondrial genomes of Symphyta show a biased usage of A and T rather than G and C. Protein-coding genes in Symphyta species show a lower evolutionary rate than those of Apocrita. The Ka/Ks ratios were all less than 1, indicating purifying selection of Symphyta species. Phylogenetic analyses supported the paraphyly and basal position of Symphyta in Hymenoptera. The well-supported phylogenetic relationship in the study is Tenthredinoidea + (Cephoidea + (Orussoidea + Apocrita)). PMID:26879745

  19. Molecular and phylogenetic analysis of equine piroplasms in the Republic of Korea.

    PubMed

    Seo, Min-Goo; Yun, Sun-Hee; Choi, Seong-Kyoon; Cho, Gil-Jae; Park, Yong-Soo; Cho, Kwang-Hyun; Kwon, Oh-Deog; Kwak, Dongmi

    2013-06-01

    This study was conducted to screen out horses infected with piroplasms using PCR and to assess the phylogenetic variations of the piroplasm isolates. From 2007 to 2010, a total of 224 blood samples of horses were collected from three provinces of Korea and analyzed by PCR using primers specific to the 18S rRNA of piroplasms. Out of 224 samples analyzed, only two (0.9%) horses were found positive for Theileria equi. Sequencing of the complete 18S rRNA of T. equi from the two horses (GG-7 and GG-14) whose information was submitted to the GenBank (accession nos. HM229407 and HM229408, respectively) showed 100% identity. Alignment of the complete sequences of T. equi 18S rRNA with the GenBank databases of T. equi showed a high degree of homology (98.6-99.8%). The phylogenetic analysis showed T. equi GG-7 and GG-14 clustered together with T. equi isolates from Spain, Sudan, Jordan and South Africa, indicating the possibility of a close epidemiological link among these isolates.

  20. Species identification and phylogenetic analysis of genus Nassarius (Nassariidae) based on mitochondrial genes

    NASA Astrophysics Data System (ADS)

    Li, Haitao; Lin, Duan; Fang, Hongda; Zhu, Aijia; Gao, Yang

    2010-05-01

    Genus Nassarius contains many subgenera, such as Zeuxis, Telasco, Niotha, Varicinassa, Plicarcularia, Nassarius s. str. and Reticunassa. On the basis of morphological characteristics of the shell and radula and sequences of mitochondrial cytochrome oxidase subunit I (COI) and 16S rRNA genes, Nassarius specimens collected from the South China Sea were identified and phylogenetically analyzed. Although Nassarius sp. and Nassarius ( Varicinassa) variciferus were morphologically different in their shells, few variations were found among their radular teeth and sequences of mtCOI and mt16S RNA genes. Therefore, Nassarius sp. should be classified as N. (Varicinassa) variciferus. Nassarius (Zeuxis) sp. has only a subtle difference from Nassarius (Zeuxis) algidus on the shell, but it shows obvious differences in radular teeth and DNA sequence, indicating that they are two distinct species. Sequence divergence of mtCOI and mt16S RNA genes within Nassarius species was much lower than that between species, suggesting that these two genes are suitable for Nassarius species identification. Phylogenetic analysis (neighbor-joining and maximum parsimony) based on mtCOI and mt16S rRNA genes revealed the presence of two groups in genus Nassarius and a closest relationship between subgenera Zeuxis and Telasco. Species of subgenus Plicarcularia did not form a single clade. The molecular phylogeny was not congruent with the previous morphological phylogeny. The subgeneric divisions of genus Nassarius appear to be uncertain and unreliable.

  1. Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis

    PubMed Central

    Wolf, Yuri I.; Rogozin, Igor B.; Koonin, Eugene V.

    2004-01-01

    Relative positions of nematodes, arthropods, and chordates in animal phylogeny remain uncertain. The traditional tree topology joins arthropods with chordates in a coelomate clade, whereas nematodes, which lack a coelome, occupy a basal position. However, the current leading hypothesis, based on phylogenetic trees for 18S ribosomal RNA and several proteins, joins nematodes with arthropods in a clade of molting animals, Ecdysozoa. We performed a phylogenetic analysis of over 500 sets of orthologous proteins, which are represented in plants, animals, and fungi, using maximum likelihood, maximum parsimony, and distance methods. Additionally, to increase the statistical power of topology tests, the same methods were applied to concatenated alignments of subunits of eight conserved macromolecular complexes. The majority of the methods, when applied to most of the orthologous clusters, both concatenated and individual, grouped the fly with humans to the exclusion of the nematode, in support of the coelomate phylogeny. Trees were also constructed using information on insertions and deletions in orthologous proteins, combinations of domains in multidomain proteins, and presence-absence of species in clusters of orthologs. All of these approaches supported the coelomate clade and showed concordance between evolution of protein sequences and higher-level evolutionary events, such as domain fusion or gene loss. PMID:14707168

  2. Phylogenetic analysis of Croatian orf viruses isolated from sheep and goats

    PubMed Central

    2010-01-01

    Background The Orf virus (ORFV) is the prototype of the parapoxvirus genus and it primarily causes contagious ecthyma in goats, sheep, and other ruminants worldwide. In this paper, we described the sequence and phylogenetic analysis of the B2L gene of ORFV from two natural outbreaks: i) in autochthonous Croatian Cres-breed sheep and ii) on small family goat farm. Results Sequence and phylogenetic analyses of the ORFV B2L gene showed that the Cro-Cres-12446/09 and Cro-Goat-11727/10 were not clustered together. Cro-Cres-12446/09 shared the highest similarity with ORFV NZ2 from New Zealand, and Ena from Japan; Cro-Goat-11727/10 was closest to the HuB from China and Taiping and Hoping from Taiwan. Conclusion Distinct ORFV strains are circulating in Croatia. Although ORFV infections are found ubiquitously wherever sheep and goats are farmed in Croatia, this is the first information on genetic relatedness of any Croatian ORFV with other isolates around the world. PMID:21073725

  3. Social mating system and sex-biased dispersal in mammals and birds: a phylogenetic analysis.

    PubMed

    Mabry, Karen E; Shelley, Erin L; Davis, Katie E; Blumstein, Daniel T; Van Vuren, Dirk H

    2013-01-01

    The hypothesis that patterns of sex-biased dispersal are related to social mating system in mammals and birds has gained widespread acceptance over the past 30 years. However, two major complications have obscured the relationship between these two behaviors: 1) dispersal frequency and dispersal distance, which measure different aspects of the dispersal process, have often been confounded, and 2) the relationship between mating system and sex-biased dispersal in these vertebrate groups has not been examined using modern phylogenetic comparative methods. Here, we present a phylogenetic analysis of the relationship between mating system and sex-biased dispersal in mammals and birds. Results indicate that the evolution of female-biased dispersal in mammals may be more likely on monogamous branches of the phylogeny, and that females may disperse farther than males in socially monogamous mammalian species. However, we found no support for a relationship between social mating system and sex-biased dispersal in birds when the effects of phylogeny are taken into consideration. We caution that although there are larger-scale behavioral differences in mating system and sex-biased dispersal between mammals and birds, mating system and sex-biased dispersal are far from perfectly associated within these taxa.

  4. Phylogenetic analysis of Culicoides species from France based on nuclear ITS1-rDNA sequences.

    PubMed

    Perrin, A; Cetre-Sossah, C; Mathieu, B; Baldet, T; Delecolle, J-C; Albina, E

    2006-06-01

    Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) play important roles in the transmission of viral diseases affecting wild and domestic ruminants and horses, including Bluetongue (BT) and African horse sickness (AHS) respectively. In southern Europe, BT has been largely transmitted by the classical Afro-Asian vector Culicoides imicola Kieffer. However, other species such as C. obsoletus Meigen, C. scoticus Downs & Kettle and C. pulicaris Linné may also be involved in BTV transmission. As a consequence of the discovery of C. imicola followed by BTV-2 outbreaks on the island of Corsica in October 2000, further studies on these biting midges have been carried out. To better characterize the evolution and phylogenetic relations of Culicoides, molecular analysis in parallel with a morphology-based taxonomic approach were performed. Phylogenetic analyses of French Culicoides species were undertaken using the ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) as a molecular target. This region was shown to be useful in understanding evolutionary and genetic relationships between species. Construction of several trees showed that molecular phylogeny within the genus Culicoides correlates not only with morphological-based taxonomy but also with ecological patterns.

  5. Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes.

    PubMed

    Meixner, Martin J; Lüter, Carsten; Eckert, Carsten; Itskovich, Valeria; Janussen, Dorte; von Rintelen, Thomas; Bohne, Alexandra V; Meixner, Johannes M; Hess, Wolfgang R

    2007-12-01

    Morphologic and phylogenetic analysis of freshwater sponges endemic to lakes in Central Sulawesi, Siberia and South-East Europe is presented. We also analyzed several cosmopolitan sponge species from Eurasia and North America and included sponge sequences from public databases. In agreement with previous reports [Addis, J.S., Peterson, K.J., 2005. Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences. Zool. Scr. 34, 549-557], the metaniid sponge Corvomeyenia sp. was the most deeply branching species within a monophyletic lineage of the suborder Spongillina. Pachydictyum globosum (Malawispongiidae) and Nudospongilla vasta (Spongillidae), two morphologically quite distinct species from Sulawesi were found in a joint clade with Trochospongilla (Spongillidae) rendering Trochospongilla paraphyletic. Furthermore, Ochridaspongia sp., another Malawispongiidae, clustered far away from that clade, together with Ephydatia fluviatilis, making the latter family polyphyletic. The Lubomirskiidae endemic to Lake Baikal, Lubomirskia abietina, Baikalospongia bacillifera, B. intermedia, and Swartschewskia papyracea formed a well-supported clade that was most closely linked to the genus Ephydatia (99.9% identity over a total length of 2169 concatenated nucleotide positions). Our study indicates the frequent and independent origin of sponge species endemic to different freshwater ecosystems from a few cosmopolitan founder species. The highly specific primer sets newly developed here facilitate work on the molecular phylogeny and DNA barcoding of sponges.

  6. Preliminary phylogenetic analysis of the Andean clade and the placement of new Colombian blueberries (Ericaceae, Vaccinieae)

    PubMed Central

    Pedraza-Peñalosa, Paola; Salinas, Nelson R.; Virnig, Anne Lucy S.; Wheeler, Ward C.

    2015-01-01

    Abstract The blueberry tribe Vaccinieae (Ericaceae) is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fieldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed before being named. This is particularly important, as the monophyly of many of the studied genera have not been confirmed. In order to advance our understanding of the relationships within neotropical Vaccinieae and advice the taxonomy of the new blueberry relatives, here we present the most comprehensive phylogenetic analysis for the Andean clade. Anthopterus, Demosthenesia, and Pellegrinia are among the putative Andean genera recovered as monophyletic, while other eight Andean genera were not. The analyses also showed that genera that have been traditionally widely defined are non-monophyletic and could be further split into more discrete groups. Four newly discovered Colombian Vaccinieae are placed in the monophyletic Satyria s.s. and the Psammisia I clade. Although these new species are endemic to the Colombian Western Cordillera and Chocó biogeographic region and three are not known outside of Las Orquídeas National Park, they do not form sister pairs. PMID:25987883

  7. Phylogenetic analysis of Tibetan mastiffs based on mitochondrial hypervariable region I.

    PubMed

    Ren, Zhanjun; Chen, Huiling; Yang, Xuejiao; Zhang, Chengdong

    2017-03-01

    Recently, the number of Tibetan mastiffs, which is a precious germplasm resource and cultural heritage, is decreasing sharply. Therefore, the genetic diversity of Tibetan mastiffs needs to be studied to clarify its phylogenetics relationships and lay the foundation for resource protection, rational development and utilization of Tibetan mastiffs. We sequenced hypervariable region I of mitochondrial DNA (mtDNA) of 110 individuals from Tibet region and Gansu province. A total of 12 polymorphic sites were identified which defined eight haplotypes of which H4 and H8 were unique to Tibetan population with H8 being identified first. The haplotype diversity (Hd: 0.808), nucleotide diversity (Pi: 0.603%), the average number of nucleotide difference (K: 3.917) of Tibetan mastiffs from Gansu were higher than those from Tibet region (Hd: 0.794; Pi: 0.589%; K: 3.831), which revealed higher genetic diversity in Gansu. In terms of total population, the genetic variation was low. The median-joining network and phylogenetic tree based on the mtDNA hypervariable region I showed that Tibetan mastiffs originated from grey wolves, as the other domestic dogs and had different history of maternal origin. The mismatch distribution analysis and neutrality tests indicated that Tibetan mastiffs were in genetic equilibrium or in a population decline.

  8. Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data.

    PubMed

    Puttick, Mark N; O'Reilly, Joseph E; Tanner, Alastair R; Fleming, James F; Clark, James; Holloway, Lucy; Lozano-Fernandez, Jesus; Parry, Luke A; Tarver, James E; Pisani, Davide; Donoghue, Philip C J

    2017-01-11

    Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.

  9. apex: phylogenetics with multiple genes.

    PubMed

    Jombart, Thibaut; Archer, Frederick; Schliep, Klaus; Kamvar, Zhian; Harris, Rebecca; Paradis, Emmanuel; Goudet, Jérome; Lapp, Hilmar

    2017-01-01

    Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases, different loci should, at least as a preliminary step, be examined and analysed separately. The r software has become a popular platform for phylogenetics, with several packages implementing distance-based, parsimony and likelihood-based phylogenetic reconstruction, and an even greater number of packages implementing phylogenetic comparative methods. Unfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. In this study, we introduce the new r package apex to fill this gap. apex implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data. In this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set.

  10. Phylogenetic analysis of the L and HN gene of ophidian paramyxoviruses. Brief report.

    PubMed

    Kindermann, J; Kübber-Heiss, A; Kerschbaumer, P; Nowotny, N

    2001-01-01

    Two reptilian paramyxoviruses, isolated from a neotropical rattlesnake (neotropical virus, NTV, ATCC VR-1408) and a bush viper (bush viper virus, BVV, ATCC VR- 1409), respectively, were analysed to determine their taxonomic position among other reptilian paramyxoviruses investigated previously by Ahne et al.. A 679 bp long region of the hemagglutinin-neuraminidase (HN) gene and a 627 bp long region of the large (L) gene were reverse transcribed, amplified by polymerase chain reaction (PCR), and sequenced. The deduced amino acid sequences were compared to mammalian paramyxoviruses belonging to the genera Respirovirus and Rubulavirus. The deduced amino acid sequences revealed 58.9 to 62% homology for the partial L protein and 41% to 47.1% homology for the partial HN protein. For phylogenetic analyses, a 518 bp L gene and a 352 bp HN gene fragment were used, both generating similar trees consisting of two distinct main groups, and some intermediate isolates. BVV clustered within group "b" while NTV clustered together with the intermediate ophidian paramyxovirus isolate Crot2-OH90.

  11. Phylogenetic Analysis of Geographically Diverse Radopholus similis via rDNA Sequence Reveals a Monomorphic Motif.

    PubMed

    Kaplan, D T; Thomas, W K; Frisse, L M; Sarah, J L; Stanton, J M; Speijer, P R; Marin, D H; Opperman, C H

    2000-06-01

    The nucleic acid sequences of rDNA ITS1 and the rDNA D2/D3 expansion segment were compared for 57 burrowing nematode isolates collected from Australia, Cameroon, Central America, Cuba, Dominican Republic, Florida, Guadeloupe, Hawaii, Nigeria, Honduras, Indonesia, Ivory Coast, Puerto Rico, South Africa, and Uganda. Of the 57 isolates, 55 were morphologically similar to Radopholus similis and seven were citrus-parasitic. The nucleic acid sequences for PCR-amplified ITS1 and for the D2/D3 expansion segment of the 28S rDNA gene were each identical for all putative R. similis. Sequence divergence for both the ITS1 and the D2/D3 was concordant with morphological differences that distinguish R. similis from other burrowing nematode species. This result substantiates previous observations that the R. similis genome is highly conserved across geographic regions. Autapomorphies that would delimit phylogenetic lineages of non-citrus-parasitic R. similis from those that parasitize citrus were not observed. The data presented herein support the concept that R. similis is comprised of two pathotypes-one that parasitizes citrus and one that does not.

  12. A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda)

    PubMed Central

    Mateus, Octávio; Benson, Roger B.J.

    2015-01-01

    Diplodocidae are among the best known sauropod dinosaurs. Several species were described in the late 1800s or early 1900s from the Morrison Formation of North America. Since then, numerous additional specimens were recovered in the USA, Tanzania, Portugal, and Argentina, as well as possibly Spain, England, Georgia, Zimbabwe, and Asia. To date, the clade includes about 12 to 15 nominal species, some of them with questionable taxonomic status (e.g., ‘Diplodocus’ hayi or Dyslocosaurus polyonychius), and ranging in age from Late Jurassic to Early Cretaceous. However, intrageneric relationships of the iconic, multi-species genera Apatosaurus and Diplodocus are still poorly known. The way to resolve this issue is a specimen-based phylogenetic analysis, which has been previously implemented for Apatosaurus, but is here performed for the first time for the entire clade of Diplodocidae. The analysis includes 81 operational taxonomic units, 49 of which belong to Diplodocidae. The set of OTUs includes all name-bearing type specimens previously proposed to belong to Diplodocidae, alongside a set of relatively complete referred specimens, which increase the amount of anatomically overlapping material. Non-diplodocid outgroups were selected to test the affinities of potential diplodocid specimens that have subsequently been suggested to belong outside the clade. The specimens were scored for 477 morphological characters, representing one of the most extensive phylogenetic analyses of sauropod dinosaurs. Character states were figured and tables given in the case of numerical characters. The resulting cladogram recovers the classical arrangement of diplodocid relationships. Two numerical approaches were used to increase reproducibility in our taxonomic delimitation of species and genera. This resulted in the proposal that some species previously included in well-known genera like Apatosaurus and Diplodocus are generically distinct. Of particular note is that the famous genus

  13. A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda).

    PubMed

    Tschopp, Emanuel; Mateus, Octávio; Benson, Roger B J

    2015-01-01

    Diplodocidae are among the best known sauropod dinosaurs. Several species were described in the late 1800s or early 1900s from the Morrison Formation of North America. Since then, numerous additional specimens were recovered in the USA, Tanzania, Portugal, and Argentina, as well as possibly Spain, England, Georgia, Zimbabwe, and Asia. To date, the clade includes about 12 to 15 nominal species, some of them with questionable taxonomic status (e.g., 'Diplodocus' hayi or Dyslocosaurus polyonychius), and ranging in age from Late Jurassic to Early Cretaceous. However, intrageneric relationships of the iconic, multi-species genera Apatosaurus and Diplodocus are still poorly known. The way to resolve this issue is a specimen-based phylogenetic analysis, which has been previously implemented for Apatosaurus, but is here performed for the first time for the entire clade of Diplodocidae. The analysis includes 81 operational taxonomic units, 49 of which belong to Diplodocidae. The set of OTUs includes all name-bearing type specimens previously proposed to belong to Diplodocidae, alongside a set of relatively complete referred specimens, which increase the amount of anatomically overlapping material. Non-diplodocid outgroups were selected to test the affinities of potential diplodocid specimens that have subsequently been suggested to belong outside the clade. The specimens were scored for 477 morphological characters, representing one of the most extensive phylogenetic analyses of sauropod dinosaurs. Character states were figured and tables given in the case of numerical characters. The resulting cladogram recovers the classical arrangement of diplodocid relationships. Two numerical approaches were used to increase reproducibility in our taxonomic delimitation of species and genera. This resulted in the proposal that some species previously included in well-known genera like Apatosaurus and Diplodocus are generically distinct. Of particular note is that the famous genus

  14. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis.

    PubMed

    Labeda, David P; Dunlap, Christopher A; Rong, Xiaoying; Huang, Ying; Doroghazi, James R; Ju, Kou-San; Metcalf, William W

    2017-04-01

    The family Streptomycetaceae, notably species in the genus Streptomyces, have long been the subject of investigation due to their well-known ability to produce secondary metabolites. The emergence of drug resistant pathogens and the relative ease of producing genome sequences has renewed the importance of Streptomyces as producers of new natural products and resulted in revived efforts in isolating and describing strains from novel environments. A previous large study of the phylogeny in the Streptomycetaceae based on 16S rRNA gene sequences provided a useful framework for the relationships among species, but did not always have sufficient resolution to provide definitive identification. Multi-locus sequence analysis of 5 house-keeping genes has been shown to provide improved taxonomic resolution of Streptomyces species in a number of previous reports so a comprehensive study was undertaken to evaluate evolutionary relationships among species within the family Streptomycetaceae where type strains are available in the ARS Culture Collection or genome sequences are available in GenBank. The results of the analysis supported the distinctiveness of Kitasatospora and Streptacidiphilus as validly named genera since they cluster outside of the phylogenetic radiation of the genus Streptomyces. There is also support for the transfer of a number of Streptomyces species to the genus Kitasatospora as well for reducing at least 31 species clusters to a single taxon. The multi-locus sequence database resulting from the study is a useful tool for identification of new isolates and the phylogenetic analysis presented also provides a road map for planning future genome sequencing efforts in the Streptomycetaceae.

  15. Phylogenetic and expression analysis of sucrose phosphate synthase isozymes in plants.

    PubMed

    Lutfiyya, Linda L; Xu, Nanfei; D'Ordine, Robert L; Morrell, James A; Miller, Philip W; Duff, Stephen M G

    2007-07-01

    In plants and microbes, sucrose phosphate synthase (SPS) is an important enzyme in sucrose biosynthesis. Several different isozymes of SPS exist in plants. Genomic and EST sequence data from Arabidopsis, rice and maize has been analyzed. This analysis has revealed that the Arabidopsis genome contains four unique SPS genes. The rice databases (Monsanto proprietary, and public databases) contain five unique full-length SPS genes. Using the Monsanto maize EST and genomic sequence databases, we have identified five full length and two partial SPS sequences, bringing the total number of presently known maize SPS genes to at least seven. Phylogenetic analysis of all known SPS sequences revealed several putative evolutionary branches of SPS. We have classified SPS genes into three major groups in higher plants, all with distinct features from the known microbial SPS genes. Furthermore, this analysis suggests evolutionary divergence of monocotyledonous (monocot) and dicotyledonous (dicot) SPS sequences. The evidence suggests that several gene duplication events occurred at various points during evolution, both before and after the monocot/dicot split. It appears that at least one of the major forms of SPS genes may have evolved after the divergence of monocots and dicots. In addition, several more recent gene duplication events may have occurred after maize/rice speciation, giving rise to additional SPS genes in maize. Some of the variants lack one or more of the presently known regulatory sites, implying that this evolutionary divergence may have given rise to enzymes with functional differences. We present evidence from transcript distribution studies using cDNA libraries as well as transcriptional profiling experiments and propose that specific SPS genes have diverse patterns of expression that are sometimes responsive to environmental signals. Our data suggests that higher plant SPS isozymes differ with respect to their patterns of expression and regulation and that

  16. Amino acid sequence of myoglobin from the chiton Liolophura japonica and a phylogenetic tree for molluscan globins.

    PubMed

    Suzuki, T; Furukohri, T; Okamoto, S

    1993-02-01

    Myoglobin was isolated from the radular muscle of the chiton Liolophura japonica, a primitive archigastropodic mollusc. Liolophura contains three monomeric myoglobins (I, II, and III), and the complete amino acid sequence of myoglobin I has been determined. It is composed of 145 amino acid residues, and the molecular mass was calculated to be 16,070 D. The E7 distal histidine, which is replaced by valine or glutamine in several molluscan globins, is conserved in Liolophura myoglobin. The autoxidation rate at physiological conditions indicated that Liolophura oxymyoglobin is fairly stable when compared with other molluscan myoglobins. The amino acid sequence of Liolophura myoglobin shows low homology (11-21%) with molluscan dimeric myoglobins and hemoglobins, but shows higher homology (26-29%) with monomeric myoglobins from the gastropodic molluscs Aplysia, Dolabella, and Bursatella. A phylogenetic tree was constructed from 19 molluscan globin sequences. The tree separated them into two distinct clusters, a cluster for muscle myoglobins and a cluster for erythrocyte or gill hemoglobins. The myoglobin cluster is divided further into two subclusters, corresponding to monomeric and dimeric myoglobins, respectively. Liolophura myoglobin was placed on the branch of monomeric myoglobin lineage, showing that it diverged earlier from other monomeric myoglobins. The hemoglobin cluster is also divided into two subclusters. One cluster contains homodimeric, heterodimeric, tetrameric, and didomain chains of erythrocyte hemoglobins of the blood clams Anadara, Scapharca, and Barbatia. Of special interest is the other subcluster. It consists of three hemoglobin chains derived from the bacterial symbiontharboring clams Calyptogena and Lucina, in which hemoglobins are supposed to play an important role in maintaining the symbiosis with sulfide bacteria.

  17. Using Phylogenetic Analysis to Detect Market Substitution of Atlantic Salmon for Pacific Salmon: An Introductory Biology Laboratory Experiment

    ERIC Educational Resources Information Center

    Cline, Erica; Gogarten, Jennifer

    2012-01-01

    We describe a laboratory exercise developed for the cell and molecular biology quarter of a year-long majors' undergraduate introductory biology sequence. In an analysis of salmon samples collected by students in their local stores and restaurants, DNA sequencing and phylogenetic analysis were used to detect market substitution of Atlantic salmon…

  18. Molecular epidemiology and phylogenetic analysis of HA gene of influenza A(H1N1)pdm09 strain during 2010-2014 in Dalian, North China.

    PubMed

    Han, Yan; Sun, Nan; Lv, Qiu-Yue; Liu, Dan-Hong; Liu, Da-Peng

    2016-10-01

    The objective of the present study was to evaluate the epidemiology of influenza A(H1N1)pdm09 and its hemagglutinin (HA) molecular and phylogenetic analysis during 2010-2014 in Dalian, North China. A total of 3717 influenza-like illness (ILI) cases were tested by real-time PCR and 493 were found to be positive. Out of these 493 cases, 121 were subtype influenza A(H1N1)pdm09, of which 14 cases were reported in 2010-2011, 29 in 2012-2013, and 78 in 2013-2014. HA coding regions of 45 isolates were compared to that of the vaccine strain A/California/7/09(H1N1), and a number of variations were detected. P83S, S185T, S203T, R223Q, and I321V mutations were observed in all of the Dalian isolates. Furthermore, a high proportion >71 % of the strains possessed the variation D97N and K283E. Phylogenetic analysis confirmed the close match of the majority of circulating strains with the vaccine strains. However, it also reveals a trend of strains to accumulate amino acid variations and form new phylogenetic groups.

  19. Phylogenetic distribution of apolipoproteins A-I and E in vertebrates as determined by Western blot analysis.

    PubMed

    Duggan, A E; Callard, I P

    2001-08-01

    A putative apolipoprotein E (apoE) has been identified in the HDL and VHDL fractions of the turtle. This observation is of particular interest considering apoE has been reported absent in the domestic hen (Hermier et al., '95; Biochim Biophys Acta: 105-118, 1995) and thus presumed absent in nonmammalian vertebrates altogether. As a result, partial amino acid sequencing of this protein was performed and revealed that one fragment shared 41% sequence identity to human apoE. Western blot analysis using antisera to apoE demonstrated cross-reactivity to a 34-kDa protein (putative apoE) in turtle plasma. Further investigation using anti-apoE antibody in Western blot analysis detected immunoreactive apoE in the plasma of lamprey, spiny dogfish, skate, and alligator, but not in flounder, newt or python; its absence in several species of birds was confirmed. Using anti-apoA-I antibody, apoA-I was detected in all vertebrate groups except a representative teleost (flounder). Apo-A-I antibody cross-reacted weakly with some putative apoE proteins (chicken, spiny dogfish and skate) and the reverse was true for anti-apoE, which cross-reacted with putative apoA-I in birds, reptiles, and elasmobranchs, confirming the molecular similarity and phylogenetic relatedness of these two proteins.

  20. Phylogenetic analysis using E2 gene of classical swine fever virus reveals a new subgenotype in China.

    PubMed

    Jiang, Da-Liang; Gong, Wen-Jie; Li, Run-Cheng; Liu, Guo-Hua; Hu, Yun-Fei; Ge, Meng; Wang, Shu-Qin; Yu, Xing-Long; Tu, Changchun

    2013-07-01

    Outbreaks of classical swine fever (CSF) have caused serious economic consequences in China. Phylogenetic analysis based on full-length E2 gene sequences showed that five classical swine fever virus (CSFV) isolates collected from Hunan province in 2011 and 2012, together with seven other isolates from neighboring provinces, Guangdong (5) and Guangxi (2), could be classified as a new subgenotype 2.1c, which may have been endemic in the south of China for at least fourteen years. Subgenotype 2.1c isolates share 90.2-94.9% and 89.9-93.8% nucleotide sequence similarity separately with those of subgenotype 2.1a and 2.1b in E2 gene, which are lower than the nucleotide identities between subgenotype 2.1a and 2.1b (91.1-95.7%). Further analysis based on a partial E2 gene sequence (216 nt) indicated that subgenotype 2.1c isolates are also circulating in Thailand. Alignment of E2 amino acid sequences showed that subgenotype 2.1c isolates exhibit a SPA → TPV substitution at positions 777 and 779 compared with subgenotypes 2.1a and 2.1b.

  1. The glyceraldehyde-3-phosphate dehydrogenase homologue is differentially regulated in phases of Paracoccidioides brasiliensis: molecular and phylogenetic analysis.

    PubMed

    Barbosa, Mônica S; Cunha Passos, Daniela A; Felipe, M Sueli S; Jesuíno, Rosália S A; Pereira, Maristela; de Almeida Soares, Célia M

    2004-07-01

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays important roles in various cellular processes. Here we report the sequence and analysis of a novel developmentally regulated gene and cDNA (Pbgadph), encoding a GAPDH homologue (PbGAPDH), of the pathogenic dimorphic fungus Paracoccidioides brasiliensis. We have analyzed the protein, the cDNA and genomic sequences to provide insights into the structure, function, and potential regulation of PbGAPDH. That Pbgapdh encodes PbGAPDH was demonstrated by micro-sequencing of the native protein homologue isolated from the fungus proteome. The deduced amino acid sequence of Pbgapdh showed identity to those of from other species (88-76%). Phylogenetic analysis indicated that GAPDH could be useful for the determination of evolutionary relationships. Expression of the Pbgapdh gene and the cognate protein were developmentally regulated in phases of P. brasiliensis, with a higher expression in the yeast parasitic phase and was induced during the transition from mycelium to yeast and decreased during the reverse process, transition from yeast to mycelium.

  2. Isolation and phylogenetic analysis of canine distemper virus among domestic dogs in Vietnam.

    PubMed

    Nguyen, Dung Van; Suzuki, Junko; Minami, Shohei; Yonemitsu, Kenzo; Nagata, Nao; Kuwata, Ryusei; Shimoda, Hiroshi; Vu, Chien Kim; Truong, Thuy Quoc; Maeda, Ken

    2017-01-20

    Canine distemper virus (CDV) is one of the most serious pathogens found in many species of carnivores, including domestic dogs. In this study, hemagglutinin (H) genes were detected in five domestic Vietnamese dogs with diarrhea, and two CDVs were successfully isolated from dogs positive for H genes. The complete genome of one isolate, CDV/dog/HCM/33/140816, was determined. Phylogenetic analysis showed that all Vietnamese CDVs belonged to the Asia-1 genotype. In addition, the H proteins of Vietnamese CDV strains were the most homologous to those of Chinese CDVs (98.4% to 99.3% identity). These results indicated that the Asia-1 genotype of CDV was the predominant genotype circulating among the domestic dog population in Vietnam and that transboundary transmission of CDV has occurred between Vietnam and China.

  3. Phylogenetic analysis of canine distemper virus in domestic dogs in Nanjing, China.

    PubMed

    Bi, Zhenwei; Wang, Yongshan; Wang, Xiaoli; Xia, Xingxia

    2015-02-01

    Canine distemper virus (CDV) infects a broad range of carnivores, including wild and domestic Canidae. The hemagglutinin gene, which encodes the attachment protein that determines viral tropism, has been widely used to determine the relationship between CDV strains of different lineages circulating worldwide. We determined the full-length H gene sequences of seven CDV field strains detected in domestic dogs in Nanjing, China. A phylogenetic analysis of the H gene sequences of CDV strains from different geographic regions and vaccine strains was performed. Four of the seven CDV strains were grouped in the same cluster of the Asia-1 lineage to which the vast majority of Chinese CDV strains belong, whereas the other three were clustered within the Asia-4 lineage, which has never been detected in China. This represents the first record of detection of strains of the Asia-4 lineage in China since this lineage was reported in Thailand in 2013.

  4. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.

    PubMed

    Trifinopoulos, Jana; Nguyen, Lam-Tung; von Haeseler, Arndt; Minh, Bui Quang

    2016-07-08

    This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary models including mixture and partition models. W-IQ-TREE performs fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and tree topology tests. All computations are conducted on a dedicated computer cluster and the users receive the results via URL or email. W-IQ-TREE is available at http://iqtree.cibiv.univie.ac.at It is free and open to all users and there is no login requirement.

  5. Phylogenetic analysis of the genus Lensia (Cnidaria, Hydrozoa, Siphonophora), based on the species morphology.

    PubMed

    Nishiyama, Eric Y; Ribeiro, Guilherme C; Oliveira, Otto M P

    2016-07-01

    Siphonophores are poorly studied despite their abundance and ecological importance in marine ecosystems. The genus Lensia Totton, 1932 contains the highest number of species within Siphonophora, but systematic studies of these organisms are scarce in the literature. This study presents a phylogenetic analysis for fifteen species of Lensia based on morphological data. The material for this study was obtained during two oceanographic campaigns made along the southeastern Brazilian coast. A total of twenty two characters of the anterior nectophore morphology were scored. The shortest trees were searched using parsimony (under different weighting regimes). All analyses provided the same topology: (M. kochi (D. dispar + D. bojani) (L. leloupi (L. havock (L. conoidea (L. subtilis; L. meteori; L. hardy; L. fowleri; (L. subtiloides (L. hotspur; L. cossack; L. campanella)); (L. multicristata (L. hunter (L. lelouveteau + L. grimaldii))). The monophyly of the genus Lensia is supported by the hydroecium measuring up to 1/4 the height of the nectosac.

  6. Detection and phylogenetic analysis of hepatitis E viruses from mongooses in Okinawa, Japan.

    PubMed

    Nidaira, Minoru; Takahashi, Kazuaki; Ogura, Go; Taira, Katsuya; Okano, Shou; Kudaka, Jun; Itokazu, Kiyomasa; Mishiro, Shunji; Nakamura, Masaji

    2012-12-01

    Hepatitis E virus (HEV) infection has previously been reported in wild mongooses on Okinawa Island; to date however, only one HEV RNA sequence has been identified in a mongoose. Hence, this study was performed to detect HEV RNA in 209 wild mongooses on Okinawa Island. Six (2.9%) samples tested positive for HEV RNA. Phylogenetic analysis revealed that 6 HEV RNAs belonged to genotype 3 and were classified into groups A and B. In group B, mongoose-derived HEV sequences were very similar to mongoose HEV previously detected on Okinawa Island, as well as to those of a pig. This investigation emphasized the possibility that the mongoose is a reservoir animal for HEV on Okinawa Island.

  7. Dietary niche breadth in a local community of passerine birds: an analysis using phylogenetic contrasts.

    PubMed

    Brandl, R; Kristín, A; Leisler, B

    1994-06-01

    The analysis of a local community of forest passerines (13 species) using phylogenetic contrasts shows a correlation between body size of bird species and mean prey size, minimum prey size, maximum prey size and the size range of dietary items. This suggests that larger birds drop small prey taxa from their prey list, because of the difficulty of capturing very small prey, for energetic reasons or because of microhabitat usage. We find some support for the third hypothesis. Dietary niche breadth calculated across prey taxa is not related to body size. Dietary niche breadth, however, is correlated with size-corrected measurements of the bill and locomotor apparatus. Long and slender bills increase the dietary niche breadth. Thus subtle differences constrain foraging and the techniques of extracting certain prey taxa form crevices. Dietary niche breadth and foraging diversity are positively correlated with population density: at least locally dietary generalists occur at higher breeding densities than specialists.

  8. Phylogenetic analysis and characterization of Korean orf virus from dairy goats: case report.

    PubMed

    Oem, Jae-Ku; Roh, In-Soon; Lee, Kyung-Hyun; Lee, Kyoung-Ki; Kim, Hye-Ryoung; Jean, Young-Hwa; Lee, O-Soo

    2009-10-16

    An outbreak of orf virus infection in dairy goats in Korea was investigated. Suspected samples of the skin and lip of affected goats were sent to the laboratory for more exact diagnosis. Orf virus was detected by electron microscopy and viral DNA was identified by PCR. To reveal the genetic characteristics of the Korean strain (ORF/09/Korea), the sequences of the major envelope protein (B2L) and orf virus interferon resistance (VIR) genes were determined and then compared with published reference sequences. Phylogenetic analysis revealed that the ORF/09/Korea strain was closest to the isolates (Taiping) from Taiwan. This is believed to be the first report on the molecular characterization of orf virus in Korea.

  9. Phylogenetic analysis of Newcastle disease virus isolates occurring in India during 1989-2013.

    PubMed

    Desingu, P A; Singh, S D; Dhama, K; Karthik, K; Vinodh Kumar, O R; Malik, Y S

    2016-06-01

    The study details characterization of Newcastle disease virus (NDV) isolates recovered from commercial poultry flocks (chicken) and wild birds (crane) of India during the time period from 1989 to 2013. Phylogenetic analysis revealed that most of the NDV isolates belongs to class II, genotype XIIIa and a chicken isolate (108/BAREILLY/AD-IVRI/91) was of genotype VI, where it showed diversity of 3 % from the other viruses belonging to same genotype. Another chicken isolate (75/RAMPUR/AD-IVRI/89) grouped in genotype III and showed 4 % diversity with viruses of genotype III. The crane origin NDV identified as of genotype II corresponding to the vaccine virus. This appears to be the first report about existence of genotype XIIIa and its ancestral viruses are circulating in India for the last two decades in different species of birds. Furthermore, genetically distinct viruses belonging to genotypes II, III and VI are also circulating in India.

  10. Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis.

    PubMed

    Kitano, Takashi; Noda, Reiko; Takenaka, Osamu; Saitou, Naruya

    2009-06-01

    The primate ABO blood group gene encodes a glycosyl transferase (either A or B type), and is known to have large coalescence times among the allelic lineages in human. We determined nucleotide sequences of ca. 2.2kb of this gene for 23 individuals of three gibbon species (agile gibbon, white-handed gibbon, and siamang), and observed a total of 24 haplotypes. We found relics of five ancient intragenic recombinations, occurred during ca. 2-7 million years ago, through a phylogenetic network analysis. The coalescence time between A and B alleles estimate precede the divergence (ca. 8MYA) of siamang and common gibbon lineages. This establishes the coexistence of divergent allelic lineages of the ABO blood group gene for a long period in the ancestral gibbon species, and strengthens the non-neutral evolution for this gene.

  11. Isolation and phylogenetic analysis of canine distemper virus among domestic dogs in Vietnam

    PubMed Central

    NGUYEN, Dung Van; SUZUKI, Junko; MINAMI, Shohei; YONEMITSU, Kenzo; NAGATA, Nao; KUWATA, Ryusei; SHIMODA, Hiroshi; VU, Chien Kim; TRUONG, Thuy Quoc; MAEDA, Ken

    2016-01-01

    Canine distemper virus (CDV) is one of the most serious pathogens found in many species of carnivores, including domestic dogs. In this study, hemagglutinin (H) genes were detected in five domestic Vietnamese dogs with diarrhea, and two CDVs were successfully isolated from dogs positive for H genes. The complete genome of one isolate, CDV/dog/HCM/33/140816, was determined. Phylogenetic analysis showed that all Vietnamese CDVs belonged to the Asia-1 genotype. In addition, the H proteins of Vietnamese CDV strains were the most homologous to those of Chinese CDVs (98.4% to 99.3% identity). These results indicated that the Asia-1 genotype of CDV was the predominant genotype circulating among the domestic dog population in Vietnam and that transboundary transmission of CDV has occurred between Vietnam and China. PMID:27746406

  12. A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1

    PubMed Central

    Reisman, Steven; Hatzopoulos, Thomas; Läufer, Konstantin; Thiruvathukal, George K.; Putonti, Catherine

    2016-01-01

    As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 sequences. Phylogenetic analyses were conducted for >6,000 HIV-1 sequences revealing spatial and temporal factors influence the evolution of the individual genes uniquely. Nevertheless, signatures of origin can be extrapolated even despite increased globalization. The approach developed here can easily be customized for any species of interest. PMID:26819543

  13. Phylogenetic analysis of β-xylanase SRXL1 of Sporisorium reilianum and its relationship with families (GH10 and GH11) of Ascomycetes and Basidiomycetes

    PubMed Central

    Álvarez-Cervantes, Jorge; Díaz-Godínez, Gerardo; Mercado-Flores, Yuridia; Gupta, Vijai Kumar; Anducho-Reyes, Miguel Angel

    2016-01-01

    In this paper, the amino acid sequence of the β-xylanase SRXL1 of Sporisorium reilianum, which is a pathogenic fungus of maize was used as a model protein to find its phylogenetic relationship with other xylanases of Ascomycetes and Basidiomycetes and the information obtained allowed to establish a hypothesis of monophyly and of biological role. 84 amino acid sequences of β-xylanase obtained from the GenBank database was used. Groupings analysis of higher-level in the Pfam database allowed to determine that the proteins under study were classified into the GH10 and GH11 families, based on the regions of highly conserved amino acids, 233–318 and 180–193 respectively, where glutamate residues are responsible for the catalysis. PMID:27040368

  14. [Phylogenetic relationships and intraspecific variation of D-genome Aegilops L. as revealed by RAPD analysis].

    PubMed

    Goriunova, S V; Kochieva, E Z; Chikida, N N; Pukhal'skiĭ, V A

    2004-05-01

    RAPD analysis was carried out to study the genetic variation and phylogenetic relationships of polyploid Aegilops species, which contain the D genome as a component of the alloploid genome, and diploid Aegilops tauschii, which is a putative donor of the D genome for common wheat. In total, 74 accessions of six D-genome Aegilops species were examined. The highest intraspecific variation (0.03-0.21) was observed for Ae. tauschii. Intraspecific distances between accessions ranged 0.007-0.067 in Ae. cylindrica, 0.017-0.047 in Ae. vavilovii, and 0.00-0.053 in Ae. juvenalis. Likewise, Ae. ventricosa and Ae. crassa showed low intraspecific polymorphism. The among-accession difference in alloploid Ae. ventricosa (genome DvNv) was similar to that of one parental species, Ae. uniaristata (N), and substantially lower than in the other parent, Ae. tauschii (D). The among-accession difference in Ae. cylindrica (CcDc) was considerably lower than in either parent, Ae. tauschii (D) or Ae. caudata (C). With the exception of Ae. cylindrica, all D-genome species--Ae. tauschii (D), Ae. ventricosa (DvNv), Ae. crassa (XcrDcrl and XcrDcrlDcr2), Ae. juvenalis (XjDjUj), and Ae. vavilovii (XvaDvaSva)--formed a single polymorphic cluster, which was distinct from clusters of other species. The only exception, Ae. cylindrica, did not group with the other D-genome species, but clustered with Ae. caudata (C), a donor of the C genome. The cluster of these two species was clearly distinct from the cluster of the other D-genome species and close to a cluster of Ae. umbellulata (genome U) and Ae. ovata (genome UgMg). Thus, RAPD analysis for the first time was used to estimate and to compare the interpopulation polymorphism and to establish the phylogenetic relationships of all diploid and alloploid D-genome Aegilops species.

  15. A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis

    PubMed Central

    2015-01-01

    Background Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of housekeeping genes, has been shown to be promising and powerful for defining bacterial species, and, in this study, it was applied to Bradyrhizobium, species, increasing our understanding of the diversity of nitrogen-fixing bacteria. Description Classification of bacteria of agronomic importance is relevant to biodiversity, as well as to biotechnological manipulation to improve agricultural productivity. We propose the construction of an online database that will provide information and tools using MLSA to improve phylogenetic and taxonomic characterization of Bradyrhizobium, allowing the comparison of genomic sequences with those of type and representative strains of each species. Conclusion A database for the taxonomic and phylogenetic identification of the Bradyrhizobium, genus, using MLSA, will facilitate the use of biological data available through an intuitive web interface. Sequences stored in the on-line database can be compared with multiple sequences of other strains with simplicity and agility through multiple alignment algorithms and computational routines integrated into the database. The proposed database and software tools are available at http://mlsa.cnpso.embrapa.br, and can be used, free of charge, by researchers worldwide to classify Bradyrhizobium, strains; the database and software can be applied to

  16. Phylogenetic analysis of cercospora and mycosphaerella based on the internal transcribed spacer region of ribosomal DNA.

    PubMed

    Goodwin, S B; Dunkle, L D; Zismann, V L

    2001-07-01

    ABSTRACT Most of the 3,000 named species in the genus Cercospora have no known sexual stage, although a Mycosphaerella teleomorph has been identified for a few. Mycosphaerella is an extremely large and important genus of plant pathogens, with more than 1,800 named species and at least 43 associated anamorph genera. The goal of this research was to perform a large-scale phylogenetic analysis to test hypotheses about the past evolutionary history of Cercospora and Mycosphaerella. Based on the phylogenetic analysis of internal transcribed spacer (ITS) sequence data (ITS1, 5.8S rRNA gene, ITS2), the genus Mycosphaerella is monophyletic. In contrast, many anamorph genera within Mycosphaerella were polyphyletic and were not useful for grouping species. One exception was Cercospora, which formed a highly supported monophyletic group. Most Cercospora species from cereal crops formed a subgroup within the main Cercospora cluster. Only species within the Cercospora cluster produced the toxin cercosporin, suggesting that the ability to produce this compound had a single evolutionary origin. Intraspecific variation for 25 taxa in the Mycosphaerella clade averaged 1.7 nucleotides (nts) in the ITS region. Thus, isolates with ITS sequences that differ by two or more nucleotides may be distinct species. ITS sequences of groups I and II of the gray leaf spot pathogen Cercospora zeae-maydis differed by 7 nts and clearly represent different species. There were 6.5 nt differences on average between the ITS sequences of the sorghum pathogen Cercospora sorghi and the maize pathogen Cercospora sorghi var. maydis, indicating that the latter is a separate species and not simply a variety of Cercospora sorghi. The large monophyletic Mycosphaerella cluster contained a number of anamorph genera with no known teleomorph associations. Therefore, the number of anamorph genera related to Mycosphaerella may be much larger than suspected previously.

  17. Interspecific phylogenetic analysis enhances intraspecific phylogeographical inference: a case study in Pinus lambertiana.

    PubMed

    Liston, Aaron; Parker-Defeniks, Mariah; Syring, John V; Willyard, Ann; Cronn, Richard

    2007-09-01

    Pinus lambertiana (sugar pine) is an economically and ecologically important conifer with a 1600-km latitudinal range extending from Oregon, USA, to northern Baja California, Mexico. Like all North American white pines (subsect. Strobus), sugar pine is highly susceptible to white pine blister rust, a disease caused by the fungus Cronartium ribicola. We conducted a chloroplast DNA (cpDNA) survey of Pinus subsect. Strobus with comprehensive geographical sampling of P. lambertiana. Sequence analysis of 12 sugar pine individuals revealed strong geographical differentiation for two chloroplast haplotypes. A diagnostic restriction site survey of an additional 72 individuals demarcated a narrow 150-km contact zone in northeastern California. In the contact zone, maternal (megagametophtye) and paternal (embryo) haplotypes were identified in 31 single seeds, demonstrating bidirectional pollen flow extending beyond the range of maternal haplotypes. The frequencies of the Cr1 allele for white pine blister rust major gene resistance, previously determined for 41 seed zones, differ significantly among seed zones that are fixed for the alternate haplotypes, or contain a mixture of both haplotypes. Interspecific phylogenetic analysis reveals that the northern sugar pine haplotype belongs to a clade that includes Pinus albicaulis (whitebark pine) and all of the East Asian white pines. Furthermore, there is little cpDNA divergence between northern sugar pine and whitebark pine (dS = 0.00058). These results are consistent with a Pleistocene migration of whitebark pine into North America and subsequent chloroplast introgression from whitebark pine to sugar pine. This study demonstrates the importance of placing phylogeographical results in a broader phylogenetic context.

  18. Phylogenetic analysis of nasal avian schistosomes (Trichobilharzia) from aquatic birds in Mazandaran Province, northern Iran.

    PubMed

    Fakhar, Mahdi; Ghobaditara, Maryam; Brant, Sara V; Karamian, Mehdi; Gohardehi, Shaban; Bastani, Reza

    2016-04-01

    Nasal schistosomes are trematodes in the family Schistosomatidae, many members of which are causative agents of human cercarial dermatitis (HCD). Little is known about the species diversity and distribution of nasal dwelling schistosomes of water birds, particularly in countries outside of Europe; even less is known in countries like Iran. Nasal schistosomes are of particular interest since these species migrate via the central nervous system to the nasal cavity once they penetrate their host. Thus, there must be efforts to determine the incidence of HCD due to nasal schistosomes. HCD outbreaks are reported seasonally in Mazandaran Province, northern Iran, an area well known for rice cultivation leading to increased person contact with water and infected snails. Such places include favorable habitat for both domestic ducks year round, and wild migratory ducks in the winter through spring. Recent reports have detected the presence of both nasal and visceral schistosomes in ducks in this area but with little species characterization. In this study, we examine a diversity of aquatic birds to determine the distribution, prevalence and bird host use of nasal schistosomes. We apply for the first time a molecular identification and phylogenetic analysis of these schistosomes. From 2012 to 2014, the nasal cavity of 508 aquatic birds from Mazandaran Province were examined that included species in Anseriformes, Gruiformes, Charadriiformes and Phoenicopteriformes. Nasal schistosomes were found in 45 (8.9%) birds belonging to Anseriformes (Anas platyrhynchos and Anas clypeata). Phylogenetic analysis of the nuclear internal transcribed spacer 1 rDNA and the mitochondrial cytochrome oxidase1 gene of isolated eggs revealed that all samples grouped in a sister clade to the European Trichobilharzia regenti. However, Trichobilharzia from this study were more similar to a unique haplotype of Trichobilharzia, isolated from the nasals of an A. clypeata in France. The genetic and

  19. Phylogenetic meta-analysis of the functional traits of clonal plants foraging in changing environments.

    PubMed

    Xie, Xiu-Fang; Song, Yao-Bin; Zhang, Ya-Lin; Pan, Xu; Dong, Ming

    2014-01-01

    Foraging behavior, one of the adaptive strategies of clonal plants, has stimulated a tremendous amount of research. However, it is a matter of debate whether there is any general pattern in the foraging traits (functional traits related to foraging behavior) of clonal plants in response to diverse environments. We collected data from 97 published papers concerning the relationships between foraging traits (e.g., spacer length, specific spacer length, branch intensity and branch angle) of clonal plants and essential resources (e.g., light, nutrients and water) for plant growth and reproduction. We incorporated the phylogenetic information of 85 plant species to examine the universality of foraging hypotheses using phylogenetic meta-analysis. The trends toward forming longer spacers and fewer branches in shaded environments were detected in clonal plants, but no evidence for a relation between foraging traits and nutrient availability was detected, except that there was a positive correlation between branch intensity and nutrient availability in stoloniferous plants. The response of the foraging traits of clonal plants to water availability was also not obvious. Additionally, our results indicated that the foraging traits of stoloniferous plants were more sensitive to resource availability than those of rhizomatous plants. In consideration of plant phylogeny, these results implied that the foraging traits of clonal plants (notably stoloniferous plants) only responded to light intensity in a general pattern but did not respond to nutrient or water availability. In conclusion, our findings on the effects of the environment on the foraging traits of clonal plants avoided the confounding effects of phylogeny because we incorporated phylogeny into the meta-analysis.

  20. Detection and phylogenetic analysis of infectious pancreatic necrosis virus in Chile.

    PubMed

    Tapia, D; Eissler, Y; Torres, P; Jorquera, E; Espinoza, J C; Kuznar, J

    2015-10-27

    Infectious pancreatic necrosis virus (IPNV) is the etiological agent of a highly contagious disease that is endemic to salmon farming in Chile and causes great economic losses to the industry. Here we compared different diagnostic methods to detect IPNV in field samples, including 3 real-time reverse transcription PCR (qRT-PCR) assays, cell culture isolation, and indirect fluorescent antibody test (IFAT). Additionally, we performed a phylogenetic analysis to investigate the genogroups prevailing in Chile, as well as their geographic distribution and virulence. The 3 qRT-PCR assays used primers that targeted regions of the VP2 and VP1 genes of the virus and were tested in 46 samples, presenting a fair agreement within their results. All samples were positive for at least 2 of the qRT-PCR assays, 29 were positive for cell culture, and 23 for IFAT, showing less sensitivity for these latter 2 methods. For the phylogenetic analysis, portions of 1180 and 523 bp of the VP2 region of segment A were amplified by RT-PCR, sequenced and compared with sequences from reference strains and from isolates reported by previous studies carried out in Chile. Most of the sequenced isolates belonged to genogroup 5 (European origin), and 5 were classified within genogroup 1 (American origin). Chilean isolates formed clusters within each of the genogroups found, evidencing a clear differentiation from the reference strains. To our knowledge, this is the most extensive study completed for IPNV in Chile, covering isolates from sea- and freshwater salmon farms and showing a high prevalence of this virus in the country.

  1. Phylogenetic analysis and comparison between cow and buffalo (including Egyptian buffaloes) mitochondrial displacement-loop regions.

    PubMed

    Ramadan, Hassan A I; El-Hefnawi, Mahmoud M

    2008-08-01

    Mitochondrial DNA (mtDNA) analysis has been used extensively for phylogenetic analysis studies and systematics. The displacement loop (D-loop) region inside the mtDNA is a non-coding part whose analysis can indicate variations between closely related populations. This paper reports for the first time the characterization and analysis of the complete sequence of the D-loop region from Egyptian buffaloes and analysis in conjunction with previously published Indian and European Bubalus bubalis and Bos sub-tribe sequences. In the entire D-loop of the Egyptian buffaloes, we identified four haplotypes and nine polymorphic sites from the nine sequenced D-loop regions--while in the studied set of buffaloes we identified 28 polymorphic sites in the entire D-loop, and 49 polymorphic sites in the case of cows. Alignment between buffaloes and cows to evaluate the characteristics of the D-loop region showed that the second region of the conserved sequence block (CSB2) is apparently the most variable region in the D-loop between cows and buffaloes, with four insertions in all buffaloes and two substitutions, followed by the second region of the extended termination associated sequence (ETAS2) with a substitution rate of 1/10. The Egyptian buffaloes were shown to be closest to the Italian counterparts, exemplifying the closeness of ethnicity and the history of civilization of that region.

  2. Sequencing and phylogenetic analysis of neurotoxin gene from an environmental isolate of Clostridium sp.: comparison with other clostridial neurotoxins.

    PubMed

    Dixit, Aparna; Alam, Syed Imteyaz; Singh, Lokendra

    2006-07-01

    A Clostridium sp. isolated from intestine of decaying fish exhibited 99% sequence identity with C. tetani at 16S rRNA level. It produced a neurotoxin that was neutralized by botulinum antitoxin (A+B+E) as well as tetanus antitoxin. The gene fragments for light chain, C-terminal and N-terminal regions of the heavy chain of the toxin were amplified using three reported primer sets for tetanus neurotoxin (TeNT). The neurotoxin gene fragments were cloned in Escherichia coli and sequenced. The sequences obtained exhibited approximately 98, 99 and 98% sequence identity with reported gene sequences of TeNT/LC, TeNT/HC and TeNT/HN, respectively. The phylogenetic interrelationship between the neurotoxin gene of Clostridium sp. with previously reported gene sequences of Clostridium botulinum A to G and C. tetani was examined by analysis of differences in the nucleotide sequences. Six amino acids were substituted at four different positions in the light chain of neurotoxin from the isolate when compared with the reported closest sequence of TeNT. Of these, four were located in the beta15 motif at a solvent inaccessible, buried region of the protein molecule. One of these substitutions were on the solvent accessible surface residue of alpha1 motif, previously shown to have strong sequence conservation. A substitution of two amino acids observed in N-terminal region of heavy chain were buried residues, located in the beta21 and beta37 motifs showing variability in other related sequences. The C-terminal region responsible for binding to receptor was conserved, showing no changes in the amino acid sequence.

  3. Phylogenetic Analysis of Local-Scale Tree Soil Associations in a Lowland Moist Tropical Forest

    PubMed Central

    Schreeg, Laura A.; Kress, W. John; Erickson, David L.; Swenson, Nathan G.

    2010-01-01

    Background Local plant-soil associations are commonly studied at the species-level, while associations at the level of nodes within a phylogeny have been less well explored. Understanding associations within a phylogenetic context, however, can improve our ability to make predictions across systems and can advance our understanding of the role of evolutionary history in structuring communities. Methodology/Principal Findings Here we quantified evolutionary signal in plant-soil associations using a DNA sequence-based community phylogeny and several soil variables (e.g., extractable phosphorus, aluminum and manganese, pH, and slope as a proxy for soil water). We used published plant distributional data from the 50-ha plot on Barro Colorado Island (BCI), Republic of Panamá. Our results suggest some groups of closely related species do share similar soil associations. Most notably, the node shared by Myrtaceae and Vochysiaceae was associated with high levels of aluminum, a potentially toxic element. The node shared by Apocynaceae was associated with high extractable phosphorus, a nutrient that could be limiting on a taxon specific level. The node shared by the large group of Laurales and Magnoliales was associated with both low extractable phosphorus and with steeper slope. Despite significant node-specific associations, this study detected little to no phylogeny-wide signal. We consider the majority of the ‘traits’ (i.e., soil variables) evaluated to fall within the category of ecological traits. We suggest that, given this category of traits, phylogeny-wide signal might not be expected while node-specific signals can still indicate phylogenetic structure with respect to the variable of interest. Conclusions Within the BCI forest dynamics plot, distributions of some plant taxa are associated with local-scale differences in soil variables when evaluated at individual nodes within the phylogenetic tree, but they are not detectable by phylogeny-wide signal. Trends

  4. An improved model for whole genome phylogenetic analysis by Fourier transform.

    PubMed

    Yin, Changchuan; Yau, Stephen S-T

    2015-10-07

    and demonstrates that the improved DFT dissimilarity measure is an efficient and effective similarity measure of DNA sequences. Due to its high efficiency and accuracy, the proposed DFT similarity measure is successfully applied on phylogenetic analysis for individual genes and large whole bacterial genomes.

  5. Enhanced heat stability and kinetic parameters of maize endosperm ADPglucose pyrophosphorylase by alteration of phylogenetically identified amino acids.

    PubMed

    Boehlein, Susan K; Shaw, Janine R; Georgelis, Nikolaos; Hannah, L Curtis

    2014-02-01

    ADP-glucose pyrophosphorylase (AGPase) controls the rate-limiting step in starch biosynthesis and is regulated at various levels. Cereal endosperm enzymes, in contrast to other plant AGPases, are particularly heat labile and transgenic studies highlight the importance of temperature for cereal yield. Previously, a phylogenetic approach identified Type II and positively selected amino acid positions in the large subunit of maize endosperm AGPase. Glycogen content, kinetic parameters and heat stability were measured in AGPases having mutations in these sites and interesting differences were observed. This study expands on our earlier evolutionary work by determining how all Type II and positively selected sites affect kinetic constants, heat stability and catalytic rates at increased temperatures. Variants with enhanced properties were identified and combined into one gene, designated Sh2-E. Enhanced properties include: heat stability, enhanced activity at 37 °C, activity at 55 °C, reduced Ka and activity in the absence of activator. The resulting enzyme exhibited all improved properties of the various individual changes. Additionally, Sh2-E was expressed with a small subunit variant with enhanced enzyme properties resulting in an enzyme that has exceptional heat stability, a high catalytic rate at increased temperatures and significantly decreased Km values for both substrates in the absence of the activator.

  6. Prevalence and phylogenetic analysis of HTLV-1 in a segregated population in Iran.

    PubMed

    Rafatpanah, Houshang; Torkamani, Mahmood; Valizadeh, Narges; Vakili, Rosita; Meshkani, Baratali; Khademi, Hassan; Gerayli, Sina; Mozhgani, Sayed Hamid Reza; Rezaee, Seyed Abdolrahim

    2016-07-01

    Human T-lymphotropic virus type 1 (HTLV-1) infection is an important health issue that affects a variety of endemic areas. The Khorasan province, mainly its capital Mashhad in northeastern Iran, was reported to be as one of these endemic regions. Torbat-e Heydarieh, a large city Southwest border to Mashhad with a segregated population was investigated for the prevalence and associated risk factors of HTLV-1 infection in 400 randomly selected individuals. Blood samples were tested for the presence of HTLV-1 antibodies via the ELISA method and then were confirmed by an Immunoblot test. For the presence of HTLV-1 in lymphocytes of infected subjects, PCR was performed on LTR and TAX regions. DNA sequencing of LTR fragment was also carried out to determine the phylogenetic of HTLV-1, using the Maximum likelihood method. HTLV-1 sero-reactivity (sero-prevalence) among the study population was 2% (8/400), of which 1.25% had HTLV-1 provirus in lymphocytes (actual prevalence). HTLV-1 infection was significantly associated with the age, marital status, and history of blood transfusion (P < 0.05). However, there were no statistical differences between HTLV-1 infection, and gender, surgery, and hospitalization. In regression analysis, age showed the most significant correlation with the infection (P = 0.006, OR = 4.33). Based on our phylogenetic study, the HTLV-1 prevalent sequence type of Torbat-e Heydarieh belongs to the cosmopolitan subtype A. HTLV-1 prevalence in Torbat-e Heydarieh (1.25%) is low comparing to those of both Mashhad (2-3%) and Neishabour (3.5-5%) in the province of Khorasan. Thus, traveling mobility and population mixing such as marriage, bureaucratic affairs, occupation, and economic activities could be the usual routs of HTLV-1 new wave of spreading in this segregated city.

  7. Phylogenetic analysis reveals a high prevalence of Sporothrix brasiliensis in feline sporotrichosis outbreaks.

    PubMed

    Rodrigues, Anderson Messias; de Melo Teixeira, Marcus; de Hoog, G Sybren; Schubach, Tânia Maria Pacheco; Pereira, Sandro Antonio; Fernandes, Geisa Ferreira; Bezerra, Leila Maria Lopes; Felipe, Maria Sueli; de Camargo, Zoilo Pires

    2013-01-01

    Sporothrix schenckii, previously assumed to be the sole agent of human and animal sporotrichosis, is in fact a species complex. Recently recognized taxa include S. brasiliensis, S. globosa, S. mexicana, and S. luriei, in addition to S. schenckii sensu stricto. Over the last decades, large epidemics of sporotrichosis occurred in Brazil due to zoonotic transmission, and cats were pointed out as key susceptible hosts. In order to understand the eco-epidemiology of feline sporotrichosis and its role in human sporotrichosis a survey was conducted among symptomatic cats. Prevalence and phylogenetic relationships among feline Sporothrix species were investigated by reconstructing their phylogenetic origin using the calmodulin (CAL) and the translation elongation factor-1 alpha (EF1α) loci in strains originated from Rio de Janeiro (RJ, n = 15), Rio Grande do Sul (RS, n = 10), Paraná (PR, n = 4), São Paulo (SP, n =3) and Minas Gerais (MG, n = 1). Our results showed that S. brasiliensis is highly prevalent among cats (96.9%) with sporotrichosis, while S. schenckii was identified only once. The genotype of Sporothrix from cats was found identical to S. brasiliensis from human sources confirming that the disease is transmitted by cats. Sporothrix brasiliensis presented low genetic diversity compared to its sister taxon S. schenckii. No evidence of recombination in S. brasiliensis was found by split decomposition or PHI-test analysis, suggesting that S. brasiliensis is a clonal species. Strains recovered in states SP, MG and PR share the genotype of the RJ outbreak, different from the RS clone. The occurrence of separate genotypes among strains indicated that the Brazilian S. brasiliensis epidemic has at least two distinct sources. We suggest that cats represent a major host and the main source of cat and human S. brasiliensis infections in Brazil.

  8. Molecular detection of the oyster parasite Mikrocytos mackini, and a preliminary phylogenetic analysis.

    PubMed

    Carnegie, Ryan B; Meyer, Gary R; Blackbourn, Janice; Cochennec-Laureau, Nathalie; Berthe, Franck C J; Bower, Susan M

    2003-04-24

    The protistan parasite Mikrocytos mackini, the causative agent of Denman Island disease in the oyster Crassostrea gigas in British Columbia, Canada, is of wide concern because it can infect other oyster species and because its life cycle, mode of transmission, and origins are unknown. PCR and fluorescent in situ hybridization (FISH) assays were developed for M. mackini, the PCR assay was validated against standard histopathological diagnosis, and a preliminary phylogenetic analysis of the M. mackini small-subunit ribosomal RNA gene (SSU rDNA) was undertaken. A PCR designed specifically not to amplify host DNA generated a 544 bp SSU rDNA fragment from M. mackini-infected oysters and enriched M. mackini cell isolates, but not from uninfected control oysters. This fragment was confirmed by FISH to be M. mackini SSU rDNA. A M. mackini-specific PCR was then designed which detected 3 to 4x more M. mackini infections in 1056 wild oysters from Denman Island, British Columbia, than standard histopathology. Mikrocytos mackini prevalence estimates based on both PCR and histopathology increased (PCR from 4.4 to 7.4%, histopathology from 1.2 to 2.1%) when gross lesions were processed in addition to standard samples (i.e. transverse sections for histopathology, left outer palp DNA for PCR). The use of histopathology and tissue imprints plus PCR, and standard samples plus observed gross lesions, represented a 'total evidence' approach that provided the most realistic estimates of the true prevalence of M. mackini. Maximum parsimony and evolutionary distance phylogenetic analyses suggested that M. mackini may be a basal eukaryote, although it is not closely related to other known protistan taxa.

  9. First molecular detection and phylogenetic analysis of Anaplasma phagocytophilum in shelter dogs in Seoul, Korea.

    PubMed

    Lee, Sukyee; Lee, Seung-Hun; VanBik, Dorene; Kim, Neung-Hee; Kim, Kyoo-Tae; Goo, Youn-Kyoung; Rhee, Man Hee; Kwon, Oh-Deog; Kwak, Dongmi

    2016-07-01

    In this study, the status of Anaplasma phagocytophilum infection was assessed in shelter dogs in Seoul, Korea, with PCR and phylogenetic analyses. Nested PCR on 1058 collected blood samples revealed only one A. phagocytophilum positive sample (female, age <1year, mixed breed, collected from the north of the Han River). The genetic variability of A. phagocytophilum was evaluated by genotyping, using the 16S rRNA, groEL, and msp2 gene sequences of the positive sample. BLASTn analysis revealed that the 16S rRNA, groEL, and msp2 genes had 99.6%, 99.9%, and 100% identity with the following sequences deposited in GenBank: a cat 16S rRNA sequence from Korea (KR021166), a rat groEL sequence from Korea (KT220194), and a water deer msp2 sequence from Korea (HM752099), respectively. Phylogenetic analyses classified the groEL gene into two distinct groups (serine and alanine), whereas the msp2 gene showed a general classification into two groups (USA and Europe) that were further subgrouped according to region. To the best of our knowledge, this study is the first to describe the molecular diagnosis of A. phagocytophilum in dogs reared in Korea. In addition, the high genetic identity of the 16S rRNA and groEL sequences between humans and dogs from the same region suggests a possible epidemiological relation. Given the conditions of climate change, tick ecology, and recent incidence of human granulocytic anaplasmosis in Korea, the findings of this study underscore the need to establish appropriate control programs for tick-borne diseases in Korea.

  10. Phylogenetic analysis of Antrodia species and Antrodia camphorata inferred from internal transcribed spacer region.

    PubMed

    Chiu, Hua-Hsien

    2007-04-01

    The species of Antrodia are one of the difficult-to-classify and obscure groups of poroid Aphyllophorales based on morphological appearance. However, it is becoming increasingly important to reliably identify the entire suite of Antrodia camphorata strains and Antrodia species due to the potential pharmaceutical value of their biologically active ingredients. In this study, the internal transcribed spacer (ITS) region of the ribosomal RNA gene (rDNA) was sequenced and phylogenetically analyzed in a number of Antrodia fungal species and strains. ITS amplicons from the Antrodia species tested ranged in size from 543 to 610 bp; the size of the ITS of A. camphorata strains ranged from 592 to 596 bp. The overall sizes of ITS2 and 5.8S ribosomal RNA gene of all A. camphorata strains tested in this study were shown to be 217 and 158 bp, respectively. A phylogenetic analysis of ITS data generated, which included sequences of 11 A. camphorata strains and nine other Antrodia species, showed three clearly distinct groups. Group 1 includes A. camphorata, Antrodia salmonea, and Antrodia carbinca strains. Within Group 2, Antrodia sinuosa and Antrodia xantha were clustered together. Group 3 contained Antrodia albida, A. heteromorpha, A. serialis, and A. malicola. The observed sequence diversity among ITS alleles provided an effective tool for differentiating strains of A. camphorata, A. salmonea, A. xantha, A. sinuosa, or A. serialis. Polymorphisms arising within the ITS1-5.8S-ITS2 region can provide practical markers for establishing a foundation for the further expansion of an ITS sequence database of medically important fungi.

  11. Phylogenetic Analysis Reveals a High Prevalence of Sporothrix brasiliensis in Feline Sporotrichosis Outbreaks

    PubMed Central

    Rodrigues, Anderson Messias; de Melo Teixeira, Marcus; de Hoog, G. Sybren; Schubach, Tânia Maria Pacheco; Pereira, Sandro Antonio; Fernandes, Geisa Ferreira; Bezerra, Leila Maria Lopes; Felipe, Maria Sueli; de Camargo, Zoilo Pires

    2013-01-01

    Sporothrix schenckii, previously assumed to be the sole agent of human and animal sporotrichosis, is in fact a species complex. Recently recognized taxa include S. brasiliensis, S. globosa, S. mexicana, and S. luriei, in addition to S. schenckii sensu stricto. Over the last decades, large epidemics of sporotrichosis occurred in Brazil due to zoonotic transmission, and cats were pointed out as key susceptible hosts. In order to understand the eco-epidemiology of feline sporotrichosis and its role in human sporotrichosis a survey was conducted among symptomatic cats. Prevalence and phylogenetic relationships among feline Sporothrix species were investigated by reconstructing their phylogenetic origin using the calmodulin (CAL) and the translation elongation factor-1 alpha (EF1α) loci in strains originated from Rio de Janeiro (RJ, n = 15), Rio Grande do Sul (RS, n = 10), Paraná (PR, n = 4), São Paulo (SP, n = 3) and Minas Gerais (MG, n = 1). Our results showed that S. brasiliensis is highly prevalent among cats (96.9%) with sporotrichosis, while S. schenckii was identified only once. The genotype of Sporothrix from cats was found identical to S. brasiliensis from human sources confirming that the disease is transmitted by cats. Sporothrix brasiliensis presented low genetic diversity compared to its sister taxon S. schenckii. No evidence of recombination in S. brasiliensis was found by split decomposition or PHI-test analysis, suggesting that S. brasiliensis is a clonal species. Strains recovered in states SP, MG and PR share the genotype of the RJ outbreak, different from the RS clone. The occurrence of separate genotypes among strains indicated that the Brazilian S. brasiliensis epidemic has at least two distinct sources. We suggest that cats represent a major host and the main source of cat and human S. brasiliensis infections in Brazil. PMID:23818999

  12. Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information.

    PubMed

    Hill, Natascha; Leow, Alexander; Bleidorn, Christoph; Groth, Detlef; Tiedemann, Ralph; Selbig, Joachim; Hartmann, Stefanie

    2013-06-01

    Many deep evolutionary divergences still remain unresolved, such as those among major taxa of the Lophotrochozoa. As alternative phylogenetic markers, the intron-exon structure of eukaryotic genomes and the patterns of absence and presence of spliceosomal introns appear to be promising. However, given the potential homoplasy of intron presence, the phylogenetic analysis of this data using standard evolutionary approaches has remained a challenge. Here, we used Mutual Information (MI) to estimate the phylogeny of Protostomia using gene structure data, and we compared these results with those obtained with Dollo Parsimony. Using full genome sequences from nine Metazoa, we identified 447 groups of orthologous sequences with 21,732 introns in 4,870 unique intron positions. We determined the shared absence and presence of introns in the corresponding sequence alignments and have made this data available in "IntronBase", a web-accessible and downloadable SQLite database. Our results obtained using Dollo Parsimony are obviously misled through systematic errors that arise from multiple intron loss events, but extensive filtering of data improved the quality of the estimated phylogenies. Mutual Information, in contrast, performs better with larger datasets, but at the same time it requires a complete data set, which is difficult to obtain for orthologs from a large number of taxa. Nevertheless, Mutual Information-based distances proved to be useful in analyzing this kind of data, also because the estimation of MI-based distances is independent of evolutionary models and therefore no pre-definitions of ancestral and derived character states are necessary.

  13. Genome Sequences and Phylogenetic Analysis of K88- and F18-Positive Porcine Enterotoxigenic Escherichia coli

    PubMed Central

    Shepard, Sara M.; Danzeisen, Jessica L.; Isaacson, Richard E.; Seemann, Torsten; Achtman, Mark

    2012-01-01

    Porcine enterotoxigenic Escherichia coli (ETEC) continues to result in major morbidity and mortality in the swine industry via postweaning diarrhea. The key virulence factors of ETEC strains, their serotypes, and their fimbrial components have been well studied. However, most studies to date have focused on plasmid-encoded traits related to colonization and toxin production, and the chromosomal backgrounds of these strains have been largely understudied. Here, we generated the genomic sequences of K88-positive and F18-positive porcine ETEC strains and examined the phylogenetic distribution of clinical porcine ETEC strains and their plasmid-associated genetic content. The genomes of porcine ETEC strains UMNK88 and UMNF18 were both found to contain remarkable plasmid complements containing known virulence factors, potential novel virulence factors, and antimicrobial resistance-associated elements. The chromosomes of these strains also possessed several unique genomic islands containing hypothetical genes with similarity to classical virulence factors, although phage-associated genomic islands dominated the accessory genomes of these strains. Phylogenetic analysis of 78 clinical isolates associated with neonatal and porcine diarrhea revealed that a limited subset of porcine ETEC lineages exist that generally contain common toxin and fimbrial profiles, with many of the isolates belonging to the ST10, ST23, and ST169 multilocus sequencing types. These lineages were generally distinct from existing human ETEC database isolates. Overall, most porcine ETEC strains appear to have emerged from a limited subset of E. coli lineages that either have an increased propensity to carry plasmid-encoded virulence factors or have the appropriate ETEC core genome required for virulence. PMID:22081385

  14. Structural, Biochemical, and Phylogenetic Analyses Suggest That Indole-3-Acetic Acid Methyltransferase Is an Evolutionarily Ancient Member of the SABATH Family

    SciTech Connect

    Zhao,N.; Ferrer, J.; Ross, J.; Guan, J.; Yang, Y.; Pichersky, E.; Noel, J.; Chen, F.

    2008-01-01

    The plant SABATH protein family encompasses a group of related small-molecule methyltransferases (MTs) that catalyze the S-adenosyl-L-methionine-dependent methylation of natural chemicals encompassing widely divergent structures. Indole-3-acetic acid (IAA) methyltransferase (IAMT) is a member of the SABATH family that modulates IAA homeostasis in plant tissues through methylation of IAA's free carboxyl group. The crystal structure of Arabidopsis (Arabidopsis thaliana) IAMT (AtIAMT1) was determined and refined to 2.75 Angstroms resolution. The overall tertiary and quaternary structures closely resemble the two-domain bilobed monomer and the dimeric arrangement, respectively, previously observed for the related salicylic acid carboxyl methyltransferase from Clarkia breweri (CbSAMT). To further our understanding of the biological function and evolution of SABATHs, especially of IAMT, we analyzed the SABATH gene family in the rice (Oryza sativa) genome. Forty-one OsSABATH genes were identified. Expression analysis showed that more than one-half of the OsSABATH genes were transcribed in one or multiple organs. The OsSABATH gene most similar to AtIAMT1 is OsSABATH4. Escherichia coli-expressed OsSABATH4 protein displayed the highest level of catalytic activity toward IAA and was therefore named OsIAMT1. OsIAMT1 exhibited kinetic properties similar to AtIAMT1 and poplar IAMT (PtIAMT1). Structural modeling of OsIAMT1 and PtIAMT1 using the experimentally determined structure of AtIAMT1 reported here as a template revealed conserved structural features of IAMTs within the active-site cavity that are divergent from functionally distinct members of the SABATH family, such as CbSAMT. Phylogenetic analysis revealed that IAMTs from Arabidopsis, rice, and poplar (Populus spp.) form a monophyletic group. Thus, structural, biochemical, and phylogenetic evidence supports the hypothesis that IAMT is an evolutionarily ancient member of the SABATH family likely to play a critical role in

  15. Molecular Phylogenetic Analysis of Archaeal Intron-Containing Genes Coding for rRNA Obtained from a Deep-Subsurface Geothermal Water Pool

    PubMed Central

    Takai, Ken; Horikoshi, Koki

    1999-01-01

    Molecular phylogenetic analysis of a naturally occurring microbial community in a deep-subsurface geothermal environment indicated that the phylogenetic diversity of the microbial population in the environment was extremely limited and that only hyperthermophilic archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA sequences contained intron-like sequences, some of which had open reading frames with repeated homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of these homing endonucleases suggested the possible phylogenetic relationship among archaeal rRNA-encoded homing endonucleases. PMID:10584021

  16. Tyrosine hydroxylase in the european eel (Anguilla anguilla): cDNA cloning, brain distribution, and phylogenetic analysis.

    PubMed

    Boularand, S; Biguet, N F; Vidal, B; Veron, M; Mallet, J; Vincent, J D; Dufour, S; Vernier, P

    1998-08-01

    We report the isolation of a full-length eel tyrosine hydroxylase (TH) cDNA that is characterized by a long 3' untranslated region and by a diversity restricted to the 3' end owing to the differential use of three polyadenylation signals. The longest eel TH mRNA was distinctive in the presence of four pentameric elements (AUUUA) in the AU-rich 3' noncoding region. Such a diversity could provide the basis of posttranscriptional or translational regulation of eel TH gene expression. Comparison of the eel TH sequence with those of other aromatic amino acid hydroxylases (TH, tryptophan hydroxylase, and phenylalanine hydroxylase) and phylogenetic analysis confirmed that the N-terminal regulatory domain is highly divergent, contrasting with the conservation of the catalytic core of the enzyme. Molecular phylogenies including the available sequences of the three hydroxylase genes suggested that the duplication of their common ancestor occurred before the emergence of arthropods. The regional expression of the eel TH mRNA was studied by semiquantitative PCR, northern blots, and in situ hybridization and compared with the immunocytochemical localization of TH protein. The data showed that TH mRNA is mostly expressed in the olfactory and hypothalamic areas, whereas sparse TH-expressing cell bodies are present in the telencephalic region and brainstem. No labeling was detected in the mesencephalic area, in striking contrast with that found in amphibians and amniotes.

  17. Comparative Mitochondrial Genome Analysis of Eligma narcissus and other Lepidopteran Insects Reveals Conserved Mitochondrial Genome Organization and Phylogenetic Relationships

    PubMed Central

    Dai, Li-Shang; Zhu, Bao-Jian; Zhao, Yue; Zhang, Cong-Fen; Liu, Chao-Liang

    2016-01-01

    In this study, we sequenced the complete mitochondrial genome of Eligma narcissus and compared it with 18 other lepidopteran species. The mitochondrial genome (mitogenome) was a circular molecule of 15,376 bp containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and an adenine (A) + thymine (T) − rich region. The positive AT skew (0.007) indicated the occurrence of more As than Ts. The arrangement of 13 PCGs was similar to that of other sequenced lepidopterans. All PCGs were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which was initiated by the CGA sequence, as observed in other lepidopterans. The results of the codon usage analysis indicated that Asn, Ile, Leu, Tyr and Phe were the five most frequent amino acids. All tRNA genes were shown to be folded into the expected typical cloverleaf structure observed for mitochondrial tRNA genes. Phylogenetic relationships were analyzed based on the nucleotide sequences of 13 PCGs from other insect mitogenomes, which confirmed that E. narcissus is a member of the Noctuidae superfamily. PMID:27222440

  18. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

    PubMed

    Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A

    2012-09-21

    Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity.

  19. Phylogenetic analysis of avian poxviruses among free-ranging birds of Virginia.

    PubMed

    Adams, Cary J; Feldman, Sanford H; Sleeman, Jonathan M

    2005-12-01

    Polymerase chain reaction was used to amplify a portion of the avian poxvirus core 4b gene of infected free-ranging birds that presented at the Wildlife Center of Virginia during the 2003 and early 2004 years. The species of bird infected were a great blue heron (Ardea herodias), two American crows (Corvus brachyrhyncos), two American robins (Turdus migratorius), two mourning doves (Zenaida macroura), a red-tailed hawk (Buteo jamaicensis), a blue-gray gnatcatcher (Polioptila caerulea), a northern mockingbird (Mimus polyglottos), a house finch (Carpodacus mexicanus), and a northern cardinal (Cardinalis cardinalis). Phylogenetic analysis was performed using the consensus sequences determined for each avian case in Virginia in combination with avian poxvirus core 4b gene sequence from isolates previously described in Europe and that of vaccinia virus. Alignment of DNA sequences identified areas of point mutations and, in the case of a single mourning dove, the incorporation of a triplet of nucleotides. Maximum-likelihood analysis grouped the 2003-2004 Virginia avian poxviruses into a clade distinct from those reported in European free-ranging birds, with the exception of a single case in a mourning dove that clustered within one European clade. The cladogram that resulted from our analysis of the European isolates is in agreement with those previously published. This study identified a distinct clade of avian poxvirus unique from four clades previously described and associated with epornitics in free-ranging birds, where the core 4b gene DNA sequence has been the basis of comparison.

  20. An enhanced calibration of a recently released megatree for the analysis of phylogenetic diversity.

    PubMed

    Gastauer, M; Meira-Neto, J A A

    2016-04-19

    Dated or calibrated phylogenetic trees, in which branch lengths correspond to evolutionary divergence times between nodes, are important requirements for computing measures of phylogenetic diversity or phylogenetic community structure. The increasing knowledge about the diversification and evolutionary divergence times of vascular plants requires a revision of the age estimates used for the calibration of phylogenetic trees by the bladj algorithm of the Phylocom 4.2 package. Comparing the recently released megatree R20120829.new with two calibrated vascular plant phylogenies provided in the literature, we found 242 corresponding nodes. We modified the megatree (R20120829mod.new), inserting names for all corresponding nodes. Furthermore, we provide files containing age estimates from both sources for the updated calibration of R20120829mod.new. Applying these files consistently in analyses of phylogenetic community structure or diversity serves to avoid erroneous measures and ecological misinterpretation.

  1. Phylogenetic Analysis of Stenotrophomonas spp. Isolates Contributes to the Identification of Nosocomial and Community-Acquired Infections

    PubMed Central

    Cerezer, Vinicius Godoy; Pasternak, Jacyr; Franzolin, Marcia Regina; Moreira-Filho, Carlos Alberto

    2014-01-01

    Stenotrophomonas ssp. has a wide environmental distribution and is also found as an opportunistic pathogen, causing nosocomial or community-acquired infections. One species, S. maltophilia, presents multidrug resistance and has been associated with serious infections in pediatric and immunocompromised patients. Therefore, it is relevant to conduct resistance profile and phylogenetic studies in clinical isolates for identifying infection origins and isolates with augmented pathogenic potential. Here, multilocus sequence typing was performed for phylogenetic analysis of nosocomial isolates of Stenotrophomonas spp. and, environmental and clinical strains of S. maltophilia. Biochemical and multidrug resistance profiles of nosocomial and clinical strains were determined. The inferred phylogenetic profile showed high clonal variability, what correlates with the adaptability process of Stenotrophomonas to different habitats. Two clinical isolates subgroups of S. maltophilia sharing high phylogenetic homogeneity presented intergroup recombination, thus indicating the high permittivity to horizontal gene transfer, a mechanism involved in the acquisition of antibiotic resistance and expression of virulence factors. For most of the clinical strains, phylogenetic inference was made using only partial ppsA gene sequence. Therefore, the sequencing of just one specific fragment of this gene would allow, in many cases, determining whether the infection with S. maltophilia was nosocomial or community-acquired. PMID:24818127

  2. Spatial and phylogenetic analysis of the vesicular stomatitis virus epidemic in the southwestern United States in 2004-2006

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The southwestern United States has been incidentally affected by vesicular stomatitis virus (VSV) epidemics during the last 100 years. By the time this manuscript was written, the last episodes were reported in 2004-2006. Results of space clustering and phylogenetic analysis techniques used here sug...

  3. Inferring Cell Differentiation Processes Based on Phylogenetic Analysis of Genome-Wide Epigenetic Information: Hematopoiesis as a Model Case

    PubMed Central

    Koyanagi, Kanako O.

    2015-01-01

    How cells divide and differentiate is a fundamental question in organismal development; however, the discovery of differentiation processes in various cell types is laborious and sometimes impossible. Phylogenetic analysis is typically used to reconstruct evolutionary processes based on inherent characters. It could also be used to reconstruct developmental processes based on the developmental changes that occur during cell proliferation and differentiation. In this study, DNA methylation information from differentiated hematopoietic cells was used to perform phylogenetic analyses. The results were assessed for their validity in inferring hierarchical differentiation processes of hematopoietic cells and DNA methylation processes of differentiating progenitor cells. Overall, phylogenetic analyses based on DNA methylation information facilitated inferences regarding hematopoiesis. PMID:25638259

  4. Analysis of the complete genome of Fervidococcus fontis confirms the distinct phylogenetic position of the order Fervidicoccales and suggests its environmental function.

    PubMed

    Lebedinsky, Alexander V; Mardanov, Andrey V; Kublanov, Ilya V; Gumerov, Vadim M; Beletsky, Alexey V; Perevalova, Anna A; Bidzhieva, Salima Kh; Bonch-Osmolovskaya, Elizaveta A; Skryabin, Konstantin G; Ravin, Nikolai V

    2014-03-01

    The complete genome of the obligately anaerobic crenarchaeote Fervidicoccus fontis Kam940(T), a terrestrial hot spring inhabitant with a growth optimum of 65-70 °C, has been sequenced and analyzed. The small 1.3-Mb genome encodes several extracellular proteases and no other extracellular hydrolases. No complete pathways of carbohydrate catabolism were found. Genes coding for enzymes necessary for amino acid transamination and further oxidative decarboxylation are present. The genome encodes no mechanisms of acyl-CoA and acetyl-CoA oxidation. Two [NiFe]-hydrogenases are encoded: a membrane-bound energy-converting hydrogenase and a cytoplasmic one. The ATP-synthase is H(+)-dependent as inferred from the amino acid sequence of the membrane rotor subunit. On the whole, genome analysis shows F. fontis to be a peptidolytic heterotroph with a restricted biosynthetic potential, which is in accordance with its phenotypic properties. The analysis of phylogenetic markers and of the distribution of best blastp hits of F. fontis proteins in the available genomes of Crenarchaeota supports distinct phylogenetic position of the order Fervidicoccales as a separate lineage adjoining the heterogeneous order Desulfurococcales. In addition, certain F. fontis genomic features correlate with its adaptation to temperatures of 60-80 °C, which are lower than temperatures preferred by Desulfurococcales.

  5. Molecular Tracing of Hepatitis C Virus Genotype 1 Isolates in Iran: A NS5B Phylogenetic Analysis with Systematic Review

    PubMed Central

    Hesamizadeh, Khashayar; Alavian, Seyed Moayed; Najafi Tireh Shabankareh, Azar; Sharafi, Heidar

    2016-01-01

    Context Hepatitis C virus (HCV) is characterized by a high degree of genetic heterogeneity and classified into 7 genotypes and different subtypes. It heterogeneously distributed through various risk groups and geographical regions. A well-established phylogenetic relationship can simplify the tracing of HCV hierarchical strata into geographical regions. The current study aimed to find genetic phylogeny of subtypes 1a and 1b of HCV isolates based on NS5B nucleotide sequences in Iran and other members of Eastern Mediterranean regional office of world health organization, as well as other Middle Eastern countries, with a systematic review of available published and unpublished studies. Evidence Acquisition The phylogenetic analyses were performed based on the nucleotide sequences of NS5B gene of HCV genotype 1 (HCV-1), which were registered in the GenBank database. The literature review was performed in two steps: 1) searching studies evaluating the NS5B sequences of HCV-1, on PubMed, Scopus, and Web of Science, and 2) Searching sequences of unpublished studies registered in the GenBank database. Results In this study, 442 sequences from HCV-1a and 232 from HCV-1b underwent phylogenetic analysis. Phylogenetic analysis of all sequences revealed different clusters in the phylogenetic trees. The results showed that the proportion of HCV-1a and -1b isolates from Iranian patients probably originated from domestic sources. Moreover, the HCV-1b isolates from Iranian patients may have similarities with the European ones. Conclusions In this study, phylogenetic reconstruction of HCV-1 sequences clearly indicated for molecular tracing and ancestral relationships of the HCV genotypes in Iran, and showed the likelihood of domestic origin for HCV-1a and various origin for HCV-1b. PMID:28123445

  6. Molecular characterization and phylogenetic analysis of a novel glutenin gene (Dy10.1t) from Aegilops tauschii.

    PubMed

    Zhang, Yanzhen; Li, Qiaoyun; Yan, Yueming; Zheng, Jigang; An, Xueli; Xiao, Yinghua; Wang, Aili; Pei, Yuhe; Wang, Haibo; Hsam, Sai L K; Zeller, Friedrich J

    2006-07-01

    A novel y-type high molecular mass glutenin subunit (HMM-GS) possessing a mobility that is slightly slower than that of the subunit Dy10 obtained by SDS-PAGE, named Dy10.1t, in the wild wheat Aegilops tauschii was identified by 1- and 2-dimensional gel electrophoresis, capillary electrophoresis, and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS). The gene encoding the HMM subunit Dy10.1t was amplified with allele-specific PCR primers, and the amplified products were cloned and sequenced. The coding domain of the Dy10.1t subunit gene consisted of 1980 bp encoding a protein of 658 residues with an M rs of 68 611 Da, which was similar to the M rs determined by MALDI-TOF-MS. The deduced amino acid sequence indicated that Dy10.1t subunit displayed a greater similarity to the Dy12 subunit, differing by only 8 amino acid substitutions. Six coding region single-nucleotide polymorphisms were discovered in the Dy10.1t gene by multiple alignments (1 per 330 bp), 1 in the N-terminal domain and the others in the central repeats. Five of them resulted in residue substitutions, whereas 3 created enzyme site changes. The homology and neighbour-joining trees constructed from code domain sequences of 20 x- and y-type glutenin genes from different Triticum species separated into 2 halves, which corresponded to the x-type and y-type HMM glutenin alleles. Phylogenetic analysis revealed that the Glu-1 gene duplication event probably occurred at about 16.83 million years ago, whereas the divergence times of A, B, and D genomes within x-type and y-type halves were before 7.047 and 10.54 million years ago, respectively.

  7. Phylogenetic analysis of Chlamydia trachomatis Tarp and correlation with clinical phenotype.

    PubMed

    Lutter, Erika I; Bonner, Christine; Holland, Martin J; Suchland, Robert J; Stamm, Walter E; Jewett, Travis J; McClarty, Grant; Hackstadt, Ted

    2010-09-01

    Chlamydia trachomatis is the leading cause of infectious blindness worldwide and is the most commonly reported pathogen causing sexually transmitted infections. Tarp (translocated actin recruiting phosphoprotein), a type III secreted effector that mediates actin nucleation, is central to C. trachomatis infection. The phylogenetic analysis of tarP from reference strains as well as ocular, genital, and lymphogranuloma venereum (LGV) clinical isolates demonstrated an evolutionary relationship with disease phenotype, with LGV and ocular isolates branched into clades that were separate from the urogenital isolates. The sequence analysis of Tarp indicated a high degree of variability and identified trends within clinical groupings. Tarps from LGV strains contained the highest number of tyrosine-rich repeat regions (up to nine) and the fewest (two) predicted actin binding domains. The converse was noted for Tarp proteins from ocular isolates that contained up to four actin binding domains and as few as one tyrosine-rich repeat region. The results suggest that Tarp is among the few known genes to play a role in C. trachomatis adaptations to specific niches within the host.

  8. Molecular characterization and phylogenetic analysis of the reticuloendotheliosis virus isolated from wild birds in Northeast China.

    PubMed

    Jiang, Lili; Qi, Xiaole; Gao, Yulong; Hua, Yuping; Li, Kai; Deng, Xiaoyun; Wang, Qi; Zhang, Lizhou; Chai, Hongliang; Chen, Yuming; Yin, Chunhong; Gao, Honglei; Qin, Liting; Wang, Yongqiang; Qu, Yue; Chen, Qiang; Fan, Zhaobin; Wang, Xiaomei

    2013-09-27

    To analyze the status of reticuloendotheliosis (RE) infection of wild birds in China, 585 samples from wild birds collected in Liaoning, Jilin and Heilongjiang provinces China were investigated and analyzed. The sampled birds represent 3 orders and more than 40 species. Virus isolation and PCR amplification showed that some of the wild birds were infected with REV, and 10 REV strains were isolated. The gp90 gene from each of the 10 REV strains was amplified, cloned, and sequenced. Sequence analysis indicated that the gp90 genes of the 10 REV strains isolated in this study were more similar at the nucleotide level with the northeast Chinese strains HLJR0901 and HLJR0801 and some REV strains found in the US and Taiwan than with the early Chinese REV isolate HA9901. Furthermore, phylogenetic analysis indicated that the gp90 genes of the 10 REV strains were more similar to the REV subtype III-representing strain (CSV) than to strains 170A (subtype I) or SNV (subtype II). This is the first study to investigate the status of wild birds infected with REV. The results of this paper will not only provide necessary information for further understanding the evolution of REV, but they also identify the potential role of wild birds in REV transmission and furthers our understanding of the ecology of REV in wild bird species.

  9. Phylogenetic analysis of VP2 gene of canine parvovirus and comparison with Indian and world isolates.

    PubMed

    Kaur, G; Chandra, M; Dwivedi, P N

    2016-03-01

    Canine parvovirus (CPV) causes hemorrhagic enteritis, especially in young dogs, leading to high morbidity and mortality. It has four main antigenic types CPV-2, CPV-2a, CPV-2b and CPV-2c. Virus protein 2 (VP2) is the main capsid protein and mutations affecting VP2 gene are responsible for the evolution of various antigenic types of CPV. Full length VP2 gene from field isolates was amplified and cloned for sequence analysis. The sequences were submitted to the GenBank and were assigned Acc. Nos., viz. KP406928.1 for P12, KP406927.1 for P15, KP406930.1 for P32, KP406926.1 for Megavac-6 and KP406929.1 for NobivacDHPPi. Phylogenetic analysis indicated that the samples were forming a separate clad with vaccine strains. When the samples were compared with the world and Indian isolates, it was observed that samples formed a separate node indicating regional genetic variation in CPV.

  10. Phylogenetic relationships of seven palearctic members of the maculipennis complex inferred from ITS2 sequence analysis.

    PubMed

    Marinucci, M; Romi, R; Mancini, P; Di Luca, M; Severini, C

    1999-11-01

    The sequences of the second internal transcribed spacer (ITS2) of ribosomal DNA (rDNA) were determined from seven palearctic mosquitoes species belonging to the Anopheles maculipennis species complex, namely An. atroparvus, An. labranchiae, An. maculipennis, An. messeae, An. melanoon, An. sacharovi and An. martinius. The length of the ITS2 ranged from 280 to 300 bp, with a GC content of 49.4-54.1%. With the exception of An. messeae, negligible levels of intraspecific polymorphism and no intrapopulation variation were observed. The phylogenetic relationships among the members of the maculipennis complex were inferred by maximum-parsimony analysis of the PAUP program and the neighbour-joining and maximum-likelihood analysis of the PHYLIP program. All of the trees obtained were almost identical in topology, although the relationships among three species, i.e. An. maculipennis, An. messeae and An. melanoon, remained unresolved. The phylogenies were in good agreement with the previous gene-enzyme and polytene chromosome banding pattern studies.

  11. Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia.

    PubMed

    Chao, Q J; Li, Y D; Geng, X X; Zhang, L; Dai, X; Zhang, X; Li, J; Zhang, H J

    2014-04-14

    This is the first report of a complete mitochondrial genome sequence from Himalayan marmot (Marmota himalayana, class Marmota). We determined the M. himalayana mitochondrial (mt) genome sequence by using long-PCR methods and a primer-walking sequencing strategy with genus-specific primers. The complete mt genome of M. himalayana was 16,443 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a typical control region (CR). Gene order and orientation were identical to those in mt genomes of most vertebrates. The heavy strand showed an overall A+T content of 63.49%. AT and GC skews for the mt genome of the M. himalayana were 0.012 and -0.300, respectively, indicating a nucleotide bias against T and G. The control region was 997 bp in size and displayed some unusual features, including absence of repeated motifs and two conserved sequence blocks (CSB2 and CSB3), which is consistent with observations from two other rodent species, Sciurus vulgaris and Myoxus glis. Phylogenetic analysis of complete mt DNA sequences without the control region including 30 taxa of Rodentia was performed with Maximum-Likelihood (ML) and Bayesian Inference (BI) methods and provided strong support for Sciurognathi polyphyly and Hystricognathi monophyly. This analysis also provided evidence that M. himalayana mt DNA was closely related to that from Sciurus vulgaris (Sciuridae) and was similar to mt DNA from Myoxus glis.

  12. Phylogenetic analysis of vertebrate CXC chemokines reveals novel lineage specific groups in teleost fish.

    PubMed

    Chen, Jun; Xu, Qiaoqing; Wang, Tiehui; Collet, Bertrand; Corripio-Miyar, Yolanda; Bird, Steve; Xie, Ping; Nie, Pin; Secombes, Christopher J; Zou, Jun

    2013-10-01

    In this study, we have identified 421 molecules across the vertebrate spectrum and propose a unified nomenclature for CXC chemokines in fish, amphibians and reptiles based on phylogenetic analysis. Expanding on earlier studies in teleost fish, lineage specific CXC chemokines that have no apparent homologues in mammals were confirmed. Furthermore, in addition to the two subgroups of the CXCL8 homologues known in teleost fish, a third group was identified (termed CXCL8_L3), as was a further subgroup of the fish CXC genes related to CXCL11. Expression of the CXC chemokines found in rainbow trout, Oncorhynchus mykiss, was studied in response to stimulation with inflammatory and antiviral cytokines, and bacterial. Tissue distribution analysis revealed distinct expression profiles for these trout CXC chemokines. Lastly three of the trout chemokines, including two novel fish specific CXC chemokines containing three pairs of cysteines, were produced as recombinant proteins and their effect on trout leucocyte migration studied. These molecules increased the relative expression of CD4 and MCSFR in migrated cells in an in vitro chemotaxis assay.

  13. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

    SciTech Connect

    Meyer, F.; Paarmann, D.; D'Souza, M.; Olson, R.; Glass, E. M.; Kubal, M.; Paczian, T.; Stevens, R.; Wilke, A.; Wilkening, J.; Edwards, R. A.; Rodriguez, A.; Mathematics and Computer Science; Univ. of Chicago; San Diego State Univ.

    2008-09-19

    Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. user access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing databasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis--the available of high-performance computing for annotating the data.

  14. [Ontogenetic and phylogenetic analysis of myosin light chain proteins from skeletal muscles of loach Misgurnus fossilis].

    PubMed

    Miuge, N S; Tikhonov, A V; Ozerniuk, N D

    2005-01-01

    mRNAs of all three types of myosin light chain proteins are expressed in skeletal muscles of both larval and adult stages of loach Misgurnus fossilis (Cobitidae) and these proteins are encoded by different genes (mlc1, mlc2, and mlc3). No difference was revealed between transcripts from larval stage and adult fish for all three mlc proteins. Our approach (RT-PCR with fish-specific mlc1, mlc2, and mlc3 primers) failed to reveal the larval form of myosin light chain protein found previously by protein electrophoresis of loach fry muscle extract. Comparative analysis of the protein structure shows high homology of MLC1 and MLC3 proteins sharing a large EF-hand calcium-binding domain. Phylogenetic analysis of MLC1 from skeletal muscles of fish and other vertebrate species is concordant with the traditional phylogeny of the group. Within the Teleostei, loach MLC1 had the highest homology with other Cyprinidae, and least with Salmonidae fishes.

  15. The complete mitochondrial genome of dhole Cuon alpinus: phylogenetic analysis and dating evolutionary divergence within Canidae.

    PubMed

    Zhang, Honghai; Chen, Lei

    2011-03-01

    The dhole (Cuon alpinus) is the only existent species in the genus Cuon (Carnivora: Canidae). In the present study, the complete mitochondrial genome of the dhole was sequenced. The total length is 16672 base pairs which is the shortest in Canidae. Sequence analysis revealed that most mitochondrial genomic functional regions were highly consistent among canid animals except the CSB domain of the control region. The difference in length among the Canidae mitochondrial genome sequences is mainly due to the number of short segments of tandem repeated in the CSB domain. Phylogenetic analysis was progressed based on the concatenated data set of 14 mitochondrial genes of 8 canid animals by using maximum parsimony (MP), maximum likelihood (ML) and Bayesian (BI) inference methods. The genera Vulpes and Nyctereutes formed a sister group and split first within Canidae, followed by that in the Cuon. The divergence in the genus Canis was the latest. The divarication of domestic dogs after that of the Canis lupus laniger is completely supported by all the three topologies. Pairwise sequence divergence data of different mitochondrial genes among canid animals were also determined. Except for the synonymous substitutions in protein-coding genes, the control region exhibits the highest sequence divergences. The synonymous rates are approximately two to six times higher than those of the non-synonymous sites except for a slightly higher rate in the non-synonymous substitution between Cuon alpinus and Vulpes vulpes. 16S rRNA genes have a slightly faster sequence divergence than 12S rRNA and tRNA genes. Based on nucleotide substitutions of tRNA genes and rRNA genes, the times since divergence between dhole and other canid animals, and between domestic dogs and three subspecies of wolves were evaluated. The result indicates that Vulpes and Nyctereutes have a close phylogenetic relationship and the divergence of Nyctereutes is a little earlier. The Tibetan wolf may be an archaic

  16. Sequence and phylogenetic analysis of chicken anaemia virus obtained from backyard and commercial chickens in Nigeria.

    PubMed

    Oluwayelu, D O; Todd, D; Olaleye, O D

    2008-12-01

    This work reports the first molecular analysis study of chicken anaemia virus (CAV) in backyard chickens in Africa using molecular cloning and sequence analysis to characterize CAV strains obtained from commercial chickens and Nigerian backyard chickens. Partial VP1 gene sequences were determined for three CAVs from commercial chickens and for six CAV variants present in samples from a backyard chicken. Multiple alignment analysis revealed that the 6% and 4% nucleotide diversity obtained respectively for the commercial and backyard chicken strains translated to only 2% amino acid diversity for each breed. Overall, the amino acid composition of Nigerian CAVs was found to be highly conserved. Since the partial VP1 gene sequence of two backyard chicken cloned CAV strains (NGR/CI-8 and NGR/CI-9) were almost identical and evolutionarily closely related to the commercial chicken strains NGR-1, and NGR-4 and NGR-5, respectively, we concluded that CAV infections had crossed the farm boundary.

  17. Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences.

    PubMed

    Savolainen, V; Chase, M W; Hoot, S B; Morton, C M; Soltis, D E; Bayer, C; Fay, M F; de Bruijn, A Y; Sullivan, S; Qiu, Y L

    2000-06-01

    Following (1) the large-scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80:528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84:1-49), we present a phylogenetic analysis of flowering plants based on a second plastid gene, atpB, analyzed separately and in combination with rbcL sequences for 357 taxa. Despite some discrepancies, the atpB-based phylogenetic trees were highly congruent with those derived from the analysis of rbcL and 18S rDNA, and the combination of atpB and rbcL DNA sequences (comprising approximately 3000 base pairs) produced increased bootstrap support for many major sets of taxa. The angiosperms are divided into two major groups: noneudicots with inaperturate or uniaperturate pollen (monocots plus Laurales, Magnoliales, Piperales, Ceratophyllales, and Amborellaceae-Nymphaeaceae-Illiciaceae) and the eudicots with triaperturate pollen (particularly asterids and rosids). Based on rbcL alone and atpB/rbcL combined, the noneudicots (excluding Ceratophyllum) are monophyletic, whereas in the atpB trees they form a grade. Ceratophyllum is sister to the rest of angiosperms with rbcL alone and in the combined atpB/rbcL analysis, whereas with atpB alone, Amborellaceae, Nymphaeaceae, and Illiciaceae/Schisandraceae form a grade at the base of the angiosperms. The phylogenetic information at each codon position and the different types of substitutions (observed transitions and transversions in the trees vs. pairwise comparisons) were examined; taking into account their respective consistency and retention indices, we demonstrate that third-codon positions and transitions are the most useful characters in these phylogenetic reconstructions. This study further demonstrates that phylogenetic analysis of large matrices is feasible.

  18. Phylogenetic analysis and genetic diversity of 3' region of rtxA gene from geographically diverse strains of Moraxella bovis, Moraxella bovoculi and Moraxella ovis.

    PubMed

    Farias, Luana D'Avila; Maboni, Grazieli; Matter, Letícia Beatriz; Scherer, Charles Fernando Capinos; Libardoni, Felipe; de Vargas, Agueda Castagna

    2015-08-05

    The cytotoxin A (MbxA) is one of the main virulence factors of Moraxella bovis involved in the pathogenesis of infectious bovine keratoconjunctivitis (IBK). Moraxella ovis and Moraxella bovoculi, suspected to be associated with infectious keratitis in sheep and cattle respectively, also have a gene that encodes the cytotoxin A (movA and mbvA, respectively). The aim of this study was to determine the molecular sequence of the 3' region of the cytotoxin gene of Moraxella spp. strains isolated from clinical cases to establish phylogenetic and evolutionary comparisons. PCR amplification, nucleotide sequencing (nt) and amino acid (aa) sequence prediction were performed, followed by the sequences comparison, identity level calculation and selective pressure analysis. The phylogenetic reconstruction based on nt and aa sequences clearly differentiate M. bovis (n=15), M. bovoculi (n=11) and M. ovis (n=7) and their respective reference strains. An alignment of 843nt revealed high similarity within bacterial species (MbxA=99.9% nt and aa; MbvA=99.3% nt and 98.8% aa; MovA=99.5% nt and 99.3% aa). The similarity of partial sequences (nt 1807-2649) of MbxA in relation to MbvA and MovA ranged from 76.3 to 78.5%; similarity between MbvA and MovA ranged from 95.7 to 97.5%. A negative selection on mbvA and movA sequences was revealed by the molecular evolution analysis. The phylogenetic analysis of movA and mbvA allowed different strains of Moraxella spp. to be grouped according to the period of isolation. Sequence analysis of cytotoxin may provide insights into genetic and evolutionary relationships and into the genetic/molecular basis of Moraxella spp.

  19. Arginine kinase from the Tardigrade, Macrobiotus occidentalis: molecular cloning, phylogenetic analysis and enzymatic properties.

    PubMed

    Uda, Kouji; Ishida, Mikako; Matsui, Tohru; Suzuki, Tomohiko

    2010-10-01

    Arginine kinase (AK), which catalyzes the reversible transfer of phosphate from ATP to arginine to yield phosphoarginine and ADP, is widely distributed throughout the invertebrates. We determined the cDNA sequence of AK from the tardigrade (water bear) Macrobiotus occidentalis, cloned the sequence into pET30b plasmid, and expressed it in Escherichia coli as a 6x His-tag—fused protein. The cDNA is 1377 bp, has an open reading frame of 1080 bp, and has 5′- and 3′-untranslated regions of 116 and 297 bp, respectively. The open reading frame encodes a 359-amino acid protein containing the 12 residues considered necessary for substrate binding in Limulus AK. This is the first AK sequence from a tardigrade. From fragmented and non-annotated sequences available from DNA databases, we assembled 46 complete AK sequences: 26 from arthropods (including 19 from Insecta), 11 from nematodes, 4 from mollusks, 2 from cnidarians and 2 from onychophorans. No onychophoran sequences have been reported previously. The phylogenetic trees of 104 AKs indicated clearly that Macrobiotus AK (from the phylum Tardigrada) shows close affinity with Epiperipatus and Euperipatoides AKs (from the phylum Onychophora), and therefore forms a sister group with the arthropod AKs. Recombinant 6x His-tagged Macrobiotus AK was successfully expressed as a soluble protein, and the kinetic constants (K(m), K(d), V(ma) and k(cat)) were determined for the forward reaction. Comparison of these kinetic constants with those of AKs from other sources (arthropods, mollusks and nematodes) indicated that Macrobiotus AK is unique in that it has the highest values for k(cat) and K(d)K(m) (indicative of synergistic substrate binding) of all characterized AKs.

  20. Phylogenetic Analysis of Polygalacturonase-Producing Bacillus and Pseudomonas Isolated From Plant Waste Material

    PubMed Central

    Sohail, Muhammad; Latif, Zakia

    2016-01-01

    Background: Keeping in mind the commercial application of polygalacturonase (PG) in juice and beverages industry, bacterial strains were isolated from rotten fruits and vegetables to screen for competent producers of PG. Objectives: In this study, the plate method was used for preliminary screening of polygalacturonase-producing bacteria, while the Dinitrosalicylic Acid (DNS) method was used for quantifications of PG. Materials and Methods: Biochemically-identified polygalacturonase-producing Bacillus and Pseudomonas species were further characterized by molecular markers. The genetic diversity among these selected strains was analyzed by investigating microsatellite distribution in their genome. Out of 110 strains, 17 competent strains of Bacillus and eight strains of Pseudomonas were selected, identified and confirmed biochemically. Selected strains were characterized by 16S rRNA sequencing and data was submitted to the national center for biotechnology information (NCBI) website for accession numbers. Results: Among the Bacillus, Bacillus vallismortis (JQ990307) isolated from mango was the most competent producer of PG; producing up to 4.4 U/µL. Amongst Pseudomonas, Pseudomonas aeruginosa (JQ990314) isolated from oranges was the most competent PG producer equivalent to B. vallismortis (JQ990307). To determine genetic diversity of different strains of Pseudomonas and Bacillus varying in PG production, fingerprinting was done on the basis of Simple Sequence Repeats (SSR) or microsatellites. The data was analyzed and a phylogenetic tree was constructed using the Minitab 3 software for comparison of bacterial isolates producing different concentrations of PG. Fingerprinting showed that presence or absence of certain microsatellites correlated with the ability of PG production. Conclusions: Bacteria from biological waste were competent producers of PG and must be used on an industrial scale to cope with the demand of PG in the food industry. PMID:27099686

  1. Genetic Analysis and Phylogenetic Characterization of Pandemic (H1N1) 2009 influenza viruses that found in Nagasaki, Japan.

    PubMed

    Kawano, Hiroaki; Haruyama, Takahiro; Hayashi, Yuji; Sinoda, Yoshinori; Sonoda, Megumi; Kobayashi, Nobuyuki

    2011-01-01

    Isolation and determination of the nucleotide sequence of hemagglutinin (HA) of the pandemic (H1N1) 2009 influenza viruses found in Nagasaki, Japan, were conducted. The alignment results of the predicted HA amino acid sequences of these strains compared to the known global isolates revealed 5 specific amino acid differences located within the antigenic sites. The phylogenetic analyses revealed that the majority of the Nagasaki isolates could be classified into 6 phylogenetic clusters. Almost all isolates collected in the early season were classified into cluster I, which apparently originated from A/Nagasaki/HA-6/2009 isolated from a patient who returned from the Philippines. This cluster ceased to spread after November 2009. Between the end of August 2009 and January 2010, 5 new phylogenetic clusters (II-VI) emerged with viruses from different origins, and cluster III continuously advanced until March 2010. These results suggest that the onset of the influenza epidemic in Nagasaki originated from patient(s) who returned from the Philippines, and subsequently, various imported strains from different origins sustained the virus spread. Among the Nagasaki isolates, A/Nagasaki/HA-58/2009 having an H275Y mutation in the neuraminidase gene, which confers resistance to oseltamivir, was isolated. This is the first report in which an oseltamivir-resistant pandemic H275Y mutant was identified in Nagasaki Prefecture.

  2. Phylogenetic analysis of the incidence of lux gene horizontal transfer in Vibrionaceae.

    PubMed

    Urbanczyk, Henryk; Ast, Jennifer C; Kaeding, Allison J; Oliver, James D; Dunlap, Paul V

    2008-05-01

    Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib(2) operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib(2

  3. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae▿ †

    PubMed Central

    Urbanczyk, Henryk; Ast, Jennifer C.; Kaeding, Allison J.; Oliver, James D.; Dunlap, Paul V.

    2008-01-01

    Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib2 operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib2

  4. Towards a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing 'phyloh' as a novel phylogenetic diversity analysis tool.

    PubMed

    Sandionigi, A; Vicario, S; Prosdocimi, E M; Galimberti, A; Ferri, E; Bruno, A; Balech, B; Mezzasalma, V; Casiraghi, M

    2015-07-01

    The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity.

  5. Phylogenetic relationships and evolutionary traits in Ranunculus s.l. (Ranunculaceae) inferred from ITS sequence analysis.

    PubMed

    Hörandl, Elvira; Paun, Ovidiu; Johansson, Jan T; Lehnebach, Carlos; Armstrong, Tristan; Chen, Lixue; Lockhart, Peter

    2005-08-01

    Ranunculus is a large genus with a worldwide distribution. Phylogenetic analyses of c. 200 species of Ranunculus s.l. based on sequences of the nrITS using maximum parsimony and Bayesian inference yielded high congruence with previous cpDNA restriction site analyses, but strongly contradict previous classifications. A large core clade including Ranunculus subg. Ranunculus, subg. Batrachium, subg. Crymodes p.p., Ceratocephala, Myosurus, and Aphanostemma is separated from R. subg. Ficaria, subg. Pallasiantha, subg. Coptidium, subg. Crymodes p.p., Halerpestes, Peltocalathos, Callianthemoides, and Arcteranthis. Within the core clade, 19 clades can be described with morphological and karyological features. Several sections are not monophyletic. Parallel evolution of morphological characters in adaptation to climatic conditions may be a reason for incongruence of molecular data and morphology-based classifications. In some mountainous regions, groups of closely related species may have originated from adaptive radiation and rapid speciation. Split decomposition analysis indicated complex patterns of relationship and suggested hybridization in the apomictic R. auricomus complex, R. subg. Batrachium, and the white-flowering European alpines. The evolutionary success of the genus might be due to a combination of morphological plasticity and adaptations, hybridization and polyploidy as important factors for regional diversification, and a broad range of reproductive strategies.

  6. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

    PubMed Central

    Scaduto, Diane I.; Brown, Jeremy M.; Haaland, Wade C.; Zwickl, Derrick J.; Hillis, David M.; Metzker, Michael L.

    2010-01-01

    Phylogenetic analysis has been widely used to test the a priori hypothesis of epidemiological clustering in suspected transmission chains of HIV-1. Among studies showing strong support for relatedness between HIV samples obtained from infected individuals, evidence for the direction of transmission between epidemiologically related pairs has been lacking. During transmission of HIV, a genetic bottleneck occurs, resulting in the paraphyly of source viruses with respect to those of the recipient. This paraphyly establishes the direction of transmission, from which the source can then be inferred. Here, we present methods and results from two criminal cases, State of Washington v Anthony Eugene Whitfield, case number 04-1-0617-5 (Superior Court of the State of Washington, Thurston County, 2004) and State of Texas v Philippe Padieu, case numbers 219-82276-07, 219-82277-07, 219-82278-07, 219-82279-07, 219-82280-07, and 219-82705-07 (219th Judicial District Court, Collin County, TX, 2009), which provided evidence that direction can be established from blinded case samples. The observed paraphyly from each case study led to the identification of an inferred source (i.e., index case), whose identity was revealed at trial to be that of the defendant. PMID:21078965

  7. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis

    PubMed Central

    Gupta, Amit Kumar; Kaur, Karambir; Rajput, Akanksha; Dhanda, Sandeep Kumar; Sehgal, Manika; Khan, Md. Shoaib; Monga, Isha; Dar, Showkat Ahmad; Singh, Sandeep; Nagpal, Gandharva; Usmani, Salman Sadullah; Thakur, Anamika; Kaur, Gazaldeep; Sharma, Shivangi; Bhardwaj, Aman; Qureshi, Abid; Raghava, Gajendra Pal Singh; Kumar, Manoj

    2016-01-01

    Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (http://bioinfo.imtech.res.in/manojk/zikavr/), dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content. Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, codon context, usage bias and phylogenetic inferences at whole genome and proteome level with user-friendly visual environment. Further, glycosylation sites and molecular diagnostic primers were also analyzed. Most importantly, we also proposed potential therapeutically imperative constituents namely vaccine epitopes, siRNAs, miRNAs, sgRNAs and repurposing drug candidates. PMID:27633273

  8. Molecular characterization and phylogenetic analysis of Fasciola gigantica from western Java, Indonesia.

    PubMed

    Hayashi, Kei; Ichikawa-Seki, Madoka; Allamanda, Puttik; Wibowo, Putut Eko; Mohanta, Uday Kumar; Sodirun; Guswanto, Azirwan; Nishikawa, Yoshifumi

    2016-10-01

    Fasciola gigantica and aspermic (hybrid) Fasciola flukes are thought to be distributed in Southeast Asian countries. The objectives of this study were to investigate the distribution of these flukes from unidentified ruminants in western Java, Indonesia, and to determine their distribution history into the area. Sixty Fasciola flukes from western Java were identified as F. gigantica based on the nucleotide sequences of the nuclear phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold) genes. The flukes were then analyzed phylogenetically based on the nucleotide sequence of the mitochondrial NADH dehydrogenase subunit 1 (nad1) gene, together with Fasciola flukes from other Asian countries. All but one F. gigantica fluke were classified in F. gigantica haplogroup C, which mainly contains nad1 haplotypes detected in flukes from Thailand, Vietnam, and China. A population genetic analysis suggested that haplogroup C spread from Thailand to the neighboring countries including Indonesia together with domestic ruminants, such as the swamp buffalo, Bubalus bubalis. The swamp buffalo is one of the important definitive hosts of Fasciola flukes in Indonesia, and is considered to have been domesticated in the north of Thailand. The remaining one fluke displayed a novel nad1 haplotype that has never been detected in the reference countries. Therefore, the origin of the fluke could not be established. No hybrid Fasciola flukes were detected in this study, in contrast to neighboring Asian countries.

  9. [Phylogenetic analysis of ancient mitochondrial DNA lineages of human remains found in Yakutia].

    PubMed

    Fedorova, S A; Stepanov, A D; Adoian, M; Parik, J; Argunov, V A; Ozawa, T; Khusnutdinova, E K; Villems, R

    2008-01-01

    Molecular genetic analysis of ancient human remains are mostly based on mitochondrial DNA due to its better preservation in human skeletons in comparison with nuclear DNA. We investigated mtDNA extracted from human skeletons found in graves in Yakutia to determine their haplotypes and to compare them with lineages of modern populations. Ancient DNA was extracted from fragments of three skeletons of Yakut graves at At-Dabaan, Ojuluun and Jaraama sites (dating XVIII century) and two skeletons of Neolithic graves at Kerdugen site found in central Yakutia (Churapchinsky, Kangalassky and Megino-Kangalassky districts of Yakutia). Five different haplotypes belonging to specific Asian haplogroups were identified. Lineages of mtDNA of Yakut graves belong to haplo-groups C4a, D5a2 and B5b. Our results indicate the continuity of mitochondrial lineages in the Yakut gene pool during the last 300 years. Haplotypes of two humans from Kerdugen site graves belong to haplogroups A4 and G2a/D. We compared these haplotypes with that of 40,000 Eurasian individuals, 900 of them from Yakutia. No exact matches were found in Paleoasian populations of Chukchi, Eskimos, Koryaks and Itelmen. Phylogenetically close haplotypes (+/- 1 mutation) were found in populations of Yakuts and Evenks, as well as in some populations of China, Southern and Western Siberia.

  10. Molecular characterization and phylogenetic analysis of Newcastle disease virus isolates from healthy wild birds.

    PubMed

    Zanetti, Flavia; Berinstein, Analía; Pereda, Ariel; Taboga, Oscar; Carrillo, Elisa

    2005-12-01

    Wild waterfowl is considered a natural reservoir of potentially infectious agents and a source of pathogenic viruses like avian paramyxoviruses type 1 (APMV 1). In 1997, commercial poultry in Argentina had reached the status of being free from virulent Newcastle disease virus (NDV) infections. Vaccination and biosecurity measures are actively performed to maintain this preferential sanitary condition. However, the risk of reintroduction of pathogenic viruses is always present. In this context, we conducted a study to describe the status of wild healthy birds in a geographic region relevant for the poultry industry. The presence of anti-NDV antibodies was determined in different species in all areas sampled suggesting previous contact with NDV. Seven ND viruses were isolated and characterized as apathogenic strains by biological and molecular methods. The phylogenetic analysis revealed that the majority of the Argentinian isolates form a subgroup related to viruses of genotype II. The results presented here highlight the importance of maintaining strict biosecurity measures and vaccination programs in poultry industries in order to preserve the virulent NDV-free status for commercial flocks in the country.

  11. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis.

    PubMed

    Gupta, Amit Kumar; Kaur, Karambir; Rajput, Akanksha; Dhanda, Sandeep Kumar; Sehgal, Manika; Khan, Md Shoaib; Monga, Isha; Dar, Showkat Ahmad; Singh, Sandeep; Nagpal, Gandharva; Usmani, Salman Sadullah; Thakur, Anamika; Kaur, Gazaldeep; Sharma, Shivangi; Bhardwaj, Aman; Qureshi, Abid; Raghava, Gajendra Pal Singh; Kumar, Manoj

    2016-09-16

    Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (http://bioinfo.imtech.res.in/manojk/zikavr/), dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content. Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, codon context, usage bias and phylogenetic inferences at whole genome and proteome level with user-friendly visual environment. Further, glycosylation sites and molecular diagnostic primers were also analyzed. Most importantly, we also proposed potential therapeutically imperative constituents namely vaccine epitopes, siRNAs, miRNAs, sgRNAs and repurposing drug candidates.

  12. Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012.

    PubMed

    Namuwulya, Prossy; Abernathy, Emily; Bukenya, Henry; Bwogi, Josephine; Tushabe, Phionah; Birungi, Molly; Seguya, Ronald; Kabaliisa, Theopista; Alibu, Vincent P; Kayondo, Jonathan K; Rivailler, Pierre; Icenogle, Joseph; Bakamutumaho, Barnabas

    2014-12-01

    Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confirm measles and rubella, but molecular epidemiologic aspects of rubella circulation have so far not been documented in Uganda. Twenty throat swab or oral fluid samples collected from 12 districts during routine rash and fever surveillance between 2003 and 2012 were identified as rubella virus RNA positive and PCR products encompassing the region used for genotyping were sequenced. Phylogenetic analysis of the 20 sequences identified 19 genotype 1G viruses and 1 genotype 1E virus. Genotype-specific trees showed that the Uganda viruses belonged to specific clusters for both genotypes 1G and 1E and grouped with similar sequences from neighboring countries. Genotype 1G was predominant in Uganda. More epidemiological and molecular epidemiological data are required to determine if genotype 1E is also endemic in Uganda. The information obtained in this study will assist the immunization program in monitoring changes in circulating genotypes.

  13. Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley.

    PubMed

    Ren, Xifeng; Wang, Yonggang; Yan, Songxian; Sun, Dongfa; Sun, Genlou

    2014-04-01

    Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.

  14. Molecular phylogenetic analysis of Rhizobium sullae isolated from Algerian Hedysarum flexuosum.

    PubMed

    Aliliche, Khadidja; Beghalem, Hamida; Landoulsi, Ahmed; Chriki, Ali

    2016-07-01

    Isolates from root nodules of Hedysarum flexuosum, sampled from north region of Algeria, were analyzed on the basis of their phenotypic and molecular characteristics. They were tested for their tolerance to NaCl, pH, temperatures, antibiotics and heavy metals resistance. Interestingly, the isolate Hf_04N appeared resistant to ZnCl2 (50 μg/mL) and grew at high saline concentration up to 9 %. The phylogenetic positions of five isolates were studied by comparative sequence analysis of 16S rRNA, recA, nifH and nodD genes. There were grouped close to the Rhizobium sullae type strain in relation to their 16S rRNA, recA and nifH genes-based phylogenies. By contrast, the tree of nodD gene was not congruent with ribosomal, housekeeping and nitrogen fixation genes. We suggest that our strains have a novel nodD gene. The detection of conserved domains of NodD protein and nitrogenase reductase enzyme, confirm their ability to nodulate and fix nitrogen.

  15. Taxonomic revision and phylogenetic analysis of the flightless Mancallinae (Aves, Pan-Alcidae)

    PubMed Central

    Smith, Neil Adam

    2011-01-01

    Abstract Although flightless alcids from the Miocene and Pliocene of the eastern Pacific Ocean have been known for over 100 years, there is no detailed evaluation of diversity and systematic placement of these taxa. This is the first combined analysis of morphological and molecular data to include all extant alcids, the recently extinct Great Auk Pinguinus impennis, the mancalline auks, and a large outgroup sampling of 29 additional non-alcid charadriiforms. Based on the systematic placement of Mancallinae outside of crown clade Alcidae, the clade name Pan-Alcidae is proposed to include all known alcids. An extensive review of the Mancallinae fossil record resulted in taxonomic revision of the clade, and identification of three new species. In addition to positing the first hypothesis of inter-relationships between Mancallinae species, phylogenetic results support placement of Mancallinae as the sister taxon to all other Alcidae, indicating that flightlessness evolved at least twice in the alcid lineage. Convergent osteological characteristics of Mancallinae, the flightless Great Auk, and Spheniscidae are summarized, and implications of Mancallinae diversity, radiation, and extinction in the context of paleoclimatic changes are discussed. PMID:21594108

  16. A phylogenetic analysis of Pseudonaja (Hydrophiinae, Elapidae, Serpentes) based on mitochondrial DNA sequences.

    PubMed

    Skinner, Adam; Donnellan, Stephen C; Hutchinson, Mark N; Hutchinson, Rhonda G

    2005-11-01

    A phylogenetic analysis of mitochondrial ND4 and adjacent tRNA sequences for a geographically extensive series of specimens reveals nine major clades within Pseudonaja, of which six are largely coincident with nominal taxa (P. affinis, P. guttata, P. inframacula, P. ingrami, P. modesta, and P. textilis). The remaining three clades are composed of specimens presently referred to P. nuchalis. Two of these clades correspond with the "Darwin" and "Southern" morphs of previous authors, while the third clade incorporates the "Orange with black head" and "Pale head, grey nape" morphs. We are unable to confirm the presence of consistent karyotypic differences between "Orange with black head" and "Pale head, grey nape" specimens, however, P. inframacula, P. textilis, and P. nuchalis "Darwin" are found to exhibit distinctive karyotypes, as previously reported. These results, in conjunction with additional observations of karyotpic and morphological variation, are consistent with nine historically-independent lineages (i.e., species) within Pseudonaja. There is strong support for a clade composed of P. affinis, P. inframacula, P. ingrami, P. textilis, and the three P. nuchalis lineages, and for the relationships (P. inframacula, P. nuchalis "Southern") and (P. nuchalis "Darwin", P. nuchalis "Orange with black head"--"Pale head, grey nape" ).

  17. Phylogenetic analysis of Fosterella L.B. Sm. (Pitcairnioideae, Bromeliaceae) based on four chloroplast DNA regions.

    PubMed

    Rex, Martina; Schulte, Katharina; Zizka, Georg; Peters, Jule; Vásquez, Roberto; Ibisch, Pierre L; Weising, Kurt

    2009-06-01

    The about 31 species of Fosterella L.B. Sm. (Bromeliaceae) are terrestrial herbs with a centre of diversity in the central South American Andes. To resolve infra- and intergeneric relationships among Fosterella and their putative allies, we conducted a phylogenetic analysis based on sequence data from four chloroplast DNA regions (matK gene, rps16 intron, atpB-rbcL and psbB-psbH intergenic spacers). Sequences were generated for 96 accessions corresponding to 60 species from 18 genera. Among these, 57 accessions represented 22 of the 31 recognized Fosterella species and one undescribed morphospecies. Maximum parsimony and Bayesian inference methods yielded well-resolved phylogenies. The monophyly of Fosterella was strongly supported, as was its sister relationship with a clade comprising Deuterocohnia, Dyckia and Encholirium. Six distinct evolutionary lineages were distinguished within Fosterella. Character mapping indicated that parallel evolution of identical character states is common in the genus. Relationships between species and lineages are discussed in the context of morphological, ecological and biogeographical data as well as the results of a previous amplified fragment length polymorphism (AFLP) study.

  18. Phylogenetic and molecular dating analysis of Taiwan Blue Pheasant (Lophura swinhoii).

    PubMed

    Jiang, Lichun; Wang, Gaochao; Peng, Rui; Peng, Quekun; Zou, Fangdong

    2014-04-10

    The Swinhoe's Pheasant (Lophura swinhoii) is an endemic and most endangered species to Taiwan, China. It belongs to the genus Lophura, family Phasianidae. To further investigate the evolutionary history of L. swinhoii, we determined its complete mitochondrial genome and reconstructed a single, robust phylogenetic tree. Our results showed that L. swinhoii is clustered with Lophura nycthemera and forms a sister group of Lophura ignita. The genus Lophura is strongly supported as the sister taxon of the genus Crossoptilon. The molecular clock analysis showed that the genetic divergence of L. swinhoii occurred in 2.71 (1.31-4.22) Mya. The most common ancestor of L. swinhoii might have migrated from mainland of South East Asia to Taiwan Island by the land bridge at 2.71 Mya ago. Taiwan Island is separated from the mainland by the sea (Taiwan Strait) and formed a separate island at around 2.5 Mya because of the transgression and regression. Therefore, geographical isolation and climate change may accelerate the evolution of L. swinhoii. In this study, we propose a biogeographic hypothesis for speciation of the L. swinhoii based on known events of the geographic and geological history of South East Asia and southeast China, which would benefit the understanding of evolutionary history of L. swinhoii as well as other galliform birds.

  19. The complete mitochondrial genome of Epicauta chinensis (Coleoptera: Meloidae) and phylogenetic analysis among Coleopteran insects.

    PubMed

    Du, Chao; He, Shilin; Song, Xuhao; Liao, Qi; Zhang, Xiuyue; Yue, Bisong

    2016-03-10

    The blister beetle is an important resource insect due to its defensive substance cantharidin, which was widely used in pharmacology and plant protection. We determined the complete mitochondrial genome of Epicauta chinensis Laporte (Coleoptera: Tenebrionoidae: Meloidae). The circular genome is 15,717 bp long, encoding 13 protein-coding genes (PCGs), two ribosomal RNAs and 22 tRNAs and containing a A+T-rich region with gene arrangement identical to other Coleopteran species. Twelve PCGs start with typical ATN codon, while ATP8 gene initiate with GTT for first report in Insecta. All PCGs terminate with conventional stop codon TAA or TAG. All tRNAs in E. chinensis are predicted to fold into typical cloverleaf secondary structure, except tRNA-Ser(AGN), in which the dihydrouracil arm (DHU arm) could not form stable stem-loop structure. The secondary structure of lrRNA and srRNA comprises 48 helices and 32 helices respectively. The 1101 bp A+T-rich region contains a 15 bp poly-T stretch and microsatellite-like repeats rather than large tandem repetitive sequences. Phylogenetic analysis, based on 13 PCGs of 45 Coleopteran species, show that E. chinensis grouped with Tenebrionidae species. It also support the topology of (((Chrysomelidae+Curculionoidea)+(Cucujoidea+Cleroidea))+Tenebrionoidea) within Cucujiformia.

  20. PHYLOGENETIC ANALYSIS AND AUTECOLOGY OF SPORE-FORMING BACTERIA FROM HYPERSALINE ENVIRONMENTS.

    PubMed

    Gladka, G V; Romanovskaya, V A; Tashyreva, H O; Tashyrev, O B

    2015-01-01

    Multi-resistant to extreme factors spore-forming bacteria of Bacillus genus are isolated from hypersaline environments of the Crimea (Ukraine) and the Dead Sea (Israel). Phylogenetic analysis showed distinction of dominating extremophilic culturable species in studied regions. In Crimean environments they are B. mojavensis and B. simplex, in the Dead Sea ecosystem--B. subtilis subsp. spizizenii, B. subtilis subsp. subtilis, B. licheniformis and B. simplex. Isolates are simultaneously halotolerant and resistant to UV radiation. Strains isolated from the Dead Sea and the Crimea environments were resistant to UV: LD90 and LD99.99 made 100-170 J/m2 and 750-1500 J/m2 respectively. Spores showed higher UV-resistance (LD99.99-2500 J/m2) than the vegetative cells. However the number of spores made 0.02-0.007% of the whole cell population, and should not significantly affect the UV LD99.99 value. Isolates of both environments were halotolerant in the range of 0.1-10% NaCl and thermotolerant in the range of 20-50 °C, and didn't grow at 15 °C. Survival strategy of spore-forming bacteria from hypersaline environments under high UV radiation level can be performed by spore formation which minimize cell damage as well as efficient DNA-repair systems that remove damages.

  1. A phylogenetic analysis of the emberizid sparrows based on three mitochondrial genes.

    PubMed

    Carson, Rebecca J; Spicer, Greg S

    2003-10-01

    Previous molecular phylogenetic studies have examined the taxonomic relationships among a number of typical emberizid sparrow genera. To help clarify these relationships, we sequenced a 1673 base pair fragment for the complete sequence of three mitochondrial genes: adenosine triphosphatase (Atp8 and Atp6) and cytochrome oxidase subunit III (COIII) for 38 sparrow species, along with Passerina amoena (Cardinalidae) and Piranga ludoviciana (Thraupidae) which were selected as the outgroups. Our analysis confirms the monophyly of traditional genera such as Junco, Melospiza, and Zonotrichia. Although Calcarius and Plectrophenax are often thought to be putative emberizids, all our analyses placed these genera basal to all other sparrows examined. As observed with Calcarius, Spizella did not form a monophyletic group, with S. arborea being the sister-taxon to Passerella iliaca. Our analyses also suggest that Aimophila ruficeps is probably more closely related to the "brown towhees" (Pipilo aberti, P. crissalis, and P. fuscus) than its putative congeners. The genus Ammodramus was also not monophyletic, since it appears that Passerculus sandwichensis is more closely related to A. henslowii and A. leconteii then either one is related to its congener A. savannarum. Finally, our analyses exhibited other unsuspected associations, such as the sister-taxon relationships between Amphispiza bilineata and the Chondestes grammacus/Calamospiza melanocorys clade, and Amphispiza belli and Pooecetes gramineus.

  2. The Basic Helix-Loop-Helix Protein Family: Comparative Genomics and Phylogenetic Analysis

    PubMed Central

    Ledent, Valérie; Vervoort, Michel

    2001-01-01

    The basic Helix-Loop-Helix (bHLH) proteins are transcription factors that play important roles during the development of various metazoans including fly, nematode, and vertebrates. They are also involved in human diseases, particularly in cancerogenesis. We made an extensive search for bHLH sequences in the completely sequenced genomes of Caenorhabditis elegans and of Drosophila melanogaster. We found 35 and 56 different genes, respectively, which may represent the complete set of bHLH of these organisms. A phylogenetic analysis of these genes, together with a large number (>350) of bHLH from other sources, led us to define 44 orthologous families among which 36 include bHLH from animals only, and two have representatives in both yeasts and animals. In addition, we identified two bHLH motifs present only in yeast, and four that are present only in plants; however, the latter number is certainly an underestimate. Most animal families (35/38) comprise fly, nematode, and vertebrate genes, suggesting that their common ancestor, which lived in pre-Cambrian times (600 million years ago) already owned as many as 35 different bHLH genes. PMID:11337472

  3. Nucleotide sequence and phylogenetic analysis of a new potexvirus: Malva mosaic virus.

    PubMed

    Côté, Fabien; Paré, Christine; Majeau, Nathalie; Bolduc, Marilène; Leblanc, Eric; Bergeron, Michel G; Bernardy, Michael G; Leclerc, Denis

    2008-01-01

    A filamentous virus isolated from Malva neglecta Wallr. (common mallow) and propagated in Chenopodium quinoa was grown, cloned and the complete nucleotide sequence was determined (GenBank accession # DQ660333). The genomic RNA is 6858 nt in length and contains five major open reading frames (ORFs). The genomic organization is similar to members and the viral encoded proteins shared homology with the group of the Potexvirus genus in the Flexiviridae family. Phylogenetic analysis revealed a close relationship with narcissus mosaic virus (NMV), scallion virus X (ScaVX) and, to a lesser extent, to Alstroemeria virus X (AlsVX) and pepino mosaic virus (PepMV). A novel putative pseudoknot structure is predicted in the 3'-UTR of a subgroup of potexviruses, including this newly described virus. The consensus GAAAA sequence is detected at the 5'-end of the genomic RNA and experimental data strongly suggest that this motif could be a distinctive hallmark of this genus. The name Malva mosaic virus is proposed.

  4. How did pygmy shrews colonize Ireland? Clues from a phylogenetic analysis of mitochondrial cytochrome b sequences.

    PubMed Central

    Mascheretti, Silvia; Rogatcheva, Margarita B; Gündüz, Islam; Fredga, Karl; Searle, Jeremy B

    2003-01-01

    There is a long-standing debate as to how Ireland attained its present fauna; we help to inform this debate with a molecular study of one species. A 1110 base pair fragment of the mitochondrial cytochrome b gene was sequenced in 74 specimens of the pygmy shrew, Sorex minutus, collected from throughout its western Palaearctic range. Phylogenetic analysis of these sequences revealed several well-supported lineages. Most of the 65 haplotypes belonged to a northern lineage, which ranged from Britain in the west to Lake Baikal in the east. The other lineages were largely limited to Iberia, Italy and the Balkans. One exception, however, was a lineage found in both Ireland and Andorra. This affinity, and the large difference between the mitochondrial sequences of Irish and British individuals, suggest that pygmy shrews did not colonize Ireland via a land connection from Britain, as has been previously supposed, but instead were introduced by boat from southwest continental Europe. All the Irish pygmy shrews analysed were identical or very similar in cytochrome b sequence, suggesting an extreme founding event. PMID:12908980

  5. Genetic and phylogenetic analysis of a novel parvovirus isolated from chickens in Guangxi, China.

    PubMed

    Feng, Bin; Xie, Zhixun; Deng, Xianwen; Xie, Liji; Xie, Zhiqin; Huang, Li; Fan, Qin; Luo, Sisi; Huang, Jiaoling; Zhang, Yanfang; Zeng, Tingting; Wang, Sheng; Wang, Leyi

    2016-11-01

    A previously unidentified chicken parvovirus (ChPV) strain, associated with runting-stunting syndrome (RSS), is now endemic among chickens in China. To explore the genetic diversity of ChPV strains, we determined the first complete genome sequence of a novel ChPV isolate (GX-CH-PV-7) identified in chickens in Guang Xi, China, and showed moderate genome sequence similarity to reference strains. Analysis showed that the viral genome sequence is 86.4 %-93.9 % identical to those of other ChPVs. Genetic and phylogenetic analyses showed that this newly emergent GX-CH-PV-7 is closely related to Gallus gallus enteric parvovirus isolate ChPV 798 from the USA, indicating that they may share a common ancestor. The complete DNA sequence is 4612 bp long with an A+T content of 56.66 %. We determined the first complete genome sequence of a previously unidentified ChPV strain to elucidate its origin and evolutionary status.

  6. Molecular and phylogenetic analysis of Anaplasma spp. in sheep and goats from six provinces of China

    PubMed Central

    Zhang, Yan; Lv, Yali; Zhang, Feifei; Zhang, Wenjing; Wang, Jinhong; Cui, Yanyan; Wang, Rongjun; Jian, Fuchun; Zhang, Longxian

    2016-01-01

    Members of the genus Anaplasma are important emerging tick-borne pathogens in both humans and animals in tropical and subtropical areas. Here, we investigated the presence of Anaplasma spp. in 621 sheep and 710 goats from six provinces of China. Polymerase chain reaction (PCR) and DNA sequencing were conducted to determine the prevalence of Anaplasma (A.) phagocytophilum, A. ovis and A. bovis targeting the 16S ribosomal RNA or the major surface protein 4 gene. PCR revealed Anaplasma in 39.0% (240/621) of sheep and 45.5% (323/710) of goats. The most frequently detected species was A. ovis (88/621, 14.2% for sheep; 129/710, 18.2% for goats), followed by A. bovis (60/621, 9.7% for sheep; 74/710, 10.4% for goats) and A. phagocytophilum (33/621, 5.3% for sheep; 15/710, 2.1% for goats). Additionally, eight sheep and 20 goats were found to be infected with three pathogens simultaneously. DNA sequencing confirmed the presence of these three Anaplasma species in the investigated areas, and phylogenetic analysis indicated that there was geographic segregation to a certain extent, as well as a relationship between the host and cluster of A. ovis. The results of the present study provide valuable data that helps understand the epidemiology of anaplasmosis in ruminants from China. PMID:27456776

  7. HIV-1 Phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues

    PubMed Central

    Lamers, Susanna L.; Gray, Rebecca R.; Salemi, Marco; Huysentruyt, Leanne C.; McGrath, Michael

    2010-01-01

    Brain infection by the human immunodeficiency virus type 1 (HIV-1) has been investigated in many reports with a variety of conclusions concerning the time of entry and degree of viral compartmentalization. To address these diverse findings, we sequenced HIV-1 gp120 clones from a wide range of brain, peripheral and meningeal tissues from five patients who died from several HIV-1 associated disease pathologies. High-resolution phylogenetic analysis confirmed previous studies that showed a significant degree of compartmentalization in brain and peripheral tissue subpopulations. Some intermixing between the HIV-1 subpopulations was evident, especially in patients that died from pathologies other than HIV-associated dementia. Interestingly, the major tissue harboring virus from both the brain and peripheral tissues was the meninges. These results show that 1) HIV-1 is clearly capable of migrating out of the brain, 2) the meninges are the most likely primary transport tissues, and 3) infected brain macrophages comprise an important HIV reservoir during highly active antiretroviral therapy. PMID:21055482

  8. Phylogenetic analysis of the expansion of the MATH-BTB gene family in the grasses.

    PubMed

    Juranić, Martina; Dresselhaus, Thomas

    2014-01-01

    MATH-BTB proteins are known to act as substrate-specific adaptors of cullin3 (CUL3)-based ubiquitin E3 ligases to target protein for ubiquitination. In a previous study we reported the presence of 31 MATH-BTB genes in the maize genome and determined the regulatory role of the MATH-BTB protein MAB1 during meiosis to mitosis transition. In contrast to maize, there are only 6 homologous genes in the model plant Arabidopsis, while this family has largely expanded in grasses. Here, we report a phylogenetic analysis of the MATH-BTB gene family in 9 land plant species including various mosses, eudicots, and grasses. We extend a previous classification of the plant MATH-BTB family and additionally arrange the expanded group into 5 grass-specific clades. Synteny studies indicate that expansion occurred to a large extent due to local gene duplications. Expression studies of 3 closely related MATH-BTB genes in maize (MAB1-3) indicate highly specific expression pattern. In summary, this work provides a solid base for further studies comparing genetic and functional information of the MATH-BTB family especially in the grasses.

  9. Phylogenetic analysis of the expansion of the MATH-BTB gene family in the grasses

    PubMed Central

    Juranić, Martina; Dresselhaus, Thomas

    2014-01-01

    MATH-BTB proteins are known to act as substrate-specific adaptors of cullin3 (CUL3)-based ubiquitin E3 ligases to target protein for ubiquitination. In a previous study we reported the presence of 31 MATH-BTB genes in the maize genome and determined the regulatory role of the MATH-BTB protein MAB1 during meiosis to mitosis transition. In contrast to maize, there are only 6 homologous genes in the model plant Arabidopsis, while this family has largely expanded in grasses. Here, we report a phylogenetic analysis of the MATH-BTB gene family in 9 land plant species including various mosses, eudicots, and grasses. We extend a previous classification of the plant MATH-BTB family and additionally arrange the expanded group into 5 grass-specific clades. Synteny studies indicate that expansion occurred to a large extent due to local gene duplications. Expression studies of 3 closely related MATH-BTB genes in maize (MAB1–3) indicate highly specific expression pattern. In summary, this work provides a solid base for further studies comparing genetic and functional information of the MATH-BTB family especially in the grasses. PMID:24614623

  10. Identification, molecular and phylogenetic analysis of poxvirus in skin lesions of southern right whale.

    PubMed

    Fiorito, Carla; Palacios, Carlos; Golemba, Marcelo; Bratanich, Ana; Argüelles, Maria Belen; Fazio, Ana; Bertellotti, Marcelo; Lombardo, Daniel

    2015-10-16

    Poxvirus skin disease has been reported in several species of cetaceans, principally in odontocetes, and a single report in mysticetes. Southern right whales Eubalaena australis in Peninsula Valdes, Argentina, show a variety of skin lesions of unknown etiology, and the number of these lesions has increased in recent years. Samples from dead whales were taken in order to establish the etiology of these lesions. One calf and one adult presented ring-type lesions, characterized by a circumscribed and slightly raised area of skin. Lesions were histologically characterized by the presence of microvesicles and vacuolated cells in the stratum spinosum, along with hyperplasia of the stratum corneum and eosinophilic inclusion bodies in the cytoplasm of the epithelial cells. Transmission electron microscopy showed aggregations of virions with typical poxvirus morphology. PCR of cetacean poxvirus (CPV) DNA polymerase, DNA topoisomerase I and parapoxvirus DNA polymerase gene fragments was done, and confirmed the presence of poxvirus in one sample. Phylogenetic analysis showed that the detected poxvirus belongs to the CPV-2 group. This is the first confirmed report of poxvirus in southern right whales in Argentina.

  11. [Phylogenetic reconstructions in the genus Capra (Bovidae, Artiodactyla) based on the mitochondrial DNA analysis].

    PubMed

    Kazanskaia, E Iu; Kuznetsova, M V; Danilkin, A A

    2007-02-01

    Mitochondrial genome fragments were examined in all species of the genus Capra (Bovidae, Artiodactyla). Phylogenetic analysis was carried out using 59 cytochrome b gene sequences (392 bp), and 22 sequences of the mtDNA variable fragment (402 bp). In the control region, two unique deletions were revealed. One of the deletions was found only in Capra cilindricornis (17 bp), while another one grouped C. caucasica with C. aegagrus (1 bp). The group of Caucasian wild goats splits into two clades, and furthermore, the sequences of C. caucasica demonstrate remarkable similarity to the sequences of C. aegagrus, while C. cylindricus seems to have evolved independently for a long period of time. It was demonstrated that C. pyrenaica and C. ibex were extremely close to one another. Capra sibirica formed an outer group relative to the other species, and according to our data, was the most ancient species of the genus. On the contrary, genetic distance separating C. falconeri (the most independent species of the genus related to its morphology) from the other species is small.

  12. Evolution in Australasian mangrove forests: multilocus phylogenetic analysis of the Gerygone warblers (Aves: Acanthizidae).

    PubMed

    Nyári, Árpád S; Joseph, Leo

    2012-01-01

    The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae). The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci). Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea) from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster.

  13. Predicting MicroRNA Biomarkers for Cancer Using Phylogenetic Tree and Microarray Analysis

    PubMed Central

    Wang, Hsiuying

    2016-01-01

    MicroRNAs (miRNAs) are shown to be involved in the initiation and progression of cancers in the literature, and the expression of miRNAs is used as an important cancer prognostic tool. The aim of this study is to predict high-confidence miRNA biomarkers for cancer. We adopt a method that combines miRNA phylogenetic structure and miRNA microarray data analysis to discover high-confidence miRNA biomarkers for colon, prostate, pancreatic, lung, breast, bladder and kidney cancers. There are 53 miRNAs selected through this method that either have potential to involve a single cancer’s development or to involve several cancers’ development. These miRNAs can be used as high-confidence miRNA biomarkers of these seven investigated cancers for further experiment validation. miR-17, miR-20, miR-106a, miR-106b, miR-92, miR-25, miR-16, miR-195 and miR-143 are selected to involve a single cancer’s development in these seven cancers. They have the potential to be useful miRNA biomarkers when the result can be confirmed by experiments. PMID:27213352

  14. Integration of Morphological Data into Molecular Phylogenetic Analysis: Toward the Identikit of the Stylasterid Ancestor

    PubMed Central

    Puce, Stefania; Pica, Daniela; Schiaparelli, Stefano; Negrisolo, Enrico

    2016-01-01

    Stylasteridae is a hydroid family including 29 worldwide-distributed genera, all provided with a calcareous skeleton. They are abundant in shallow and deep waters and represent an important component of marine communities. In the present paper, we studied the evolution of ten morphological characters, currently used in stylasterid taxonomy, using a phylogenetic approach. Our results indicate that stylasterid morphology is highly plastic and that many events of independent evolution and reversion have occurred. Our analysis also allows sketching a possible identikit of the stylasterid ancestor. It had calcareous skeleton, reticulate-granular coenosteal texture, polyps randomly arranged, gastrostyle, and dactylopore spines, while lacking a gastropore lip and dactylostyles. If the ancestor had single or double/multiple chambered gastropore tube is uncertain. These data suggest that the ancestor was similar to the extant genera Cyclohelia and Stellapora. Our investigation is the first attempt to integrate molecular and morphological information to clarify the stylasterid evolutionary scenario and represents the first step to infer the stylasterid ancestor morphology. PMID:27537333

  15. Phylogenetic and Comparative Sequence Analysis of Thermostable Alpha Amylases of kingdom Archea, Prokaryotes and Eukaryotes.

    PubMed

    Huma, Tayyaba; Maryam, Arooma; Rehman, Shahid Ur; Qamar, Muhammad Tahir Ul; Shaheen, Tayyaba; Haque, Asma; Shaheen, Bushra

    2014-01-01

    Alpha amylase family is generally defined as a group of enzymes that can hydrolyse and transglycosylase α-(1, 4) or α-(1, 6) glycosidic bonds along with the preservation of anomeric configuration. For the comparative analysis of alpha amylase family, nucleotide sequences of seven thermo stable organisms of Kingdom Archea i.e. Pyrococcus furiosus (100-105°C), Kingdom Prokaryotes i.e. Bacillus licheniformis (90-95°C), Geobacillus stearothermophilus (75°C), Bacillus amyloliquefaciens (72°C), Bacillus subtilis (70°C) and Bacillus KSM K38 (55°C) and Eukaryotes i.e. Aspergillus oryzae (60°C) were selected from NCBI. Primary structure composition analysis and Conserved sequence analysis were conducted through Bio Edit tools. Results from BioEdit shown only three conserved regions of base pairs and least similarity in MSA of the above mentioned alpha amylases. In Mega 5.1 Phylogeny of thermo stable alpha amylases of Kingdom Archea, Prokaryotes and Eukaryote was handled by Neighbor-Joining (NJ) algorithm. Mega 5.1 phylogenetic results suggested that alpha amylases of thermo stable organisms i.e. Pyrococcus furiosus (100-105°C), Bacillus licheniformis (90-95°C), Geobacillus stearothermophilus (75°C) and Bacillus amyloliquefaciens (72°C) are more distantly related as compared to less thermo stable organisms. By keeping in mind the characteristics of most thermo stable alpha amylases novel and improved features can be introduced in less thermo stable alpha amylases so that they become more thermo tolerant and productive for industry.

  16. A comprehensive phylogenetic analysis of termites (Isoptera) illuminates key aspects of their evolutionary biology.

    PubMed

    Inward, Daegan J G; Vogler, Alfried P; Eggleton, Paul

    2007-09-01

    The first comprehensive combined molecular and morphological phylogenetic analysis of the major groups of termites is presented. This was based on the analysis of three genes (cytochrome oxidase II, 12S and 28S) and worker characters for approximately 250 species of termites. Parsimony analysis of the aligned dataset showed that the monophyly of Hodotermitidae, Kalotermitidae and Termitidae were well supported, while Termopsidae and Rhinotermitidae were both paraphyletic on the estimated cladogram. Within Termitidae, the most diverse and ecologically most important family, the monophyly of Macrotermitinae, Foraminitermitinae, Apicotermitinae, Syntermitinae and Nasutitermitinae were all broadly supported, but Termitinae was paraphyletic. The pantropical genera Termes, Amitermes and Nasutitermes were all paraphyletic on the estimated cladogram, with at least 17 genera nested within Nasutitermes, given the presently accepted generic limits. Key biological features were mapped onto the cladogram. It was not possible to reconstruct the evolution of true workers unambiguously, as it was as parsimonious to assume a basal evolution of true workers and subsequent evolution of pseudergates, as to assume a basal condition of pseudergates and subsequent evolution of true workers. However, true workers were only found in species with either separate- or intermediate-type nests, so that the mapping of nest habit and worker type onto the cladogram were perfectly correlated. Feeding group evolution, however, showed a much more complex pattern, particularly within the Termitidae, where it proved impossible to estimate unambiguously the ancestral state within the family (which is associated with the loss of worker gut flagellates). However, one biologically plausible optimization implies an initial evolution from wood-feeding to fungus-growing, proposed as the ancestral condition within the Termitidae, followed by the very early evolution of soil-feeding and subsequent re

  17. Phylogenetic Analysis of Bacterial Communities in Mesophilic and Thermophilic Bioreactors Treating Pharmaceutical Wastewater

    PubMed Central

    LaPara, Timothy M.; Nakatsu, Cindy H.; Pantea, Lisa; Alleman, James E.

    2000-01-01

    The phylogenetic diversity of the bacterial communities supported by a seven-stage, full-scale biological wastewater treatment plant was studied. These reactors were operated at both mesophilic (28 to 32°C) and thermophilic (50 to 58°C) temperatures. Community fingerprint analysis by denaturing gradient gel electrophoresis (DGGE) of the PCR-amplified V3 region of the 16S rRNA gene from the domain Bacteria revealed that these seven reactors supported three distinct microbial communities. A band-counting analysis of the PCR-DGGE results suggested that elevated reactor temperatures corresponded with reduced species richness. Cloning of nearly complete 16S rRNA genes also suggested a reduced species richness in the thermophilic reactors by comparing the number of clones with different nucleotide inserts versus the total number of clones screened. While these results imply that elevated temperature can reduce species richness, other factors also could have impacted the number of populations that were detected. Nearly complete 16S rDNA sequence analysis showed that the thermophilic reactors were dominated by members from the β subdivision of the division Proteobacteria (β-proteobacteria) in addition to anaerobic phylotypes from the low-G+C gram-positive and Synergistes divisions. The mesophilic reactors, however, included at least six bacterial divisions, including Cytophaga-Flavobacterium-Bacteroides, Synergistes, Planctomycetes, low-G+C gram-positives, Holophaga-Acidobacterium, and Proteobacteria (α-proteobacteria, β-proteobacteria, γ-proteobacteria and δ-proteobacteria subdivisions). The two PCR-based techniques detected the presence of similar bacterial populations but failed to coincide on the relative distribution of these phylotypes. This suggested that at least one of these methods is insufficiently quantitative to determine total community biodiversity—a function of both the total number of species present (richness) and their relative distribution

  18. Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence.

    PubMed

    Fukushima, Masao; Kakinuma, Kenichi; Kawaguchi, Ryuji

    2002-08-01

    Phylogenetic analysis of about 200 strains of Salmonella, Shigella, and Escherichia coli was carried out using the nucleotide sequence of the gene for DNA gyrase B (gyrB), which was determined by directly sequencing PCR fragments. The results establish a new phylogenetic tree for the classification of Salmonella, Shigella, and Escherichia coli in which Salmonella forms a cluster separate from but closely related to Shigella and E. coli. In comparison with 16S rRNA analysis, the gyrB sequences indicated a greater evolutionary divergence for the bacteria. Thus, in screening for the presence of bacteria, the gyrB gene might be a useful tool for differentiating between closely related species of bacteria such as Shigella spp. and E. coli. At present, 16S rRNA sequence analysis is an accurate and rapid method for identifying most unknown bacteria to the genus level because the highly conserved 16S rRNA region is easy to amplify; however, analysis of the more variable gyrB sequence region can identify unknown bacteria to the species level. In summary, we have shown that gyrB sequence analysis is a useful alternative to 16S rRNA analysis for constructing the phylogenetic relationships of bacteria, in particular for the classification of closely related bacterial species.

  19. Comparative cytogenetic analysis of some species of the Dendropsophus microcephalus group (Anura, Hylidae) in the light of phylogenetic inferences

    PubMed Central

    2013-01-01

    Background Dendropsophus is a monophyletic anuran genus with a diploid number of 30 chromosomes as an important synapomorphy. However, the internal phylogenetic relationships of this genus are poorly understood. Interestingly, an intriguing interspecific variation in the telocentric chromosome number has been useful in species identification. To address certain uncertainties related to one of the species groups of Dendropsophus, the D. microcephalus group, we carried out a cytogenetic analysis combined with phylogenetic inferences based on mitochondrial sequences, which aimed to aid in the analysis of chromosomal characters. Populations of Dendropsophus nanus, Dendropsophus walfordi, Dendropsophus sanborni, Dendropsophus jimi and Dendropsophus elianeae, ranging from the extreme south to the north of Brazil, were cytogenetically compared. A mitochondrial region of the ribosomal 12S gene from these populations, as well as from 30 other species of Dendropsophus, was used for the phylogenetic inferences. Phylogenetic relationships were inferred using maximum parsimony and Bayesian analyses. Results The species D. nanus and D. walfordi exhibited identical karyotypes (2n = 30; FN = 52), with four pairs of telocentric chromosomes and a NOR located on metacentric chromosome pair 13. In all of the phylogenetic hypotheses, the paraphyly of D. nanus and D. walfordi was inferred. D. sanborni from Botucatu-SP and Torres-RS showed the same karyotype as D. jimi, with 5 pairs of telocentric chromosomes (2n = 30; FN = 50) and a terminal NOR in the long arm of the telocentric chromosome pair 12. Despite their karyotypic similarity, these species were not found to compose a monophyletic group. Finally, the phylogenetic and cytogenetic analyses did not cluster the specimens of D. elianeae according to their geographical occurrence or recognized morphotypes. Conclusions We suggest that a taxonomic revision of the taxa D. nanus and D. walfordi is quite necessary. We also

  20. Phylogenetic Analysis of Algal Symbionts Associated with Four North American Amphibian Egg Masses

    PubMed Central

    Kim, Eunsoo; Lin, Yuan; Kerney, Ryan; Blumenberg, Lili; Bishop, Cory

    2014-01-01

    Egg masses of the yellow-spotted salamander Ambystoma maculatum form an association with the green alga “Oophila amblystomatis” (Lambert ex Wille), which, in addition to growing within individual egg capsules, has recently been reported to invade embryonic tissues and cells. The binomial O. amblystomatis refers to the algae that occur in A. maculatum egg capsules, but it is unknown whether this population of symbionts constitutes one or several different algal taxa. Moreover, it is unknown whether egg masses across the geographic range of A. maculatum, or other amphibians, associate with one or multiple algal taxa. To address these questions, we conducted a phylogeographic study of algae sampled from egg capsules of A. maculatum, its allopatric congener A. gracile, and two frogs: Lithobates sylvatica and L. aurora. All of these North American amphibians form associations with algae in their egg capsules. We sampled algae from egg capsules of these four amphibians from localities across North America, established representative algal cultures, and amplified and sequenced a region of 18S rDNA for phylogenetic analysis. Our combined analysis shows that symbiotic algae found in egg masses of four North American amphibians are closely related to each other, and form a well-supported clade that also contains three strains of free-living chlamydomonads. We designate this group as the ‘Oophila’ clade, within which the symbiotic algae are further divided into four distinct subclades. Phylogenies of the host amphibians and their algal symbionts are only partially congruent, suggesting that host-switching and co-speciation both play roles in their associations. We also established conditions for isolating and rearing algal symbionts from amphibian egg capsules, which should facilitate further study of these egg mass specialist algae. PMID:25393119

  1. The complete mitochondrial genome of Choristoneura longicellana (Lepidoptera: Tortricidae) and phylogenetic analysis of Lepidoptera.

    PubMed

    Wu, Yu-Peng; Zhao, Jin-Liang; Su, Tian-Juan; Luo, A-Rong; Zhu, Chao-Dong

    2016-10-10

    To better understand the diversity and phylogeny of Lepidoptera, the complete mitochondrial genome of Choristoneura longicellana (=Hoshinoa longicellana) was determined. It is a typical circular duplex molecule with 15,759bp in length, containing the standard metazoan set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an A+T-rich region. All of the inferred tRNA secondary structures show the common cloverleaf pattern, with the exception of trnS1(AGN), which lacks the DHU arm. The rrnL of C. Longicellana is the longest in sequenced lepidopterans. C. Longicellana has the same gene order as all lepidopteran species currently available in GenBank. There are 5 overlapping regions ranging from 1bp to 8bp and 14 intergenic spacers ranging from 1bp to 48bp. In addition, there are four similar tandem macro-satellite regions with the lengths of 101bp, 98bp, 92bp, and 92bp respectively in the A+T-rich regions of C. longicellana. We sampled 89 species representing 13 superfamilies, and reconstructed their relationship among Lepidoptera by Bayesian Inference and Maximum Likelihood analysis. The topology of the two phylogenetic analysis trees is identical roughly, except for Cossoidea in different locations, the positions of Cossoidea, Copromorphoidea, Gelechioidea, Zygaenoidea were not determined based the limited sampling. (Geometroidea+(Noctuoidea+Bombycoidea)) form the Macrolepidoptera "core". Pyraloidea group with the "core" Macrolepidoptera. Papilionoidea are not Macrolepidoptera. The Hesperiidae (represent Hesperioidea) is nested in the Papilionoidea, and closely related to Pieridae and Papilionidae. The well-known relationship of (Nymphalidae+(Riodinidae+Lycaenidae)) is recovered in this paper.

  2. Phylogenetic analysis of algal symbionts associated with four North American amphibian egg masses.

    PubMed

    Kim, Eunsoo; Lin, Yuan; Kerney, Ryan; Blumenberg, Lili; Bishop, Cory

    2014-01-01

    Egg masses of the yellow-spotted salamander Ambystoma maculatum form an association with the green alga "Oophila amblystomatis" (Lambert ex Wille), which, in addition to growing within individual egg capsules, has recently been reported to invade embryonic tissues and cells. The binomial O. amblystomatis refers to the algae that occur in A. maculatum egg capsules, but it is unknown whether this population of symbionts constitutes one or several different algal taxa. Moreover, it is unknown whether egg masses across the geographic range of A. maculatum, or other amphibians, associate with one or multiple algal taxa. To address these questions, we conducted a phylogeographic study of algae sampled from egg capsules of A. maculatum, its allopatric congener A. gracile, and two frogs: Lithobates sylvatica and L. aurora. All of these North American amphibians form associations with algae in their egg capsules. We sampled algae from egg capsules of these four amphibians from localities across North America, established representative algal cultures, and amplified and sequenced a region of 18S rDNA for phylogenetic analysis. Our combined analysis shows that symbiotic algae found in egg masses of four North American amphibians are closely related to each other, and form a well-supported clade that also contains three strains of free-living chlamydomonads. We designate this group as the 'Oophila' clade, within which the symbiotic algae are further divided into four distinct subclades. Phylogenies of the host amphibians and their algal symbionts are only partially congruent, suggesting that host-switching and co-speciation both play roles in their associations. We also established conditions for isolating and rearing algal symbionts from amphibian egg capsules, which should facilitate further study of these egg mass specialist algae.

  3. Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi.

    PubMed

    Ast, Jennifer C; Dunlap, Paul V

    2004-05-01

    The luminous marine bacterium Photobacterium mandapamensis was synonymized several years ago with Photobacterium leiognathi based on a high degree of phenotypic and genetic similarity. To test the possibility that P. leiognathi as now formulated, however, actually contains two distinct bacterial groups reflecting the earlier identification of P. mandapamensis and P. leiognathi as separate species, we compared P. leiognathi strains isolated from light-organ symbiosis with leiognathid fishes (i.e., ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1) with strains from seawater originally described as P. mandapamensis and later synonymized as P. leiognathi (i.e., ATCC 27561(T) and ATCC 33981) and certain strains initially identified as P. leiognathi (i.e., PL-721, PL-741, 554). Analysis of the 16S rRNA and gyrB genes did not resolve distinct clades, affirming a close relationship among these strains. However, strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 were found to bear a luxF gene in the lux operon ( luxABFE), whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 lack this gene ( luxABE). Phylogenetic analysis of the luxAB(F)E region confirmed this distinction. Furthermore, ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 all produced a higher level of luminescence on high-salt medium, as previously described for PL-721, whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 all produced a higher level of luminescence on low-salt medium, a characteristic of P. leiognathi from leiognathid fish light organs. These results demonstrate that P. leiognathi contains two evolutionarily and phenotypically distinct clades, P. leiognathi subsp. leiognathi (strains ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1), and P. leiognathi subsp. mandapamensis (strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554).

  4. Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants

    PubMed Central

    Prall, Wil; Hendy, Oliver

    2016-01-01

    Plant adaptation to external pressures depends on functional diversity in cytochrome P450 (CYP) enzymes. CYPs contain structural domains necessary for the characteristic P450 fold that allows monooxygenation, but they also have great variation in substrate binding affinity. Plant genomes typically contain hundreds of CYPs that contribute to essential functions and species-specific metabolism. The CYP72A subfamily is conserved in angiosperms but its contribution to physiological functions is largely unknown. With genomic information available for many plants, a focused analysis of CYP subfamily diversity is important to understand the contributions of these enzymes to plant evolution. This study examines the extent to which independent gene duplication and evolution have contributed to structural diversification of CYP72A enzymes in different plant lineages. CYP72A genes are prevalent across angiosperms, but the number of genes within each genome varies greatly. The prevalence of CYP72As suggest that the last common ancestor of flowering plants contained a CYP72A sequence, but gene duplication and retention has varied greatly for this CYP subfamily. Sequence comparisons show that CYP72As are involved in species-specific metabolic functions in some plants while there is likely functional conservation between closely related species. Analysis of structural and functional domains within groups of CYP72As reveals clade-specific residues that contribute to functional constraints within subsets of CYP72As. This study provides a phylogenetic framework that allows comparisons of structural features within subsets of the CYP72A subfamily. We examined a large number of sequences from a broad collection of plant species to detect patterns of functional conservation across the subfamily. The evolutionary relationships between CYPs in plant genomes are an important component in understanding the evolution of biochemical diversity in plants. PMID:27669508

  5. An Insight into the Triabin Protein Family of American Hematophagous Reduviids: Functional, Structural and Phylogenetic Analysis.

    PubMed

    Hernández-Vargas, María J; Santibáñez-López, Carlos E; Corzo, Gerardo

    2016-02-15

    A transcriptomic analysis of the saliva of T. pallidipennis together with a short proteomic analysis were carried out to reveal novel primary structures of the lipocalin/triabin protein families in this reduviid. Although triabins share some structural characteristics to lipocalins and they are classified as in the calcyn/lipocalin superfamily, triabins differ from lipocalins in the direction of β-strands in the general conformation of the β-barrel. The triabin protein family encompasses a wide variety of proteins, which disrupt the hemostasis of warm-blooded animals. Likewise, the function of proteins classified as triabins includes proteins that are carriers of small molecules, protease inhibitors, binders of specific cell-surface receptors as well as proteins that form complexes with other macromolecules. For example, triabin and pallidipin from the saliva of T. pallidipennis are thrombin and platelet aggregation inhibitors, respectively; triplatin from T. infestans binds to thromboxane A2; and nitrophorin from Rhodnius prolixus carries nitric oxide. Therefore, based on 42 new transcriptome sequences of triabins from the salivary glands of T. pallidipennis reported at present, and on triabin sequences of other American hematophagous reduviids already reported in the literature, subfamilies of triabins were proposed following phylogenetic analyses and functional characterization of triabin members. Eight subfamilies of proteins were recognized with known functions, which were the nitrophorin and amine binding proteins, Rhodnius prolixus aggregation inhibitor, triafestin, triatin, dipetalodipin and pallidipin, triplatin and infestilin, dimiconin and triabin, and procalin subfamilies. Interestingly, 70% of the analyzed sequences came from these eight subfamilies because there was no biological function associated with them, implying the existence of a vast number of proteins with potential novel biological activities.

  6. An Insight into the Triabin Protein Family of American Hematophagous Reduviids: Functional, Structural and Phylogenetic Analysis

    PubMed Central

    Hernández-Vargas, María J.; Santibáñez-López, Carlos E.; Corzo, Gerardo

    2016-01-01

    A transcriptomic analysis of the saliva of T. pallidipennis together with a short proteomic analysis were carried out to reveal novel primary structures of the lipocalin/triabin protein families in this reduviid. Although triabins share some structural characteristics to lipocalins and they are classified as in the calcyn/lipocalin superfamily, triabins differ from lipocalins in the direction of β-strands in the general conformation of the β-barrel. The triabin protein family encompasses a wide variety of proteins, which disrupt the hemostasis of warm-blooded animals. Likewise, the function of proteins classified as triabins includes proteins that are carriers of small molecules, protease inhibitors, binders of specific cell-surface receptors as well as proteins that form complexes with other macromolecules. For example, triabin and pallidipin from the saliva of T. pallidipennis are thrombin and platelet aggregation inhibitors, respectively; triplatin from T. infestans binds to thromboxane A2; and nitrophorin from Rhodnius prolixus carries nitric oxide. Therefore, based on 42 new transcriptome sequences of triabins from the salivary glands of T. pallidipennis reported at present, and on triabin sequences of other American hematophagous reduviids already reported in the literature, subfamilies of triabins were proposed following phylogenetic analyses and functional characterization of triabin members. Eight subfamilies of proteins were recognized with known functions, which were the nitrophorin and amine binding proteins, Rhodnius prolixus aggregation inhibitor, triafestin, triatin, dipetalodipin and pallidipin, triplatin and infestilin, dimiconin and triabin, and procalin subfamilies. Interestingly, 70% of the analyzed sequences came from these eight subfamilies because there was no biological function associated with them, implying the existence of a vast number of proteins with potential novel biological activities. PMID:26891325

  7. Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants.

    PubMed

    Prall, Wil; Hendy, Oliver; Thornton, Leeann E

    Plant adaptation to external pressures depends on functional diversity in cytochrome P450 (CYP) enzymes. CYPs contain structural domains necessary for the characteristic P450 fold that allows monooxygenation, but they also have great variation in substrate binding affinity. Plant genomes typically contain hundreds of CYPs that contribute to essential functions and species-specific metabolism. The CYP72A subfamily is conserved in angiosperms but its contribution to physiological functions is largely unknown. With genomic information available for many plants, a focused analysis of CYP subfamily diversity is important to understand the contributions of these enzymes to plant evolution. This study examines the extent to which independent gene duplication and evolution have contributed to structural diversification of CYP72A enzymes in different plant lineages. CYP72A genes are prevalent across angiosperms, but the number of genes within each genome varies greatly. The prevalence of CYP72As suggest that the last common ancestor of flowering plants contained a CYP72A sequence, but gene duplication and retention has varied greatly for this CYP subfamily. Sequence comparisons show that CYP72As are involved in species-specific metabolic functions in some plants while there is likely functional conservation between closely related species. Analysis of structural and functional domains within groups of CYP72As reveals clade-specific residues that contribute to functional constraints within subsets of CYP72As. This study provides a phylogenetic framework that allows comparisons of structural features within subsets of the CYP72A subfamily. We examined a large number of sequences from a broad collection of plant species to detect patterns of functional conservation across the subfamily. The evolutionary relationships between CYPs in plant genomes are an important component in understanding the evolution of biochemical diversity in plants.

  8. Enteroviral infection outbreak in the Republic of Belarus: principal characteristics and phylogenetic analysis of etiological agents.

    PubMed

    Amvrosieva, Tamara V; Paklonskaya, Natallia V; Biazruchka, Aliaksei A; Kazinetz, Olga N; Bohush, Zoya F; Fisenko, Elena G

    2006-06-01

    For the last decade enterovirus outbreaks were registered in all of six districts of Belarus. Two of them, reported in 1997 (in Gomel) and in 2003 (in Minsk), were the most extensive and involved 461 and 1,351 patients respectively. Virus ECHO 30 was identified as the dominant etiologic agent of the outbreak in 1997 whereas co-circulation of ECHO 30, ECHO 6 and Coxsackievirus B5 took place in 2003. Analysis of clinical manifestations during the Minsk outbreak revealed unusually high rate of severe clinical forms of infection including aseptic meningitis, encephalitis and myocardial disorders. Epidemiologic observation was ordinary for enterovirus epidemics in temperate climates: the peak of the outbreak was recorded during summer-autumn period of 2003, and 0-14 years old children predominated. Data from the case-control study indicated that illness was associated with drinking water from community water system. Also the laboratory examination demonstrated contamination of different water samples with the epidemic virus serotypes and sequence analysis showed high level of genetic similarity between waterborne and clinical isolates. For these reasons the outbreak should be classified as a waterborne one. Phylogenetic reconstruction showed that all Belarusian ECHO 30 isolates belong to the major genotype of ECHO 30 which has been circulating for last 15 years in Europe and North America. Viral agents of 2003 were very similar and substantially differed from isolates of 1997. Comparison of nucleotide sequences of isolates from myocarditis patients revealed their considerable genetic similarity with ECHO 30 isolates from patients with aseptic meningitis and from water. The results of the study draw attention to the importance of virological control of tap and bottled water as a relevant measure aimed at reduction of epidemiological risks.

  9. Networks in a Large-Scale Phylogenetic Analysis: Reconstructing Evolutionary History of Asparagales (Lilianae) Based on Four Plastid Genes

    PubMed Central

    Chase, Mark W.; Kim, Joo-Hwan

    2013-01-01

    Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses. PMID:23544071

  10. Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis.

    PubMed

    Broughton, R E; Stanley, S E; Durrett, R T

    2000-12-01

    Nucleotide transitions are frequently down-weighted relative to transversions in phylogenetic analysis. This is based on the assumption that transitions, by virtue of their greater evolutionary rate, exhibit relatively more homoplasy and are therefore less reliable phylogenetic characters. Relative amounts of homoplastic and consistent transition and transversion changes in mitochondrial protein coding genes were determined from character-state reconstructions on a highly corroborated phylogeny of mammals. We found that although homoplasy was related to evolutionary rates and was greater for transitions, the absolute number of consistent transitions greatly exceeded the number of consistent transversions. Consequently, transitions provided substantially more useful phylogenetic information than transversions. These results suggest that down-weighting transitions may be unwarranted in many cases. This conclusion was supported by the fact that a range of transition: transversion weighting schemes applied to various mitochondrial genes and genomic partitions rarely provided improvement in phylogenetic estimates relative to equal weighting, and in some cases weighting transitions more heavily than transversions was most effective.

  11. Full genome characterization and phylogenetic analysis of hepatitis B virus in gibbons and a caretaker in Central Kalimantan, Indonesia.

    PubMed

    Utsumi, Takako; Wahyuni, Rury Mega; Lusida, Maria Inge; Yano, Yoshihiko; Priambada, Nur Purba; Amin, Mochamad; Purwono, Priyo Budi; Istimagfiroh, Anittaqwa; Soetjipto; Brulé, Aurélien; Hotta, Hak; Hayashi, Yoshitake

    2015-03-01

    Hepatitis B virus (HBV) from gibbons was characterized, and the possibility of horizontal transmission between gibbons and humans was examined in a gibbon rehabilitation center in Central Kalimantan, Indonesia. Ten gibbons that were positive for the hepatitis B surface antigen (HBsAg) on arrival and 13 caretakers for those gibbons were included in this study. The duration of stay at the rehabilitation center ranged from 1 to 10 years. Serological and molecular analyses were performed. Six gibbons were positive for HBsAg, whereas HBV DNA was detected in all ten of the gibbons sampled. On the other hand, HBsAg was detected in only 1 of the 13 caretakers. HBV samples from seven gibbons and from the one infected human were chosen for complete genome sequencing. A phylogenetic analysis revealed that the cluster of gibbon strains in this study was distinct from strains previously reported from other countries. In the pre-S1 region, we found a unique amino acid residue substitution (P89K), three insertions between T87 and L88 in the genomes of three gibbons, and a 33-nucleotide deletion at the start of pre-S1 that is common in non-human primates. The caretaker sample was identified as HBV subgenotype B3, the most common type in Indonesia. For the complete HBV sequences, the similarity between gibbons in this study and other non-human primate and human HBV isolates was 90-91.9 % and 85.5-89.6 %, respectively. In conclusion, the gibbon HBV genotype was influenced by geographic location and species. To the best of our knowledge, this is the first report characterizing the HBV genes and genomes of indigenous gibbons in Indonesia.

  12. Comprehensive Phylogenetic Analysis Sheds Light on the Diversity and Origin of the MLO Family of Integral Membrane Proteins

    PubMed Central

    Kusch, Stefan; Pesch, Lina; Panstruga, Ralph

    2016-01-01

    Mildew resistance Locus O (MLO) proteins are polytopic integral membrane proteins that have long been considered as plant-specific and being primarily involved in plant–powdery mildew interactions. However, research in the past decade has revealed that MLO proteins diverged into a family with several clades whose members are associated with different physiological processes. We provide a largely increased dataset of MLO amino acid sequences, comprising nearly all major land plant lineages. Based on this comprehensive dataset, we defined seven phylogenetic clades and reconstructed the likely evolution of the MLO family in embryophytes. We further identified several MLO peptide motifs that are either conserved in all MLO proteins or confined to one or several clades, supporting the notion that clade-specific diversification of MLO functions is associated with particular sequence motifs. In baker’s yeast, some of these motifs are functionally linked to transmembrane (TM) transport of organic molecules and ions. In addition, we attempted to define the evolutionary origin of the MLO family and found that MLO-like proteins with highly diverse membrane topologies are present in green algae, but also in the distinctly related red algae (Rhodophyta), Amoebozoa, and Chromalveolata. Finally, we discovered several instances of putative fusion events between MLO proteins and different kinds of proteins. Such Rosetta stone-type hybrid proteins might be instructive for future analysis of potential MLO functions. Our findings suggest that MLO is an ancient protein that possibly evolved in unicellular photosynthetic eukaryotes, and consolidated in land plants with a conserved topology, comprising seven TM domains and an intrinsically unstructured C-terminus. PMID:26893454

  13. Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic.

    PubMed

    Fischer, Cristine D B; Gräf, Tiago; Ikuta, Nilo; Lehmann, Fernanda K M; Passos, Daniel T; Makiejczuk, Aline; Silveira, Marcos A T; Fonseca, André S K; Canal, Cláudio W; Lunge, Vagner R

    2016-07-01

    Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study investigates the phylodynamics and amino-acid signatures of CDV epidemic in South America by analyzing a large dataset compiled from publicly available sequences and also by collecting new samples from Brazil. A population of 175 dogs with canine distemper (CD) signs was sampled, from which 89 were positive for CDV, generating 42 new CDV sequences. Phylogenetic analysis of the new and publicly available sequences revealed that Brazilian sequences mainly clustered in South America 1 (SA1) clade, which has its origin estimated to the late 1980's. The reconstruction of the demographic history in SA1 clade showed an epidemic expanding until the recent years, doubling in size every nine years. SA1 clade epidemic distinguished from the world CDV epidemic by the emergence of the R580Q strain, a very rare and potentially detrimental substitution in the viral genome. The R580Q substitution was estimated to have happened in one single evolutionary step in the epidemic history in SA1 clade, emerging shortly after introduction to the continent. Moreover, a high prevalence (11.9%) of the Y549H mutation was observed among the domestic dogs sampled here. This finding was associated (p<0.05) with outcome-death and higher frequency in mixed-breed dogs, the later being an indicator of a continuous exchange of CDV strains circulating among wild carnivores and domestic dogs. The results reported here highlight the diversity of the worldwide CDV epidemic and reveal local features that can be valuable for combating the disease.

  14. Molecular epidemiology and phylogenetic analysis of diverse bovine astroviruses associated with diarrhea in cattle and water buffalo calves in China.

    PubMed

    Alfred, Niyokwishimira; Liu, Huan; Li, Mu Lan; Hong, Shao Feng; Tang, Hai Bo; Wei, Zu Zhang; Chen, Ying; Li, Fa Kai; Zhong, Yi Zhi; Huang, Wei Jian

    2015-06-01

    Astroviruses are the principal causative agents of gastroenteritis in humans and have been associated with diarrhea in other mammals as well as birds. However, astroviral infection of animals had been poorly studied. In the present study, 211 rectal swabs collected from cattle and water buffalo calves with mild to severe diarrhea were tested for bovine astrovirus (BAstV) by RT-PCR. Results: 92/211 (43.6%) samples were positive for BAstV, at a rate of 46.10% (71/154) in cattle and 36.84% (21/57) in water buffalo. Phylogenetic analysis based on the partial and full-length of 25 ORF2 amino acid sequences obtained in this study classified the Guangxi BAstVs isolates into five subgroups under the genus of Mamastrovirus, genotype MAstV33, which suggested that the water buffalo was a new host of this genogroup that previously included only cattle and roe deer. Despite the origin of the host, the Guangxi BAstV isolates were closely related to the BAstV Hong Kong isolates (B18/HK and B76-2/HK), but highly divergent from the BAstV NeuroS1 isolate previously associated with neurologic disease in cattle in the U.S.A. Nucleotide sequence-based characterization of the ORF1b/ORF2 junction and corresponding overlapping regions showed distinctive properties, which may be common to BAstVs. Our results suggested that cattle and water buffalo are prone to infection of closely related astroviruses, which probably evolved from the same ancestor. The current study described astroviruses in water buffalo for the first time and is thus far among the largest epidemiological investigations of BAstV infection in cattle conducted in China.

  15. Comprehensive Phylogenetic Analysis Sheds Light on the Diversity and Origin of the MLO Family of Integral Membrane Proteins.

    PubMed

    Kusch, Stefan; Pesch, Lina; Panstruga, Ralph

    2016-03-26

    Mildew resistanceLocusO(MLO) proteins are polytopic integral membrane proteins that have long been considered as plant-specific and being primarily involved in plant-powdery mildew interactions. However, research in the past decade has revealed that MLO proteins diverged into a family with several clades whose members are associated with different physiological processes. We provide a largely increased dataset of MLO amino acid sequences, comprising nearly all major land plant lineages. Based on this comprehensive dataset, we defined seven phylogenetic clades and reconstructed the likely evolution of the MLO family in embryophytes. We further identified several MLO peptide motifs that are either conserved in all MLO proteins or confined to one or several clades, supporting the notion that clade-specific diversification of MLO functions is associated with particular sequence motifs. In baker's yeast, some of these motifs are functionally linked to transmembrane (TM) transport of organic molecules and ions. In addition, we attempted to define the evolutionary origin of the MLO family and found that MLO-like proteins with highly diverse membrane topologies are present in green algae, but also in the distinctly related red algae (Rhodophyta), Amoebozoa, and Chromalveolata. Finally, we discovered several instances of putative fusion events between MLO proteins and different kinds of proteins. Such Rosetta stone-type hybrid proteins might be instructive for future analysis of potential MLO functions. Our findings suggest that MLO is an ancient protein that possibly evolved in unicellular photosynthetic eukaryotes, and consolidated in land plants with a conserved topology, comprising seven TM domains and an intrinsically unstructured C-terminus.

  16. A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals novel NS5 mutation

    PubMed Central

    Schmidt, DJ; Pickett, BE; Camacho, D; Comach, G; Xhaja, K; Lennon, NJ; Rizzolo, K; de Bosch, N; Becerra, A; Nogueira, ML; Mondini, A; da Silva, EV; Vasconcelos, PF; Muñoz-Jordán, JL; Santiago, GA; Ocazionez, R; Gehrke, L; Lefkowitz, EJ; Birren, BW; Henn, MR; Bosch, I

    2013-01-01

    Dengue virus currently causes 50-100 million infections annually. Comprehensive knowledge about the evolution of Dengue in response to selection pressure is currently unavailable, but would greatly enhance vaccine design efforts. In the current study, we sequenced 187 new dengue virus serotype 3(DENV-3) genotype III whole genomes isolated from Asia and the Americas. We analyzed them together with previously-sequenced isolates to gain a more detailed understanding of the evolutionary adaptations existing in this prevalent American serotype. In order to analyze the phylogenetic dynamics of DENV-3 during outbreak periods; we incorporated datasets of 48 and 11 sequences spanning two major outbreaks in Venezuela during 2001 and 2007-2008 respectively. Our phylogenetic analysis of newly sequenced viruses shows that subsets of genomes cluster primarily by geographic location, and secondarily by time of virus isolation. DENV-3 genotype III sequences from Asia are significantly divergent from those from the Americas due to their geographical separation and subsequent speciation. We measured amino acid variation for the E protein by calculating the Shannon entropy at each position between Asian and American genomes. We found a cluster of 7 amino acid substitutions having high variability within E protein domain III, which has previously been implicated in serotype-specific neutralization escape mutants. No novel mutations were found in the E protein of sequences isolated during either Venezuelan outbreak. Shannon entropy analysis of the NS5 polymerase mature protein revealed that a G374E mutation, in a region that contributes to interferon resistance in other flaviviruses by interfering with JAK-STAT signaling was present in both the Asian and American sequences from the 2007-2008 Venezuelan outbreak, but was absent in the sequences from the 2001 Venezuelan outbreak. In addition to E, several NS5 amino acid changes were unique to the 2007-2008 epidemic in Venezuela and may

  17. Identification and phylogenetic analysis of contagious ecthyma virus from camels (Camelus dromedarius) in Iran.

    PubMed

    Oryan, Ahmad; Mosadeghhesari, Mahboobe; Zibaee, Saeed; Mohammadi, Ali

    2017-03-24

    Contagious ecthyma is a highly contagious disease affecting domestic and wild ruminants such as sheep, goats and camels. The identification and characterisation of a parapoxvirus (PPV) infecting camels is described here. The virus was detected in dromedary camels (Camelus dromedarius) from Kerman and Shiraz in Iran. PPV-specific amplification by polymerase chain reaction (PCR) further confirmed that the disease was associated with PPV infection. Phylogenetic analysis of ORF011 (B2L) gene sequences showed 99.79% and 82.13% similarity of the PPV identified in this study with the Jodhpur isolate and the bovine papular stomatitis virus (BPSV) isolates (CE41), respectively. Moreover, phylogenetic analysis of the ORF045 gene indicated that the Shiraz sample was in all probability closely related to VR634 and to F00.120R and PCPV776. In conclusion, the results suggest that camel PPV (CPPV) is a likely cause of contagious ecthyma in dromedary camels in Iran.

  18. Complete mitochondrial genome of the Indian peafowl (Pavo cristatus), with phylogenetic analysis in phasianidae.

    PubMed

    Zhou, Tai-Cheng; Sha, Tao; Irwin, David M; Zhang, Ya-Ping

    2015-01-01

    Pavo cristatus, known as the Indian peafowl, is endemic to India and Sri Lanka and has been domesticated for its ornamental and food value. However, its phylogenetic status is still debated. Here, to clarify the phylogenetic status of P. cristatus within Phasianidae, we analyzed its mitochondrial genome (mtDNA). The complete mitochondrial DNA (mtDNA) genome was determined using 34 pairs of primers. Our data show that the mtDNA genome of P. cristatus is 16,686 bp in length. Molecular phylogenetic analyses of P. cristatus was performed along with 22 complete mtDNA genomes belonging to other species in Phasianidae using Bayesian and maximum likelihood methods, where Aythya americana and Anas platyrhynchos were used as outgroups. Our results show that P. critatus has its closest genetic affinity with Pavo muticus and belongs to clade that contains Gallus, Bambusicola and Francolinus.

  19. Phylogenetic analysis of Bacillus cereus isolates from severe systemic infections using multilocus sequence typing scheme.

    PubMed

    Vassileva, Maria; Torii, Keizo; Oshimoto, Megumi; Okamoto, Akira; Agata, Norio; Yamada, Keiko; Hasegawa, Tadao; Ohta, Michio

    2006-01-01

    Bacillus cereus strains from cases of severe or lethal systemic infections, including respiratory symptoms cases, were analyzed using multilocus sequence typing scheme of B. cereus MLST database. The isolates were evenly distributed between the two main clades, and 60% of them had allele profiles new to the database. Half of the collection's strains clustered in a lineage neighboring Bacillus anthracis phylogenetic origin. Strains from lethal cases with respiratory symptoms were allocated in both main clades. This is the first report of strains causing respiratory symptoms to be identified as genetically distant from B. anthracis. The phylogenetic location of the presented here strains was compared with all previously submitted to the database isolates from systemic infections, and were found to appear in the same clusters where clinical isolates from other studies had been assigned. It seems that the pathogenic strains are forming clusters on the phylogenetic tree.

  20. Phylogenetic characterization of Central/Southern European lineage 2 West Nile virus: analysis of human outbreaks in Italy and Greece, 2013-2014.

    PubMed

    Barzon, L; Papa, A; Lavezzo, E; Franchin, E; Pacenti, M; Sinigaglia, A; Masi, G; Trevisan, M; Squarzon, L; Toppo, S; Papadopoulou, E; Nowotny, N; Ulbert, S; Piralla, A; Rovida, F; Baldanti, F; Percivalle, E; Palù, G

    2015-12-01

    In recent years, West Nile virus (WNV) lineage 2 has been spreading and causing disease outbreaks in humans and animals in Europe. In order to characterize viral diversity, we performed full-length genome sequencing of WNV lineage 2 from human samples collected during outbreaks in Italy and Greece in 2013 and 2014. Phylogenetic analysis showed that these WNV lineage 2 genomes belonged to a monophyletic clade derived from a single introduction into Europe of the prototype Hungarian strain. Correlation of phylogenetic data with geospatial information showed geographical clustering of WNV genome sequences both in Italy and in Greece, indicating that the virus had evolved and diverged during its dispersal in Europe, leading to the emergence of novel genotypes, as it adapted to local ecological niches. These genotypes carried divergent conserved amino acid substitutions, which might have been relevant for viral adaptation, as suggested by selection pressure analysis and in silico and experimental modelling of sequence changes. In conclusion, the results of this study provide further information on WNV lineage 2 transmission dynamics in Europe, and emphasize the need for WNV surveillance activities to monitor viral evolution and diversity.

  1. Family structure and phylogenetic analysis of odorant receptor genes in the large yellow croaker (Larimichthys crocea)

    PubMed Central

    2011-01-01

    Background Chemosensory receptors, which are all G-protein-coupled receptors (GPCRs), come in four types: odorant receptors (ORs), vomeronasal receptors, trace-amine associated receptors and formyl peptide receptor-like proteins. The ORs are the most important receptors for detecting a wide range of environmental chemicals in daily life. Most fish OR genes have been identified from genome databases following the completion of the genome sequencing projects of many fishes. However, it remains unclear whether these OR genes from the genome databases are actually expressed in the fish olfactory epithelium. Thus, it is necessary to clone the OR mRNAs directly from the olfactory epithelium and to examine their expression status. Results Eighty-nine full-length and 22 partial OR cDNA sequences were isolated from the olfactory epithelium of the large yellow croaker, Larimichthys crocea. Bayesian phylogenetic analysis classified the vertebrate OR genes into two types, with several clades within each type, and showed that the L. crocea OR genes of each type are more closely related to those of fugu, pufferfish and stickleback than they are to those of medaka, zebrafish and frog. The reconciled tree showed 178 duplications and 129 losses. The evolutionary relationships among OR genes in these fishes accords with their evolutionary history. The fish OR genes have experienced functional divergence, and the different clades of OR genes have evolved different functions. The result of real-time PCR shows that different clades of ORs have distinct expression levels. Conclusion We have shown about 100 OR genes to be expressed in the olfactory epithelial tissues of L. crocea. The OR genes of modern fishes duplicated from their common ancestor, and were expanded over evolutionary time. The OR genes of L. crocea are closely related to those of fugu, pufferfish and stickleback, which is consistent with its evolutionary position. The different expression levels of OR genes of large

  2. Emergence of Hepatitis C Virus Genotype 4: Phylogenetic Analysis Reveals Three Distinct Epidemiological Profiles ▿

    PubMed Central

    de Bruijne, Joep; Schinkel, Janke; Prins, Maria; Koekkoek, Sylvie M.; Aronson, Sem J.; van Ballegooijen, Marijn W.; Reesink, Hendrik W.; Molenkamp, Richard; van de Laar, Thijs J. W.

    2009-01-01

    Hepatitis C virus (HCV) genotype 4 (HCV-4) infection is considered to be difficult to treat and has become increasingly prevalent in European countries, including The Netherlands. Using a molecular epidemiological approach, the present study investigates the genetic diversity and evolutionary origin of HCV-4 in Amsterdam, The Netherlands. Phylogenetic analysis of the NS5B sequences (668 bp) obtained from 133 patients newly diagnosed with HCV-4 infection over the period from 1999 to 2008 revealed eight distinct HCV-4 subtypes; the majority of HCV-4 isolates were of subtypes 4d (57%) and 4a (37%). Three distinct monophyletic clusters were identified, with each one having a specific epidemiological profile: (i) Egyptian immigrants infected with HCV-4a (n = 46), (ii) Dutch patients with a history of injecting drug use infected with HCV-4d (n = 44), and (iii) Dutch human immunodeficiency virus (HIV)-positive men who have sex with men (MSM) infected with HCV-4d (n = 26). Subsequent molecular clock analyses confirmed that the emergence of HCV-4 within these three risk groups coincided with (i) the parenteral antischistosomal therapy campaigns in Egypt (1920 to 1960), (ii) the popularity of injecting drug use in The Netherlands (1960 to 1990), and (iii) the rise in high-risk sexual behavior among MSM after the introduction of highly active antiretroviral therapy (1996 onwards). Our data show that in addition to the influx of HCV-4 strains from countries where HCV-4 is endemic, the local spread of HCV-4d affecting injecting drug users and, in recent years, especially HIV-positive MSM will further increase the relative proportion of HCV-4-infected patients in The Netherlands. HCV-4-specific agents are drastically needed to improve treatment response rates and decrease the future burden of HCV-4-related disease. PMID:19794040

  3. Molecular differentiation and phylogenetic analysis of the Egyptian foot-and-mouth disease virus SAT2.

    PubMed

    El-Shehawy, Laila I; Abu-Elnaga, Hany I; Rizk, Sonia A; Abd El-Kreem, Ahmed S; Mohamed, A A; Fawzy, Hossam G

    2014-03-01

    In February 2012, a massive new foot-and-mouth disease (FMD) outbreak struck Egypt. In this work, one-step RT-PCR assays were used for in-house detection and differentiation of foot-and-mouth disease virus (FMDV) in Egypt in this year using pan-serotypic and serotype-targeting sequence primers. FMDV SAT2 was the dominant virus in the examined isolates from the epidemic. The complete VP1 coding regions of two isolates were sequenced. The two isolates had 99.2 % sequence identity to most contemporary Egyptian SAT2 reference viruses, whereas they had 89.7-90.1 % identity to the SAT2/EGY/2/2012 isolate, which was collected from Alexandria, Egypt, and previously sequenced by WRLFMD. Phylogenetic analysis showed that Egypt had one topotype and two lineage of FMDV SAT2 in 2012. The Egyptian and the Palestinian 2012 strains were associated mainly with topotype VII, lineage SAT2/VII/Ghb-12, while the virus isolated from Alexandria Governorate belonged to the SAT2/VII/Alx-12 lineage. Topotype VII also comprised lineages that included strains isolated from Libya in 2012 and 2003. Furthermore, within the same topotype, the Egyptian SAT2/2012 isolates were related to strains from Saudi Arabia, Sudan, Eritrea, Cameroon and Nigeria. Nevertheless, more epidemiological work with neighboring countries is needed to prevent cross-border spread of disease and to reach a precise conclusion about the origin of the 2012 FMDV SAT2 emergency in the Middle East.

  4. Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree.

    PubMed

    Moore, Andrew D; Grath, Sonja; Schüler, Andreas; Huylmans, Ann K; Bornberg-Bauer, Erich

    2013-05-01

    Modularity is a hallmark of molecular evolution. Whether considering gene regulation, the components of metabolic pathways or signaling cascades, the ability to reuse autonomous modules in different molecular contexts can expedite evolutionary innovation. Similarly, protein domains are the modules of proteins, and modular domain rearrangements can create diversity with seemingly few operations in turn allowing for swift changes to an organism's functional repertoire. Here, we assess the patterns and functional effects of modular rearrangements at high resolution. Using a well resolved and diverse group of pancrustaceans, we illustrate arrangement diversity within closely related organisms, estimate arrangement turnover frequency and establish, for the first time, branch-specific rate estimates for fusion, fission, domain addition and terminal loss. Our results show that roughly 16 new arrangements arise per million years and that between 64% and 81% of these can be explained by simple, single-step modular rearrangement events. We find evidence that the frequencies of fission and terminal deletion events increase over time, and that modular rearrangements impact all levels of the cellular signaling apparatus and thus may have strong adaptive potential. Novel arrangements that cannot be explained by simple modular rearrangements contain a significant amount of repeat domains that occur in complex patterns which we term "supra-repeats". Furthermore, these arrangements are significantly longer than those with a single-step rearrangement solution, suggesting that such arrangements may result from multi-step events. In summary, our analysis provides an integrated view and initial quantification of the patterns and functional impact of modular protein evolution in a well resolved phylogenetic tree. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.

  5. Phylogenetic analysis of the Francisella-like endosymbionts of Dermacentor ticks.

    PubMed

    Scoles, Glen A

    2004-05-01

    Bacterial endosymbionts with significant homology to Francisella tularensis (gamma-proteobacteria) have been described from at least five species of ticks in three different genera, including two North American Dermacentor species [D. andersoni Stiles and D. variabilis (Say)]. The evolutionary relationships among the Francisella-like endosymbionts (FLE) from different hosts and between FLE and the arthropod-borne pathogen F. tularensis are not known. A 1,169-base fragment of the 16s rDNA and a 713-base fragment of the F. tularensis 17-kDa lipoprotein gene homolog of the FLE of six North American Dermacentor tick species [D. anderson, D. variabilis, D. albipictus (Packard), D. occidentalis Marx, D. hunteri Bishopp, and D. (Anocentor) nitens Neumann] and of Amblyomma maculatum Koch and Ornithodoros porcinus (Murry 1877, sensu Walton 1979) as outgroups, were subjected to phylogenetic analysis. These gene phylogenies were compared with a phylogeny of the same tick species constructed from a 435-base fragment of the tick mitochondrial 16s rDNA. Although the phylogenies of the FLE and their tick hosts are parallel at the genus level, the Dermacentor FLE are unresolved at the species level. The FLE and the Dermacentor ticks show little sign of co-speciation, possibly indicating that the association between these endosymbiont and the Dermacentor ticks is of a relatively recent origin. Several ticks were co-infected, either with two FLE with divergent 17-kDa lipoprotein gene sequences or with FLE and an unidentified species of spotted fever group rickettsia (alpha-proteobacteria). Infection with FLE does not seem to have precluded infection with either a second closely related gamma-proteobacterial symbiont or with a second less closely related alpha-proteobacterial symbiont.

  6. Detecting the symplesiomorphy trap: a multigene phylogenetic analysis of terebelliform annelids

    PubMed Central

    2011-01-01

    Background For phylogenetic reconstructions, conflict in signal is a potential problem for tree reconstruction. For instance, molecular data from different cellular components, such as the mitochondrion and nucleus, may be inconsistent with each other. Mammalian studies provide one such case of conflict where mitochondrial data, which display compositional biases, support the Marsupionta hypothesis, but nuclear data confirm the Theria hypothesis. Most observations of compositional biases in tree reconstruction have focused on lineages with different composition than the majority of the lineages under analysis. However in some situations, the position of taxa that lack compositional bias may be influenced rather than the position of taxa that possess compositional bias. This situation is due to apparent symplesiomorphic characters and known as "the symplesiomorphy trap". Results Herein, we report an example of the sympleisomorphy trap and how to detect it. Worms within Terebelliformia (sensu Rouse & Pleijel 2001) are mainly tube-dwelling annelids comprising five 'families': Alvinellidae, Ampharetidae, Terebellidae, Trichobranchidae and Pectinariidae. Using mitochondrial genomic data, as well as data from the nuclear 18S, 28S rDNA and elongation factor-1α genes, we revealed incongruence between mitochondrial and nuclear data regarding the placement of Trichobranchidae. Mitochondrial data favored a sister relationship between Terebellidae and Trichobranchidae, but nuclear data placed Trichobranchidae as sister to an Ampharetidae/Alvinellidae clade. Both positions have been proposed based on morphological data. Conclusions Our investigation revealed that mitochondrial data of Ampharetidae and Alvinellidae exhibited strong compositional biases. However, these biases resulted in a misplacement of Trichobranchidae, rather than Alvinellidae and Ampharetidae. Herein, we document that Trichobranchidae was apparently caught in the symplesiomorphy trap suggesting that in

  7. Expression analysis of LIM gene family in poplar, toward an updated phylogenetic classification

    PubMed Central

    2012-01-01

    Background Plant LIM domain proteins may act as transcriptional activators of lignin biosynthesis and/or as actin binding and bundling proteins. Plant LIM genes have evolved in phylogenetic subgroups differing in their expression profiles: in the whole plant or specifically in pollen. However, several poplar PtLIM genes belong to uncharacterized monophyletic subgroups and the expression patterns of the LIM gene family in a woody plant have not been studied. Findings In this work, the expression pattern of the twelve duplicated poplar PtLIM genes has been investigated by semi quantitative RT-PCR in different vegetative and reproductive tissues. As in other plant species, poplar PtLIM genes were widely expressed in the tree or in particular tissues. Especially, PtXLIM1a, PtXLIM1b and PtWLIM1b genes were preferentially expressed in the secondary xylem, suggesting a specific function in wood formation. Moreover, the expression of these genes and of the PtPLIM2a gene was increased in tension wood. Western-blot analysis confirmed the preferential expression of PtXLIM1a protein during xylem differentiation and tension wood formation. Genes classified within the pollen specific PLIM2 and PLIM2-like subgroups were all strongly expressed in pollen but also in cottony hairs. Interestingly, pairs of duplicated PtLIM genes exhibited different expression patterns indicating subfunctionalisations in specific tissues. Conclusions The strong expression of several LIM genes in cottony hairs and germinating pollen, as well as in xylem fibers suggests an involvement of plant LIM domain proteins in the control of cell expansion. Comparisons of expression profiles of poplar LIM genes with the published functions of closely related plant LIM genes suggest conserved functions in the areas of lignin biosynthesis, pollen tube growth and mechanical stress response. Based on these results, we propose a novel nomenclature of poplar LIM domain proteins. PMID:22339987

  8. Phylogenetic analysis of β-defensin-like genes of Bothrops, Crotalus and Lachesis snakes.

    PubMed

    Correa, Poliana G; Oguiura, Nancy

    2013-07-01

    Defensins are components of the vertebrate innate immune system; they comprise a diverse group of small cationic antimicrobial peptides. Among them, β-defensins have a characteristic β-sheet-rich fold plus six conserved cysteines with particular spacing and intramolecular bonds. They have been fully studied in mammals, but there is little information about them in snakes. Using a PCR approach, we described 13 β-defensin-like sequences in Bothrops and Lachesis snakes. The genes are organized in three exons and two introns, with exception of B.atrox_defensinB_01 which has only two exons. They show high similarities in exon 1, intron 1 and intron 2, but exons 2 and 3 have undergone accelerated evolution. The theoretical translated sequences encode a pre-β-defensin-like molecule with a conserved signal peptide and a mature peptide. The signal peptides are leucine-rich and the mature β-defensin-like molecules have a size around 4.5 kDa, a net charge from +2 to +11, and the conserved cysteine motif. Phylogenetic analysis was done using maximum parsimony, maximum likelihood and Bayesian analyses, and all resulted in similar topologies with slight differences. The genus Bothrops displayed two separate lineages. The reconciliation of gene trees and species tree indicated eight to nine duplications and 23 to 29 extinctions depending on the gene tree used. Our results together with previously published data indicate that the ancestral β-defensin-like gene may have three exons in vertebrates and that their evolution occurred according to a birth-and-death model.

  9. Prevalence and phylogenetic analysis of haemoplasmas from cats infected with multiple species

    PubMed Central

    Aquino, Larissa Campos; Hicks, Chelsea A.E.; Scalon, Marcela C.; Lima, Maíra G. da M.; Lemos, Marcelle dos S.; Paludo, Giane Regina; Helps, Chris R.; Tasker, Séverine

    2014-01-01

    Mycoplasma haemofelis (Mhf), ‘Candidatus Mycoplasma haemominutum’ (CMhm) and ‘Candidatus Mycoplasma turicensis’ (CMt) are agents of feline haemoplasmosis and can induce anaemia in cats. This study aimed to determine the prevalence and phylogeny of haemoplasma species in cats from Brazil's capital and surrounding areas, and whether correlation with haematological abnormalities existed. Feline haemoplasmas were found in 13.8% of 432 cats. CMhm was the most prevalent species (in 13.8% of cats), followed by Mhf (11.1%) and CMt (4.4%). Over 80% of haemoplasma-infected cats harboured two or more feline haemoplasma species: 7.1% of cats were co-infected with Mhf/CMhm, 0.4% with CMhm/CMt and 3.9% with Mhf/CMhm/CMt. Male gender was significantly associated with haemoplasma infections. No association was found between qPCR haemoplasma status and haematological variables, however CMhm relative copy numbers were correlated with red blood cell (RBC) numbers and packed cell volume (PCV). Haemoplasma 16S rRNA gene sequences (> 1 Kb) were derived from co-infected cats using novel haemoplasma species-specific primers. This allowed 16S rRNA gene sequences to be obtained despite the high level of co-infection, which precluded the use of universal 16S rRNA gene primers. Within each species, the Mhf, CMhm and CMt sequences showed > 99.8%, > 98.5% and > 98.8% identity, respectively. The Mhf, CMhm and CMt sequences showed > 99.2%, > 98.4% and > 97.8% identity, respectively, with GenBank sequences. Phylogenetic analysis showed all Mhf sequences to reside in a single clade, whereas the CMhm and CMt sequences each grouped into three distinct subclades. These phylogeny findings suggest the existence of different CMhm and CMt strains. PMID:25447887

  10. Phylogenetic analysis of faecal microbiota from captive cheetahs reveals underrepresentation of Bacteroidetes and Bifidobacteriaceae

    PubMed Central

    2014-01-01

    Background Imbalanced feeding regimes may initiate gastrointestinal and metabolic diseases in endangered felids kept in captivity such as cheetahs. Given the crucial role of the host’s intestinal microbiota in feed fermentation and health maintenance, a better understanding of the cheetah’s intestinal ecosystem is essential for improvement of current feeding strategies. We determined the phylogenetic diversity of the faecal microbiota of the only two cheetahs housed in an EAZA associated zoo in Flanders, Belgium, to gain first insights in the relative distribution, identity and potential role of the major community members. Results Taxonomic analysis of 16S rRNA gene clone libraries (702 clones) revealed a microbiota dominated by Firmicutes (94.7%), followed by a minority of Actinobacteria (4.3%), Proteobacteria (0.4%) and Fusobacteria (0.6%). In the Firmicutes, the majority of the phylotypes within the Clostridiales were assigned to Clostridium clusters XIVa (43%), XI (38%) and I (13%). Members of the Bacteroidetes phylum and Bifidobacteriaceae, two groups that can positively contribute in maintaining intestinal homeostasis, were absent in the clone libraries and detected in only marginal to low levels in real-time PCR analyses. Conclusions This marked underrepresentation is in contrast to data previously reported in domestic cats where Bacteroidetes and Bifidobacteriaceae are common residents of the faecal microbiota. Next to methodological differences, these findings may also reflect the apparent differences in dietary habits of both felid species. Thus, our results question the role of the domestic cat as the best available model for nutritional intervention studies in endangered exotic felids. PMID:24548488

  11. Prevalence and Phylogenetic Analysis of Orientia tsutsugamushi in Small Mammals in Hanoi, Vietnam.

    PubMed

    Hotta, Kozue; Pham, Hang T T; Hoang, Huong T; Trang, Tu C; Vu, Thuy N; Ung, Trang T H; Shimizu, Kenta; Arikawa, Jiro; Yamada, Akio; Nguyen, Hoa T; Nguyen, Hang L K; Le, Mai T Q; Hayasaka, Daisuke

    2016-02-01

    Rodents are important reservoirs of many human pathogens transmitted via arthropod vectors. Arthropod-borne bacteria belonging to the family Rickettsiaceae cause acute febrile diseases in humans worldwide, but the real burdens of rickettsial diseases appear to be underestimated in Hanoi, Vietnam, because differential diagnosis on the basis of clinical signs and symptoms is confounded by the presence of other tropical infectious diseases with similar signs and symptoms. To know the prevalence of bacteria of the family Rickettsiaceae among small mammals in Hanoi, 519 animals thriving in the public places were captured and examined for the presence of bacterial sequences using duplex PCR. Nucleotide sequences specific for Orientia tsutsugamushi were detected in seven samples (1.3%). Out of seven animals, two were captured in a market, whereas five were in hospitals. None of the captured small mammals tested positive for the genus Rickettsia. The nucleotide sequence analysis of the genes encoding the 47-kDa high-temperature requirement A (47-kDa HtrA) and 56-kDa type-specific antigen (TSA) showed that these seven isolates were indistinguishable from each other. O. tsutsugamushi isolated in this study was closely related phylogenetically to the Gilliam strain, which was originally isolated at the border of Assam and Burma, rather than to those isolated in the central to southern part of Vietnam. It should be emphasized that Vietnamese hospitals were heavily infested by small rodents and some of them harbored O. tsutsugamushi. Strict hygienic control should be implemented to mitigate the potential risk posed by O. tsutsugamushi in hospital settings.

  12. Phylogenetic Analysis of the Complete Mitochondrial Genome of Madurella mycetomatis Confirms Its Taxonomic Position within the Order Sordariales

    PubMed Central

    van de Sande, Wendy W. J.

    2012-01-01

    Background Madurella mycetomatis is the most common cause of human eumycetoma. The genus Madurella has been characterized by overall sterility on mycological media. Due to this sterility and the absence of other reliable morphological and ultrastructural characters, the taxonomic classification of Madurella has long been a challenge. Mitochondria are of monophyletic origin and mitochondrial genomes have been proven to be useful in phylogenetic analyses. Results The first complete mitochondrial DNA genome of a mycetoma-causative agent was sequenced using 454 sequencing. The mitochondrial genome of M. mycetomatis is a circular DNA molecule with a size of 45,590 bp, encoding for the small and the large subunit rRNAs, 27 tRNAs, 11 genes encoding subunits of respiratory chain complexes, 2 ATP synthase subunits, 5 hypothetical proteins, 6 intronic proteins including the ribosomal protein rps3. In phylogenetic analyses using amino acid sequences of the proteins involved in respiratory chain complexes and the 2 ATP synthases it appeared that M. mycetomatis clustered together with members of the order Sordariales and that it was most closely related to Chaetomium thermophilum. Analyses of the gene order showed that within the order Sordariales a similar gene order is found. Furthermore also the tRNA order seemed mostly conserved. Conclusion Phylogenetic analyses of fungal mitochondrial genomes confirmed that M. mycetomatis belongs to the order of Sordariales and that it was most closely related to Chaetomium thermophilum, with which it also shared a comparable gene and tRNA order. PMID:22701687

  13. A new African fossil caprin and a combined molecular and morphological Bayesian phylogenetic analysis of caprini (Mammalia: Bovidae).

    PubMed

    Bibi, F; Vrba, E; Fack, F

    2012-09-01

    Given that most species that have ever existed on Earth are extinct, no evolutionary history can ever be complete without the inclusion of fossil taxa. Bovids (antelopes and relatives) are one of the most diverse clades of large mammals alive today, with over a hundred living species and hundreds of documented fossil species. With the advent of molecular phylogenetics, major advances have been made in the phylogeny of this clade; however, there has been little attempt to integrate the fossil record into the developing phylogenetic picture. We here describe a new large fossil caprin species from ca. 1.9-Ma deposits from the Middle Awash, Ethiopia. To place the new species phylogenetically, we perform a Bayesian analysis of a combined molecular (cytochrome b) and morphological (osteological) character supermatrix. We include all living species of Caprini, the new fossil species, a fossil takin from the Pliocene of Ethiopia (Budorcas churcheri), and the insular subfossil Myotragus balearicus. The combined analysis demonstrates successful incorporation of both living and fossil species within a single phylogeny based on both molecular and morphological evidence. Analysis of the combined supermatrix produces superior resolution than with either the molecular or morphological data sets considered alone. Parsimony and Bayesian analyses of the data set are also compared and shown to produce similar results. The combined phylogenetic analysis indicates that the new fossil species is nested within Capra, making it one of the earliest representatives of this clade, with implications for molecular clock calibration. Geographical optimization indicates no less than four independent dispersals into Africa by caprins since the Pliocene.

  14. Phylogenetic Analysis, Lineage-Specific Expansion and Functional Divergence of seed dormancy 4-Like Genes in Plants

    PubMed Central

    Subburaj, Saminathan; Cao, Shuanghe; Xia, Xianchun; He, Zhonghu

    2016-01-01

    The rice gene seed dormancy 4 (OsSdr4) functions in seed dormancy and is a major factor associated with pre-harvest sprouting (PHS). Although previous studies of this protein family were reported for rice and other species, knowledge of the evolution of genes homologous to OsSdr4 in plants remains inadequate. Fifty four Sdr4-like (hereafter designated Sdr4L) genes were identified in nine plant lineages including 36 species. Phylogenetic analysis placed these genes in eight subfamilies (I-VIII). Genes from the same lineage clustered together, supported by analysis of conserved motifs and exon-intron patterns. Segmental duplications were present in both dicot and monocot clusters, while tandemly duplicated genes occurred only in monocot clusters indicating that both tandem and segmental duplications contributed to expansion of the grass I and II subfamilies. Estimation of the approximate ages of the duplication events indicated that ancestral Sdr4 genes evolved from a common angiosperm ancestor, about 160 million years ago (MYA). Moreover, diversification of Sdr4L genes in mono and dicot plants was mainly associated with genome-wide duplication and speciation events. Functional divergence was observed in all subfamily pairs, except IV/VIIIa. Further analysis indicated that functional constraints between subfamily pairs I/II, I/VIIIb, II/VI, II/VIIIb, II/IV, and VI/VIIIb were statistically significant. Site and branch-site model analyses of positive selection suggested that these genes were under strong adaptive selection pressure. Critical amino acids detected for both functional divergence and positive selection were mostly located in the loops, pointing to functional importance of these regions in this protein family. In addition, differential expression studies by transcriptome atlas of 11 Sdr4L genes showed that the duplicated genes may have undergone divergence in expression between plant species. Our findings showed that Sdr4L genes are functionally divergent

  15. A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions

    PubMed Central

    Makendi, Carine; Page, Andrew J.; Wren, Brendan W.; Le Thi Phuong, Tu; Clare, Simon; Hale, Christine; Goulding, David; Klemm, Elizabeth J.; Pickard, Derek; Okoro, Chinyere; Hunt, Martin; Thompson, Corinne N.; Phu Huong Lan, Nguyen; Tran Do Hoang, Nhu; Thwaites, Guy E.; Le Hello, Simon; Brisabois, Anne; Weill, François-Xavier; Baker, Stephen; Dougan, Gordon

    2016-01-01

    Salmonella enterica serovar Weltevreden (S. Weltevreden) is an emerging cause of diarrheal and invasive disease in humans residing in tropical regions. Despite the regional and international emergence of this Salmonella serovar, relatively little is known about its genetic diversity, genomics or virulence potential in model systems. Here we used whole genome sequencing and bioinformatics analyses to define the phylogenetic structure of a diverse global selection of S. Weltevreden. Phylogenetic analysis of more than 100 isolates demonstrated that the population of S. Weltevreden can be segregated into two main phylogenetic clusters, one associated predominantly with continental Southeast Asia and the other more internationally dispersed. Subcluster analysis suggested the local evolution of S. Weltevreden within specific geographical regions. Four of the isolates were sequenced using long read sequencing to produce high quality reference genomes. Phenotypic analysis in Hep-2 cells and in a murine infection model indicated that S. Weltevreden were significantly attenuated in these models compared to the classical S. Typhimurium reference strain SL1344. Our work outlines novel insights into this important emerging pathogen and provides a baseline understanding for future research studies. PMID:26867150

  16. Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phylogenetic relatedness among ascomycetous yeast genera (subphylum Saccharomycotina, phylum Ascomycota) has been uncertain. In the present study, type species of 70 currently recognized genera are compared from divergence in the nearly entire nuclear gene sequences for large subunit rRNA, small sub...

  17. Spatial and phylogenetic analysis of vesicular stomatitus virus overwintering in the United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    From 2004 through 2006, 751 vesicular stomatitis (VS) outbreaks caused by vesicular stomatitis virus serotype New Jersey (VSNJV) were reported in nine states of the southwestern United States. The normal model of the space scan statistic and phylogenetic techniques were used to test the hypothesis t...

  18. Using phylogenetic probes for quantification of stable isotope labeling and microbial community analysis

    SciTech Connect

    Brodie, Eoin L; DeSantis, Todd Z; Karaoz, Ulas; Andersen, Gary L

    2014-12-09

    Herein is described methods for a high-sensitivity means to measure the incorporation of stable isotope labeled substrates into RNA following stable isotope probing experiments (SIP). RNA is hybridized to a set of probes such as phylogenetic microarrays and isotope incorporation is quantified such as by secondary ion mass spectrometer imaging (NanoSIMS).

  19. Phylogenetic analysis of Citrus based on sequences of six nuclear genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrus has a long history of cultivation. The phylogenetic relationships between the different cultivars of citrus are not clearly understood because of hybridization, nucellar embryony and somatic mutations. Earlier studies on citrus taxonomy and phylogeny were based on isozymes analyses, microsate...

  20. Atlantic origin of the arctic biota? Evidence from phylogenetic and biogeographical analysis of the cheilostome bryozoan genus pseudoflustra.

    PubMed

    Kuklinski, Piotr; Taylor, Paul D; Denisenko, Nina V; Berning, Björn

    2013-01-01

    The intricate geological evolution of the Arctic Ocean is paralleled by complexities in the biogeographical and phylogenetical histories of the Arctic biota, including bryozoans. Here we present revised taxonomic descriptions for all known species of the bryozoan genus Pseudoflustra, and use the present-day distributions and phylogenetic relationships between these species to infer the historical biogeography of the genus. Nine species belonging to the genus Pseudoflustra are recognized in the Arctic and North Atlantic. One new species, previously identified as Ichthyaria aviculata, is described as Pseudoflustra radeki sp. nov. Another species, previously assigned to Smittoidea as S. perrieri, is transferred to Pseudoflustra. Biogeographical analysis of Pseudoflustra reveals that species distributions mostly match current patterns pertaining in the North Atlantic and Arctic Ocean. Distributions were probably shaped by recent geological history as present-day current directions in the Arctic Ocean are believed to have been similar for at least the last 120 000 years. Phylogenetic analysis of Pseudoflustra places the five Arctic-North Atlantic species in a clade crownward of a paraphyletic grouping of North Atlantic species. Given that the Arctic Ocean was fully glaciated until 18 000 years, the most likely explanation for this phylogeographical pattern is that species of Pseudoflustra colonized the Arctic relatively recently from North Atlantic sources. However, a fuller understanding of the origin of Pseudoflustra in the Arctic will require molecular and fossil data, neither of which are currently available.

  1. Atlantic Origin of the Arctic Biota? Evidence from Phylogenetic and Biogeographical Analysis of the Cheilostome Bryozoan Genus Pseudoflustra

    PubMed Central

    Kuklinski, Piotr; Taylor, Paul D.; Denisenko, Nina V.; Berning, Björn

    2013-01-01

    The intricate geological evolution of the Arctic Ocean is paralleled by complexities in the biogeographical and phylogenetical histories of the Arctic biota, including bryozoans. Here we present revised taxonomic descriptions for all known species of the bryozoan genus Pseudoflustra, and use the present-day distributions and phylogenetic relationships between these species to infer the historical biogeography of the genus. Nine species belonging to the genus Pseudoflustra are recognized in the Arctic and North Atlantic. One new species, previously identified as Ichthyaria aviculata, is described as Pseudoflustra radeki sp. nov. Another species, previously assigned to Smittoidea as S. perrieri, is transferred to Pseudoflustra. Biogeographical analysis of Pseudoflustra reveals that species distributions mostly match current patterns pertaining in the North Atlantic and Arctic Ocean. Distributions were probably shaped by recent geological history as present-day current directions in the Arctic Ocean are believed to have been similar for at least the last 120 000 years. Phylogenetic analysis of Pseudoflustra places the five Arctic-North Atlantic species in a clade crownward of a paraphyletic grouping of North Atlantic species. Given that the Arctic Ocean was fully glaciated until 18 000 years, the most likely explanation for this phylogeographical pattern is that species of Pseudoflustra colonized the Arctic relatively recently from North Atlantic sources. However, a fuller understanding of the origin of Pseudoflustra in the Arctic will require molecular and fossil data, neither of which are currently available. PMID:23536863

  2. [Genome-wide identification, phylogenetic analysis and expression profiling of the WOX family genes in Solanum lycopersicum].

    PubMed

    Li, Xiaoxu; Liu, Cheng; Li, Wei; Zhang, Zenglin; Gao, Xiaoming; Zhou, Hui; Guo, Yongfeng

    2016-05-01

    Members of the plant-specific WOX transcription factor family have been reported to play important roles in cell to cell communication as well as other physiological and developmental processes. In this study, ten members of the WOX transcription factor family were identified in Solanum lycopersicum with HMMER. Neighbor-joining phylogenetic tree, maximum-likelihood tree and Bayesian-inference tree were constructed and similar topologies were shown using the protein sequences of the homeodomain. Phylogenetic study revealed that the 25 WOX family members from Arabidopsis and tomato fall into three clades and nine subfamilies. The patterns of exon-intron structures and organization of conserved domains in Arabidopsis and tomato were consistent based on the phylogenetic results. Transcriptome analysis showed that the expression patterns of SlWOXs were different in different tissue types. Gene Ontology (GO) analysis suggested that, as transcription factors, the SlWOX family members could be involved in a number of biological processes including cell to cell communication and tissue development. Our results are useful for future studies on WOX family members in tomato and other plant species.

  3. Comparative analysis of DNA polymorphisms and phylogenetic relationships among Syzygium cumini Skeels based on phenotypic characters and RAPD technique.

    PubMed

    Singh, Jitendra P; Singh, Ak; Bajpai, Anju; Ahmad, Iffat Zareen

    2014-01-01

    The Indian black berry (Syzygium cumini Skeels) has a great nutraceutical and medicinal properties. As in other fruit crops, the fruit characteristics are important attributes for differentiation were also determined for different accessions of S. cumini. The fruit weight, length, breadth, length: breadth ratio, pulp weight, pulp content, seed weight and pulp: seed ratio significantly varied in different accessions. Molecular characterization was carried out using PCR based RAPD technique. Out of 80 RAPD primers, only 18 primers produced stable polymorphisms that were used to examine the phylogenetic relationship. A sum of 207 loci were generated out of which 201 loci found polymorphic. The average genetic dissimilarity was 97 per cent among jamun accessions. The phylogenetic relationship was also determined by principal coordinates analysis (PCoA) that explained 46.95 per cent cumulative variance. The two-dimensional PCoA analysis showed grouping of the different accessions that were plotted into four sub-plots, representing clustering of accessions. The UPGMA (r = 0.967) and NJ (r = 0.987) dendrogram constructed based on the dissimilarity matrix revealed a good degree of fit with the cophenetic correlation value. The dendrogram grouped the accessions into three main clusters according to their eco-geographical regions which given useful insight into their phylogenetic relationships.

  4. Two-Component Signal Transduction Systems of Desulfovibrio Vulgaris: Structural and Phylogenetic Analysis and Deduction of Putative Cognate Pairs

    SciTech Connect

    Zhang, Weiwen; Culley, David E.; Wu, Gang; Brockman, Fred J.

    2006-01-20

    ABSTRACT-Two-component signal transduction systems (TCSTS) composed of sensory histidine kinases (HK) and response regulators (RR), constitute a key element of the mechanism by which bacteria sense and respond to changes in environments. A large number of TCSTSs including 59 putative HKs and 55 RRs were identified from the Desulfovibrio vulgaris genome, indicating their important roles in regulation of cellular metabolism. In this study, the structural and phylogenetic analysis of all putative TCSTSs in D. vulgaris was performed. The results showed D. vulgaris contained an unexpectedly large number of hybrid-type HKs, implying that multiple-step phosphorelay may be a common signal transduction mechanism in D. vulgaris. Most TCSTS components of D. vulgaris were found clustered into several subfamilies previously recognized in other bacteria and extensive co-evolution between D. vulgaris HKs and RRs was observed, suggesting that the concordance of HKs and RRs in cognate phylogenetic groups could be indicative of cognate TCSTSs...

  5. Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboreum.

    PubMed

    Wang, Wei; Xia, Minxuan; Chen, Jie; Deng, Fenni; Yuan, Rui; Zhang, Xiaopei; Shen, Fafu

    2016-12-01

    The data presented in this paper is supporting the research article "Genome-Wide Analysis of Superoxide Dismutase Gene Family in Gossypium raimondii and G. arboreum" [1]. In this data article, we present phylogenetic tree showing dichotomy with two different clusters of SODs inferred by the Bayesian method of MrBayes (version 3.2.4), "Bayesian phylogenetic inference under mixed models" [2], Ramachandran plots of G. raimondii and G. arboreum SODs, the protein sequence used to generate 3D sructure of proteins and the template accession via SWISS-MODEL server, "SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information." [3] and motif sequences of SODs identified by InterProScan (version 4.8) with the Pfam database, "Pfam: the protein families database" [4].

  6. Lipid and Phylogenetic Analysis of a Gypsum-hosted Endoevaporitic Microbial Community

    NASA Astrophysics Data System (ADS)

    Turk, K. A.; Jahnke, L. L.; Green, S. J.; Kubo, M. D.; Vogel, M. B.; Des Marais, D. J.

    2007-12-01

    Gypsum evaporites host diverse, productive and volumetrically significant microbial communities and are relevant modern-day analogs to both Precambrian sabkha deposits and, potentially, Martian evaporites. Extensive evaporites form in subaqueous environments of high salinity ponds (>150 permil) maintained by the Exportadora de Sal, S. A. (ESSA) in Guerrero Negro, B.C.S., Mexico. A gypsarenite (reworked clastic gypsum) crust found along the southeast margin of ESSA's Pond 9 was collected in February 2004 and each vibrantly colored layer in the top centimeter was sampled. Extant microbial communities from each layer were characterized using complementary culture-independent molecular techniques, lipid biomarker analysis, and compound specific isotopic analysis. Coupling molecular analysis with lipid biomarker analysis revealed that oxygenic photosynthetic organisms dominate the surface layers (top 3 mm). Polar lipids from the surface layers consisted predominantly of glycolipids, which are characteristic of algae, cyanobacteria and green anoxygenic photosynthetic bacteria. Consistent with prior analyses of gypsum evaporites, 16S rRNA gene clone libraries indicate that cyanobacterial populations belong primarily to the genus Cyanothece. The bacterial community below the surface layers is more diverse and dominated by anaerobic organisms. Phototrophic purple sulfur bacteria, sulfate-reducing bacteria (SRB), and Bacteroidetes were particularly abundant. The relative abundances of SRB increased with depth; Desulfobacteraceae clones were distributed throughout the crust, but not at the surface, while Desulfovibrionaceae clones were found predominantly in the deepest layers. These molecular results are consistent with fatty acid biomarker analysis. δ13C values of major lipid classes in the crust and sediment range from 14 to 36‰, which is considerably lower than corresponding values for benthic Microcoleus-dominated cyanobacterial mats found at lower salinities at ESSA

  7. Sequence and phylogenetic analysis of surface protein genes of emerging H9N2 influenza viruses isolated from poultry in two geographical regions of China.

    PubMed

    Xue, Yu; Wang, Jing-Lan; Yan, Zhuan-Qiang; Li, Guang-Wei; Chen, Shun-Yan; Zhang, Xiang-Bin; Qin, Jian-Ping; Li, Hai-Yan; Chang, Shuang; Chen, Feng; Bee, Ying-Zuo; Xie, Qing-Mei

    2014-06-01

    Subtype H9N2 avian influenza viruses (AIVs) circulating in China have aroused increasing concerns for their impact on poultry and risk to public health. The present study was an attempt to elucidate the phylogenetic relationship of H9N2 AIVs in two geographically distinct regions of China where vaccination is routinely practiced. A total of 18 emerging H9N2 isolates were identified and genetically characterized. Phylogenetic analysis of hemagglutinin (HA) and neuraminidase (NA) genes confirmed that the isolates belonged to the Y280 lineage. Based on the HA genes, the isolates were subdivided into two subgroups. The viruses from Zhejiang Province were clustered together in Group I, while the isolates from Guangdong Province were clustered together in Group II. Antigenic characterization showed that the tested viruses were antigenically different when compared to the current used vaccine strain. It was notable that 14 out of total 18 isolates had an amino acid exchange (Q→L) at position 216 (226 by H3 Numbering) in the receptor-binding site, which indicated that the virus had potential affinity of binding to human like receptor. These results suggest that the emerging viruses have potential risk to public health than previously thought. Therefore, continuous surveillance studies of H9N2 influenza virus are very important to the prognosis and control of future influenza pandemics.

  8. Elongation factor-1 alpha occurs as two copies in bees: implications for phylogenetic analysis of EF-1 alpha sequences in insects.

    PubMed

    Danforth, B N; Ji, S

    1998-03-01

    We report the complete sequence of a paralogous copy of elongation factor-1 alpha (EF-1 alpha) in the honeybee, Apis mellifera (Hymenoptera: Apidae). This copy differs from a previously described copy in the positions of five introns and in 25% of the nucleotide sites in the coding regions. The existence of two paralogous copies of EF-1 alpha in Drosophila and Apis suggests that two copies of EF-1 alpha may be widespread in the holometabolous insect orders. To distinguish between a single, ancient gene duplication and parallel, independent fly and bee gene duplications, we performed a phylogenetic analysis of hexapod EF-1 alpha sequences. Unweighted parsimony analysis of nucleotide sequences suggests an ancient gene duplication event, whereas weighted parsimony analysis of nucleotides and unweighted parsimony analysis of amino acids suggests the contrary: that EF-1 alpha underwent parallel gene duplications in the Diptera and the Hymenoptera. The hypothesis of parallel gene duplication is supported both by congruence among nucleotide and amino acid data sets and by topology-dependent permutation tail probability (T-PTP) tests. The resulting tree topologies are also congruent with current views on the relationships among the holometabolous orders included in this study (Diptera, Hymenoptera, and Lepidoptera). More sequences, from diverse orders of holometabolous insects, will be needed to more accurately assess the historical patterns of gene duplication in EF-1 alpha.

  9. Phylogenetic Analysis Supports Horizontal Transmission as a Driving Force of the Spread of Avian Bornaviruses

    PubMed Central

    Rubbenstroth, Dennis; Schmidt, Volker; Rinder, Monika; Legler, Marko; Twietmeyer, Sönke; Schwemmer, Phillip; Corman, Victor M.

    2016-01-01

    Background Avian bornaviruses are a genetically diverse group of viruses initially discovered in 2008. They are known to infect several avian orders. Bornaviruses of parrots and related species (Psittaciformes) are causative agents of proventricular dilatation disease, a chronic and often fatal neurologic disease widely distributed in captive psittacine populations. Although knowledge has considerably increased in the past years, many aspects of the biology of avian bornaviruses are still undiscovered. In particular, the precise way of transmission remains unknown. Aims and Methods In order to collect further information on the epidemiology of bornavirus infections in birds we collected samples from captive and free-ranging aquatic birds (n = 738) and Passeriformes (n = 145) in Germany and tested them for the presence of bornaviruses by PCR assays covering a broad range of known bornaviruses. We detected aquatic bird bornavirus 1 (ABBV-1) in three out of 73 sampled free-ranging mute swans (Cygnus olor) and one out of 282 free-ranging Eurasian oystercatchers (Haematopus ostralegus). Canary bornavirus 1 (CnBV-1), CnBV-2 and CnBV-3 were detected in four, six and one out of 48 captive common canaries (Serinus canaria forma domestica), respectively. In addition, samples originating from 49 bornavirus-positive captive Psittaciformes were used for determination of parrot bornavirus 2 (PaBV-2) and PaBV-4 sequences. Bornavirus sequences compiled during this study were used for phylogenetic analysis together with all related sequences available in GenBank. Results of the Study Within ABBV-1, PaBV-2 and PaBV-4, identical or genetically closely related bornavirus sequences were found in parallel in various different avian species, suggesting that inter-species transmission is frequent relative to the overall transmission of these viruses. Our results argue for an important role of horizontal transmission, but do not exclude the additional possibility of vertical transmission

  10. Morphological and molecular convergences in mammalian phylogenetics.

    PubMed

    Zou, Zhengting; Zhang, Jianzhi

    2016-09-02

    Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies. However, neither the validity of this belief nor its underlying cause is known. Here comparing thousands of characters of each type that have been used for inferring the phylogeny of mammals, we find that on average morphological characters indeed experience much more convergences than amino acid sites, but this disparity is explained by fewer states per character rather than an intrinsically higher susceptibility to convergence for morphologies than sequences. We show by computer simulation and actual data analysis that a simple method for identifying and removing convergence-prone characters improves phylogenetic accuracy, potentially enabling, when necessary, the inclusion of morphologies and hence fossils for reliable tree inference.

  11. Morphological and molecular convergences in mammalian phylogenetics

    PubMed Central

    Zou, Zhengting; Zhang, Jianzhi

    2016-01-01

    Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies. However, neither the validity of this belief nor its underlying cause is known. Here comparing thousands of characters of each type that have been used for inferring the phylogeny of mammals, we find that on average morphological characters indeed experience much more convergences than amino acid sites, but this disparity is explained by fewer states per character rather than an intrinsically higher susceptibility to convergence for morphologies than sequences. We show by computer simulation and actual data analysis that a simple method for identifying and removing convergence-prone characters improves phylogenetic accuracy, potentially enabling, when necessary, the inclusion of morphologies and hence fossils for reliable tree inference. PMID:27585543

  12. PHYLOGENETIC ANALYSIS OF 16S RRNA GENE SEQUENCES REVEALS THE PREVALENCE OF MYCOBACTERIA SP., ALPHA-PROTEOBACTERIA, AND UNCULTURED BACTERIA IN DRINKING WATER MICROBIAL COMMUNITIES

    EPA Science Inventory

    Previous studies have shown that culture-based methods tend to underestimate the densities and diversity of bacterial populations inhabiting water distribution systems (WDS). In this study, the phylogenetic diversity of drinking water bacteria was assessed using sequence analysis...

  13. Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis.

    PubMed

    Johnson, James R; Owens, Krista L; Clabots, Connie R; Weissman, Scott J; Cannon, Steven B

    2006-06-01

    The evolutionary origins of extraintestinal pathogenic Escherichia coli (ExPEC) remain uncertain despite these organisms' relevance to human disease. A valid understanding of ExPEC phylogeny is needed as a framework against which the observed distribution of virulence factors and clinical associations can be analyzed. Accordingly, phylogenetic relationships were defined by multi-locus sequence analysis among 44 representatives of selected ExPEC clonal groups and the E. coli Reference (ECOR) collection. Recombination, which significantly obscured the phylogenetic signal for several strains, was dealt with by excluding strains or specific sequences. Conflicting overall phylogenies, and internal phylogenies for virulence-associated phylogenetic group B2, were inferred depending on the specific dataset (i.e., how extensively purged of recombination), outgroup (Salmonella enterica and/or Escherichia fergusonii), and analysis method (neighbor joining, maximum parsimony, maximum likelihood, or Bayesian likelihood). Nonetheless, the major E. coli phylogenetic groups A, B1, and B2 were consistently well resolved, as was a major sub-component of group D and an ECOR 37-O157:H7 clade. Moreover, nine important ExPEC clonal groups within groups B2 and D, characterized by serotypes O6:K2:H1, O18:K1:H7, O6:H31, and O4:K+:H+ (from group B2), and O1:K1:H-, O7:K1:H-, O157:K+:H (non-7), O15:K52:H1, and O11/17/77:K52:H18 ("clonal group A") (from group D), were consistently well resolved, regardless of clinical background (cystitis, pyelonephritis, neonatal meningitis, sepsis, or fecal), host group, geographical origin, and virulence profile. Among the group B2-derived clonal groups the O6:K2:H1 clade appeared basal. Within group D, "clonal group A" and the O15:K52:H1 clonal group were consistently placed with ECOR 47 and ECOR 44, respectively, as nearest neighbors. These findings clarify phylogenetic relationships among key ExPEC clonal groups but also emphasize that recombination

  14. Phylogenetic analysis of the Black Stork Ciconia nigra (Ciconiiformes: Ciconiidae) based on complete mitochondrial genome.

    PubMed

    Liu, Mengyao; Kang, Chunlan; Yan, Chaochao; Huang, Ting; Song, Xuhao; Zhang, Xiuyue; Yue, Bisong; Zeng, Tao

    2016-01-01

    The Black Stork, Ciconia nigra belongs to family Ciconiidae, which is evaluated as Least Concern by IUCN. In this study, the complete mitochondrial genome of C. nigra was first sequenced and characterized, which was 17,795 bp in length. The mt-genome has tandem repeats of 80 bp and 78 bp repeat units, and AAACAAC and AAACAAACAAC tandem repeats in D-loop region. It is notable that a single extra base "C" at position 174 was inserted in gene ND3. Bayesian inference, maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand protein-coding genes. Phylogenetic analyses showed that Ardeidae diverged earlier than Ciconiidae, Cathartida and Threskiornithidae, and Ciconiidae had closest relationship to Cathartida. C. nigra diverged first among three Ciconia birds.

  15. Phylogenetic analysis and delineation of phytoplasmas based on the secY gene

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The secY gene, located in the operator-distal part of the spc ribosomal protein operon, codes for a protein translocase subunit secY. The secY gene sequence is more variable than that of the 16S rRNA gene. Comparative phylogenetic analyses with 16S rRNA and secY gene sequences from 80 and 83 phytop...

  16. Evaluating the Phylogenetic Status of the Extinct Japanese Otter on the Basis of Mitochondrial Genome Analysis.

    PubMed

    Waku, Daisuke; Segawa, Takahiro; Yonezawa, Takahiro; Akiyoshi, Ayumi; Ishige, Taichiro; Ueda, Miya; Ogawa, Hiroshi; Sasaki, Hiroshi; Ando, Motokazu; Kohno, Naoki; Sasaki, Takeshi

    2016-01-01

    The Japanese otter lived throughout four main Japanese islands, but it has not been observed in the wild since 1979 and was declared extinct in 2012. Although recent taxonomic and molecular phylogenetic studies suggest that it should be treated as an independent species, International Union for Conservation of Nature Red List considers it as subspecies of Lutra lutra. Therefore, the taxonomic status of this species needs to be resolved. Here we determined the complete mitochondrial genome of two Japanese otters caught in Kanagawa and Kochi prefectures and five Eurasian otters (L. lutra). We reconstructed a molecular phylogenetic tree to estimate the phylogenetic position of the Japanese otter in Lutrinae using the Japanese otters and the other 11 Lutrinae species on the basis of ND5 (692 bp) and cytochrome b (1,140 bp) sequences. We observed that the two Japanese otters had close relationships with Eurasian otters, forming a monophyletic group (100% bootstrap probability). To elucidate detailed phylogenetic relationships among the Japanese and Eurasian otters, we reconstructed a maximum likelihood tree according to mitochondrial genome sequences (14,740 bp). The Japanese otter (JO1) collected in Kanagawa was deeply nested in the Eurasian otter clade, whereas the Japanese otter (JO2) collected in Kochi formed a distinct independent lineage in the Lutra clade. The estimated molecular divergences time for the ancestral lineages of the Japanese otters was 0.10 Ma (95%: 0.06-0.16 Ma) and 1.27 Ma (95%: 0.98-1.59 Ma) for JO1 and JO2 lineages, respectively. Thus, JO1 was identified as a member of L. lutra; JO2 represented the old Japanese otter lineage, which may be a distinct new species or subspecies of Lutra. We suggest that the ancestral population of the JO2 lineage migrated to Japan via the land bridge that existed between western Japanese islands and Asian continent at 1.27 Ma.

  17. Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park

    SciTech Connect

    Reysenbach, A.L.; Wickham, G.S.; Pace, N.R.

    1994-06-01

    This study uses a molecular phylogenetic approach to characterize the pink filament community at the outflow of Octopus Spring in Yellowstone National Park. The temperature range of the spring is from 84 to 88 C. The authors show that the pink filaments are most closely related to the hydrogen-oxidizing bacterium Aquifex pyrophilus and a close relative Hydrogenobacter thermophilus. 38 refs., 4 figs., 1 tab.

  18. Phylogenetic analysis of feline immunodeficiency virus in feral and companion domestic cats of New Zealand.

    PubMed

    Hayward, Jessica J; Taylor, John; Rodrigo, Allen G

    2007-03-01

    Nested PCR was used to amplify envelope V3-V6 gene fragments of feline immunodeficiency virus (FIV) from New Zealand cats. Phylogenetic analyses established that subtypes A and C predominate among New Zealand cats, with clear evidence of intersubtype recombination. In addition, 17 sequences were identified that were distinct from all known FIV clades, and we tentatively suggest these belong to a novel subtype.

  19. Evaluating the Phylogenetic Status of the Extinct Japanese Otter on the Basis of Mitochondrial Genome Analysis

    PubMed Central

    Waku, Daisuke; Segawa, Takahiro; Yonezawa, Takahiro; Akiyoshi, Ayumi; Ishige, Taichiro; Ueda, Miya; Ogawa, Hiroshi; Sasaki, Hiroshi; Ando, Motokazu; Kohno, Naoki; Sasaki, Takeshi

    2016-01-01

    The Japanese otter lived throughout four main Japanese islands, but it has not been observed in the wild since 1979 and was declared extinct in 2012. Although recent taxonomic and molecular phylogenetic studies suggest that it should be treated as an independent species, International Union for Conservation of Nature Red List considers it as subspecies of Lutra lutra. Therefore, the taxonomic status of this species needs to be resolved. Here we determined the complete mitochondrial genome of two Japanese otters caught in Kanagawa and Kochi prefectures and five Eurasian otters (L. lutra). We reconstructed a molecular phylogenetic tree to estimate the phylogenetic position of the Japanese otter in Lutrinae using the Japanese otters and the other 11 Lutrinae species on the basis of ND5 (692 bp) and cytochrome b (1,140 bp) sequences. We observed that the two Japanese otters had close relationships with Eurasian otters, forming a monophyletic group (100% bootstrap probability). To elucidate detailed phylogenetic relationships among the Japanese and Eurasian otters, we reconstructed a maximum likelihood tree according to mitochondrial genome sequences (14,740 bp). The Japanese otter (JO1) collected in Kanagawa was deeply nested in the Eurasian otter clade, whereas the Japanese otter (JO2) collected in Kochi formed a distinct independent lineage in the Lutra clade. The estimated molecular divergences time for the ancestral lineages of the Japanese otters was 0.10 Ma (95%: 0.06–0.16 Ma) and 1.27 Ma (95%: 0.98–1.59 Ma) for JO1 and JO2 lineages, respectively. Thus, JO1 was identified as a member of L. lutra; JO2 represented the old Japanese otter lineage, which may be a distinct new species or subspecies of Lutra. We suggest that the ancestral population of the JO2 lineage migrated to Japan via the land bridge that existed between western Japanese islands and Asian continent at 1.27 Ma. PMID:26938434

  20. Multigene analysis of phylogenetic relationships and divergence times of primate sucking lice (Phthiraptera: Anoplura).

    PubMed

    Light, Jessica E; Reed, David L

    2009-02-01

    Cospeciation between hosts and parasites offers a unique opportunity to use information from parasites to infer events in host evolutionary history. Although lice (Insecta: Phthiraptera) are known to cospeciate with their hosts and have frequently served as important markers to infer host evolutionary history, most molecular studies are based on only one or two markers. Resulting phylogenies may, therefore, represent gene histories (rather than species histories), and analyses of multiple molecular markers are needed to increase confidence in the results of phylogenetic analyses. Herein, we phylogenetically examine nine molecular markers in primate sucking lice (Phthiraptera: Anoplura) and we use these markers to estimate divergence times among louse lineages. Individual and combined analyses of these nine markers are, for the most part, congruent, supporting relationships hypothesized in previous studies. Only one marker, the nuclear protein-coding gene Histone 3, has a significantly different tree topology compared to the other markers. The disparate evolutionary history of this marker, however, has no significant effect on topology or nodal support in the combined phylogenetic analyses. Therefore, phylogenetic results from the combined data set likely represent a solid hypothesis of species relationships. Additionally, we find that simultaneous use of multiple markers and calibration points provides the most reliable estimates of louse divergence times, in agreement with previous studies estimating divergences among species. Estimates of phylogenies and divergence times also allow us to verify the results of [Reed, D.L., Light, J.E., Allen, J.M., Kirchman, J.J., 2007. Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice. BMC Biol. 5, 7.]; there was probable contact between gorilla and archaic hominids roughly 3 Ma resulting in a host switch of Pthirus lice from gorillas to archaic hominids. Thus, these results provide

  1. Phylogenetic analysis of fungal heterotrimeric G protein-encoding genes and their expression during dimorphism in Mucor circinelloides.

    PubMed

    Valle-Maldonado, Marco Iván; Jácome-Galarza, Irvin Eduardo; Díaz-Pérez, Alma Laura; Martínez-Cadena, Guadalupe; Campos-García, Jesús; Ramírez-Díaz, Martha Isela; Reyes-De la Cruz, Homero; Riveros-Rosas, Héctor; Díaz-Pérez, César; Meza-Carmen, Víctor

    2015-12-01

    In fungi, heterotrimeric G proteins are key regulators of biological processes such as mating, virulence, morphology, among others. Mucor circinelloides is a model organism for many biological processes, and its genome contains the largest known repertoire of genes that encode putative heterotrimeric G protein subunits in the fungal kingdom: twelve Gα (McGpa1-12), three Gβ (McGpb1-3), and three Gγ (McGpg1-3). Phylogenetic analysis of fungal Gα showed that they are divided into four distinct groups as reported previously. Fungal Gβ and Gγ are also divided into four phylogenetic groups, and to our understanding this is the first report of a phylogenetic classification for fungal Gβ and Gγ subunits. Almost all genes that encode putative heterotrimeric G subunits in M. circinelloides are differentially expressed during dimorphic growth, except for McGpg1 (Gγ) that showed very low mRNA levels at all developmental stages. Moreover, several of the subunits are expressed in a similar pattern and at the same level, suggesting that they constitute discrete complexes. For example, McGpb3 (Gβ), and McGpg2 (Gγ), are co-expressed during mycelium growth, and McGpa1, McGpb2, and McGpg2, are co-expressed during yeast development. These findings provide the conceptual framework to study the biological role of these genes during M. circinelloides morphogenesis.

  2. Phylogenetic and evolutionary analysis of NBS-encoding genes in Rosaceae fruit crops.

    PubMed

    Xu, Qiang; Wen, Xiaopeng; Deng, Xiuxin

    2007-07-01

    Phylogenetic relationships of the nucleotide binding site (NBS)-encoding resistance gene homologues (RGHs) among 12 species in five genera of Rosaceae fruit crops were evaluated. A total of 228 Rosaceous RGHs were deeply separated into two distinct clades, designated as TIR (sequences within this clade containing a Toll Interleukin-1 Receptor domain) and NonTIR (sequences lacking a TIR domain). Most Rosaceous RGH genes were phylogenetically distinct from Arabidopsis, Rice or Pine genes, except for a few Rosaceous members which grouped closely with Arabidopsis genes. Within Rosaceae, sequences from multiple species were often phylogenetically clustered together, forming heterogenous groups, however, apple- and chestnut rose-specific groups really exist. Gene duplication followed by sequence divergence were proposed as the mode for the evolution of a large number of distantly or closely related RGH genes in Rosaceae, and this mode may play a role in the generation of new resistance specificity. Positively selected sites within NBS-coding region were detected and thus nucleotide variation within NBS domain may function in determining disease resistance specificity. This study also discusses the synteny of a genomic region that encompass powdery mildew resistance locus among Malus, Prunus and Rosa, which may have potential use for fruit tree disease breeding and important gene cloning.

  3. Chromosome evolution in the annual killifish genus Cynolebias and mitochondrial phylogenetic analysis.

    PubMed

    García, G; Lalanne, A I; Aguirre, G; Cappetta, M

    2001-01-01

    Extensive chromosome variation involving Robertsonian and non-Robertsonian changes were proposed to explain chromosomal evolution within killifishes of the aplocheiloid group belonging to the order Cyprinodontiforms. In the present work we describe the karyotypes of four Cynolebias species and analyze chromosome changes by means of mitochondrial phylogenetic studies, including 10 taxa of this genus. Diploid numbers varied from 48 to 44 and the number of chromosome arms from 50 to 54. Molecular phylogenetic analyses allow us to corroborate previous hypothesis about chromosome evolution in aplocheiloid fishes. The tree topology based on a combined dataset of mitochondrial cytochrome b and 12S genes shows that recent cladogenetic events within the genus Cynolebias could have occurred by allopatric or 'in-situ' differentiation involving chromosomal rearrangements. Our analyses of approximately 10% of mitochondrial genome can be helpful in determining these recent cladogenetic events but it showed limited phylogenetic resolution at intermediate levels of divergence. This can be explained in part by the high levels of DNA sequence divergence (ranging from 0.015 to 0.245) detected at intrageneric level. Different methodological approaches suggest that chromosomal changes in Cynolebias have occurred during their differentiation, supporting the hypothesis that the unresolved basal polytomy could be the result of rapid speciation events, like a true 'star polytomy'.

  4. Taxonomic review and phylogenetic analysis of fifteen North American Entomobrya (Collembola, Entomobryidae), including four new species

    PubMed Central

    Katz, Aron D.; Giordano, Rosanna; Soto-Adames, Felipe

    2015-01-01

    Abstract The chaetotaxy of 15 species of eastern North American Entomobrya is redescribed in order to determine potential characters for the diagnosis of cryptic lineages and evaluate the diagnostic and phylogenetic utility of chaetotaxy. As a result, four new species (Entomobrya citrensis Katz & Soto-Adames, sp. n., Entomobrya jubata Katz & Soto-Adames, sp. n., Entomobrya neotenica Katz & Soto-Adames, sp. n. and Entomobrya unifasciata Katz & Soto-Adames, sp. n.) are described, and new diagnoses are provided for Entomobrya assuta Folsom, Entomobrya atrocincta Schött, Entomobrya decemfasciata (Packard), Entomobrya ligata Folsom, Entomobrya multifasciata (Tullberg), and Entomobrya quadrilineata (Bueker). Furthermore, previously undocumented levels of intraspecific variation in macrosetal pattern are reported, tempering the exclusive use of chaetotaxy for species delimitation. Phylogenetic relationships, estimated using both morphological and molecular data, indicate that Entomobrya is likely paraphyletic. The phylogenies also suggest that unreliable character homology, likely fostered by Entomobrya’s profusion of macrosetae, may limit the phylogenetic utility of chaetotaxy in groups characterized by an abundance of dorsal macrosetae. PMID:26487816

  5. Taxonomic review and phylogenetic analysis of fifteen North American Entomobrya (Collembola, Entomobryidae), including four new species.

    PubMed

    Katz, Aron D; Giordano, Rosanna; Soto-Adames, Felipe

    2015-01-01

    The chaetotaxy of 15 species of eastern North American Entomobrya is redescribed in order to determine potential characters for the diagnosis of cryptic lineages and evaluate the diagnostic and phylogenetic utility of chaetotaxy. As a result, four new species (Entomobrya citrensis Katz & Soto-Adames, sp. n., Entomobrya jubata Katz & Soto-Adames, sp. n., Entomobrya neotenica Katz & Soto-Adames, sp. n. and Entomobrya unifasciata Katz & Soto-Adames, sp. n.) are described, and new diagnoses are provided for Entomobrya assuta Folsom, Entomobrya atrocincta Schött, Entomobrya decemfasciata (Packard), Entomobrya ligata Folsom, Entomobrya multifasciata (Tullberg), and Entomobrya quadrilineata (Bueker). Furthermore, previously undocumented levels of intraspecific variation in macrosetal pattern are reported, tempering the exclusive use of chaetotaxy for species delimitation. Phylogenetic relationships, estimated using both morphological and molecular data, indicate that Entomobrya is likely paraphyletic. The phylogenies also suggest that unreliable character homology, likely fostered by Entomobrya's profusion of macrosetae, may limit the phylogenetic utility of chaetotaxy in groups characterized by an abundance of dorsal macrosetae.

  6. Complete Mitochondrial Genome of the Red Fox (Vuples vuples) and Phylogenetic Analysis with Other Canid Species.

    PubMed

    Zhong, Hua-Ming; Zhang, Hong-Hai; Sha, Wei-Lai; Zhang, Cheng-De; Chen, Yu-Cai

    2010-04-01

    The whole mitochondrial genome sequence of red fox (Vuples vuples) was determined. It had a total length of 16 723 bp. As in most mammal mitochondrial genome, it contained 13 protein coding genes, two ribosome RNA genes, 22 transfer RNA genes and one control region. The base composition was 31.3% A, 26.1% C, 14.8% G and 27.8% T, respectively. The codon usage of red fox, arctic fox, gray wolf, domestic dog and coyote followed the same pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 3 gene in the red fox. A long tandem repeat rich in AC was found between conserved sequence block 1 and 2 in the control region. In order to confirm the phylogenetic relationships of red fox to other canids, phylogenetic trees were reconstructed by neighbor-joining and maximum parsimony methods using 12 concatenated heavy-strand protein-coding genes. The result indicated that arctic fox was the sister group of red fox and they both belong to the red fox-like clade in family Canidae, while gray wolf, domestic dog and coyote belong to wolf-like clade. The result was in accordance with existing phylogenetic results.

  7. Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity.

    PubMed

    Buckley, Thomas R; James, Sam; Allwood, Julia; Bartlam, Scott; Howitt, Robyn; Prada, Diana

    2011-01-01

    We have constructed the first ever phylogeny for the New Zealand earthworm fauna (Megascolecinae and Acanthodrilinae) including representatives from other major continental regions. Bayesian and maximum likelihood phylogenetic trees were constructed from 427 base pairs from the mitochondrial large subunit (16S) rRNA gene and 661 base pairs from the nuclear large subunit (28S) rRNA gene. Within the Acanthodrilinae we were able to identify a number of well-supported clades that were restricted to continental landmasses. Estimates of nodal support for these major clades were generally high, but relationships among clades were poorly resolved. The phylogenetic analyses revealed several independent lineages in New Zealand, some of which had a comparable phylogenetic depth to monophyletic groups sampled from Madagascar, Africa, North America and Australia. These results are consistent with at least some of these clades having inhabited New Zealand since rifting from Gondwana in the Late Cretaceous. Within the New Zealand Acanthodrilinae, major clades tended to be restricted to specific regions of New Zealand, with the central North Island and Cook Strait representing major biogeographic boundaries. Our field surveys of New Zealand and subsequent identification has also revealed extensive cryptic taxonomic diversity with approximately 48 new species sampled in addition to the 199 species recognized by previous authors. Our results indicate that further survey and taxonomic work is required to establish a foundation for future biogeographic and ecological research on this vitally important component of the New Zealand biota.

  8. Phenotypic Microdiversity and Phylogenetic Signal Analysis of Traits Related to Social Interaction in Bacillus spp. from Sediment Communities.

    PubMed

    Rodríguez-Torres, María Dolores; Islas-Robles, África; Gómez-Lunar, Zulema; Delaye, Luis; Hernández-González, Ismael; Souza, Valeria; Travisano, Michael; Olmedo-Álvarez, Gabriela

    2017-01-01

    Understanding the relationship between phylogeny and predicted traits is important to uncover the dimension of the predictive power of a microbial composition approach. Numerous works have addressed the taxonomic composition of bacteria in communities, but little is known about trait heterogeneity in closely related bacteria that co-occur in communities. We evaluated a sample of 467 isolates from the Churince water system of the Cuatro Cienegas Basin (CCB), enriched for Bacillus spp. The 16S rRNA gene revealed a random distribution of taxonomic groups within this genus among 11 sampling sites. A subsample of 141 Bacillus spp. isolates from sediment, with seven well-represented species was chosen to evaluate the heterogeneity and the phylogenetic signal of phenotypic traits that are known to diverge within small clades, such as substrate utilization, and traits that are conserved deep in the lineage, such as prototrophy, swarming and biofilm formation. We were especially interested in evaluating social traits, such as swarming and biofilm formation, for which cooperation is needed to accomplish a multicellular behavior and for which there is little information from natural communities. The phylogenetic distribution of traits, evaluated by the Purvis and Fritz's D statistics approached a Brownian model of evolution. Analysis of the phylogenetic relatedness of the clusters of members sharing the trait using consenTRAIT algorithm, revealed more clustering and deeper phylogenetic signal for prototrophy, biofilm and swimming compared to the data obtained for substrate utilization. The explanation to the observed Brownian evolution of social traits could be either loss due to complete dispensability or to compensated trait loss due to the availability of public goods. Since many of the evaluated traits can be considered to be collective action traits, such as swarming, motility and biofilm formation, the observed microdiversity within taxonomic groups might be explained

  9. Molecular and phylogenetic analysis of HIV-1 variants circulating among injecting drug users in Mashhad-Iran.

    PubMed

    Naderi, H R; Tagliamonte, M; Tornesello, M L; Ciccozzi, M; Rezza, G; Farid, R; Buonaguro, F M; Buonaguro, L

    2006-09-19

    Genetic and phylogenetic information on the HIV-1 epidemic in Middle-East Countries, and in particular in Iran, are extremely limited. By March 2004, the Iranian Ministry of Health officially reported a cumulative number of 6'532 HIV positive individuals and 214 AIDS cases in the Iranian HIV-1 epidemic. The intra-venous drug users (IDUs) represent the group at highest risk for HIV-1 infection in Iran, accounting for almost 63% of all HIV-infected population. In this regards, a molecular phylogenetic study has been performed on a sentinel cohort of HIV-1 seropositive IDUs enrolled at the end of 2005 at the University of Mashhad, the largest city North East of Tehran. The study has been performed on both gag and env subgenomic regions amplified by Polymerase Chain Reaction (PCR) from peripheral blood mononuclear cells (PBMCs) and characterized by direct DNA sequence analysis. The results reported here show that the HIV-1 subtype A is circulating in this IDUs sentinel cohort. Moreover, the single phylogenetic cluster as well as the intra-group low nucleotide divergence is indicative of a recent outbreak. Unexpectedly, the Iranian samples appear to be phylogenetically derived from African Sub-Saharan subtype A viruses, raising stirring speculations on HIV-1 introduction into the IDUs epidemic in Mashhad. This sentinel study could represent the starting point for a wider molecular survey of the HIV-1 epidemics in Iran to evaluate in detail the distribution of genetic subtypes and possible natural drug-resistant variants, which are extremely helpful information to design diagnostic and therapeutic strategies.

  10. Phenotypic Microdiversity and Phylogenetic Signal Analysis of Traits Related to Social Interaction in Bacillus spp. from Sediment Communities

    PubMed Central

    Rodríguez-Torres, María Dolores; Islas-Robles, África; Gómez-Lunar, Zulema; Delaye, Luis; Hernández-González, Ismael; Souza, Valeria; Travisano, Michael; Olmedo-Álvarez, Gabriela

    2017-01-01

    Understanding the relationship between phylogeny and predicted traits is important to uncover the dimension of the predictive power of a microbial composition approach. Numerous works have addressed the taxonomic composition of bacteria in communities, but little is known about trait heterogeneity in closely related bacteria that co-occur in communities. We evaluated a sample of 467 isolates from the Churince water system of the Cuatro Cienegas Basin (CCB), enriched for Bacillus spp. The 16S rRNA gene revealed a random distribution of taxonomic groups within this genus among 11 sampling sites. A subsample of 141 Bacillus spp. isolates from sediment, with seven well-represented species was chosen to evaluate the heterogeneity and the phylogenetic signal of phenotypic traits that are known to diverge within small clades, such as substrate utilization, and traits that are conserved deep in the lineage, such as prototrophy, swarming and biofilm formation. We were especially interested in evaluating social traits, such as swarming and biofilm formation, for which cooperation is needed to accomplish a multicellular behavior and for which there is little information from natural communities. The phylogenetic distribution of traits, evaluated by the Purvis and Fritz’s D statistics approached a Brownian model of evolution. Analysis of the phylogenetic relatedness of the clusters of members sharing the trait using consenTRAIT algorithm, revealed more clustering and deeper phylogenetic signal for prototrophy, biofilm and swimming compared to the data obtained for substrate utilization. The explanation to the observed Brownian evolution of social traits could be either loss due to complete dispensability or to compensated trait loss due to the availability of public goods. Since many of the evaluated traits can be considered to be collective action traits, such as swarming, motility and biofilm formation, the observed microdiversity within taxonomic groups might be explained

  11. Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

    PubMed Central

    2011-01-01

    Background With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity. Results In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses. Conclusion A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance

  12. Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environments.

    PubMed

    Hamamura, N; Macur, R E; Korf, S; Ackerman, G; Taylor, W P; Kozubal, M; Reysenbach, A-L; Inskeep, W P

    2009-02-01

    The identification and characterization of genes involved in the microbial oxidation of arsenite will contribute to our understanding of factors controlling As cycling in natural systems. Towards this goal, we recently characterized the widespread occurrence of aerobic arsenite oxidase genes (aroA-like) from pure-culture bacterial isolates, soils, sediments and geothermal mats, but were unable to detect these genes in all geothermal systems where we have observed microbial arsenite oxidation. Consequently, the objectives of the current study were to measure arsenite-oxidation rates in geochemically diverse thermal habitats in Yellowstone National Park (YNP) ranging in pH from 2.6 to 8, and to identify corresponding 16S rRNA and aroA genotypes associated with these arsenite-oxidizing environments. Geochemical analyses, including measurement of arsenite-oxidation rates within geothermal outflow channels, were combined with 16S rRNA gene and aroA functional gene analysis using newly designed primers to capture previously undescribed aroA-like arsenite oxidase gene diversity. The majority of bacterial 16S rRNA gene sequences found in acidic (pH 2.6-3.6) Fe-oxyhydroxide microbial mats were closely related to Hydrogenobaculum spp. (members of the bacterial order Aquificales), while the predominant sequences from near-neutral (pH 6.2-8) springs were affiliated with other Aquificales including Sulfurihydrogenibium spp., Thermocrinis spp. and Hydrogenobacter spp., as well as members of the Deinococci, Thermodesulfobacteria and beta-Proteobacteria. Modified primers designed around previously characterized and newly identified aroA-like genes successfully amplified new lineages of aroA-like genes associated with members of the Aquificales across all geothermal systems examined. The expression of Aquificales aroA-like genes was also confirmed in situ, and the resultant cDNA sequences were consistent with aroA genotypes identified in the same environments. The aroA sequences

  13. Molecular cloning, expression pattern, and phylogenetic analysis of a tetraspanin CD82-like molecule in lamprey Lampetra japonica.

    PubMed

    Zhang, Xiaoping; Song, Xueying; Su, Peng; Gou, Meng; Wang, Hao; Liu, Xin; Li, Qingwei

    2016-03-01

    CD82, a member of the tetraspanins, is originally identified as an accessory molecule in T cell activation, and it participates in the formation of immune synapse both in T cells and antigen-presenting cells of jawed vertebrates. In the present study, a CD82 homologous complementary DNA (cDNA) sequence is identified in the lamprey Lampetra japonica. The open reading frame of this sequence is 801 bp long and encodes a 266-amino acid protein. The multialignment of this sequence with several typical CD82s and CD37s of jawed vertebrates shows that it also possesses their conserved four transmembrane domains and a six-cysteine motif Cys-Cys-Gly…Cys-Ser-Cys…Cys…Cys, which is a characteristic motif of CD82 and CD37 vertebrate tetraspanin sequences. Since it is close to CD82s in sequence similarity, we name it as Lja-CD82-like. From the distribution profile of the conserved motifs of CD82-like, CD82, and CD37 molecules from molluscas to mammals, it seems that the CD82s and CD37s evolved from a common ancestral gene through a gene duplication event to their modern forms by a short insertion or substitution approaches. The phylogenetic analysis indicated that CD82 and CD37 molecules of jawed vertebrates originated from a common ancestral gene which is close to agnathan CD82-like and evolved into two distinct paralogous groups maybe after the divergence of jawed and jawless vertebrates. An expression vector with trigger factor (TF) was constructed to ensure that Lja-CD82-like express in prokaryotic expression host. The expressions of Lja-CD82-like messenger RNA (mRNA) and protein in immune-related tissues of lamprey were detected by real-time quantitative polymerase chain reaction and western blotting. Results showed that the mRNA and the protein levels of Lja-CD82-like were significantly upregulated in lymphocyte-like cells, gills, and supraneural myeloid bodies after stimulation with mixed antigens, respectively. Our data provided a foundation for the further study

  14. Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: biochemical properties, structural analysis, and phylogenetic relationships.

    PubMed

    Beloqui, Ana; Pita, Marcos; Polaina, Julio; Martínez-Arias, Arturo; Golyshina, Olga V; Zumárraga, Miren; Yakimov, Michail M; García-Arellano, Humberto; Alcalde, Miguel; Fernández, Víctor M; Elborough, Kieran; Andreu, José M; Ballesteros, Antonio; Plou, Francisco J; Timmis, Kenneth N; Ferrer, Manuel; Golyshin, Peter N

    2006-08-11

    RL5, a gene coding for a novel polyphenol oxidase, was identified through activity screening of a metagenome expression library from bovine rumen microflora. Characterization of the recombinant protein produced in Escherichia coli revealed a multipotent capacity to oxidize a wide range of substrates (syringaldazine > 2,6-dimethoxyphenol > veratryl alcohol > guaiacol > tetramethylbenzidine > 4-methoxybenzyl alcohol > 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) > phenol red) over an unusually broad range of pH from 3.5 to 9.0. Apparent Km and kcat values for ABTS, syringaldazine, and 2,6-dimetoxyphenol obtained from steady-state kinetic measurements performed at 40 degrees C, pH 4.5, yielded values of 26, 0.43, and 0.45 microm and 18, 660, and 1175 s(-1), respectively. The Km values for syringaldazine and 2,6-dimetoxyphenol are up to 5 times lower, and the kcat values up to 40 times higher, than values previously reported for this class of enzyme. RL5 is a 4-copper oxidase with oxidation potential values of 745, 400, and 500 mV versus normal hydrogen electrode for the T1, T2, and T3 copper sites. A three-dimensional model of RL5 and site-directed mutants were generated to identify the copper ligands. Bioinformatic analysis of the gene sequence and the sequences and contexts of neighboring genes suggested a tentative phylogenetic assignment to the genus Bacteroides. Kinetic, electrochemical, and EPR analyses provide unequivocal evidence that the hypothetical proteins from Bacteroides thetaiotaomicron and from E. coli, which are closely related to the deduced protein encoded by the RL5 gene, are also multicopper proteins with polyphenol oxidase activity. The present study shows that these three newly characterized enzymes form a new family of functional multicopper oxidases with laccase activity related to conserved hypothetical proteins harboring the domain of unknown function DUF152 and suggests that some other of these proteins may also be laccases.

  15. A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.

    PubMed

    DiMeglio, Laura M; Staudt, Günter; Yu, Hongrun; Davis, Thomas M

    2014-01-01

    The genus Fragaria encompasses species at ploidy levels ranging from diploid to decaploid. The cultivated strawberry, Fragaria×ananassa, and its two immediate progenitors, F. chiloensis and F. virginiana, are octoploids. To elucidate the ancestries of these octoploid species, we performed a phylogenetic analysis using intron-containing sequences of the nuclear ADH-1 gene from 39 germplasm accessions representing nineteen Fragaria species and one outgroup species, Dasiphora fruticosa. All trees from Maximum Parsimony and Maximum Likelihood analyses showed two major clades, Clade A and Clade B. Each of the sampled octoploids contributed alleles to both major clades. All octoploid-derived alleles in Clade A clustered with alleles of diploid F. vesca, with the exception of one octoploid allele that clustered with the alleles of diploid F. mandshurica. All octoploid-derived alleles in clade B clustered with the alleles of only one diploid species, F. iinumae. When gaps encoded as binary characters were included in the Maximum Parsimony analysis, tree resolution was improved with the addition of six nodes, and the bootstrap support was generally higher, rising above the 50% threshold for an additional nine branches. These results, coupled with the congruence of the sequence data and the coded gap data, validate and encourage the employment of sequence sets containing gaps for phylogenetic analysis. Our phylogenetic conclusions, based upon sequence data from the ADH-1 gene located on F. vesca linkage group II, complement and generally agree with those obtained from analyses of protein-encoding genes GBSSI-2 and DHAR located on F. vesca linkage groups V and VII, respectively, but differ from a previous study that utilized rDNA sequences and did not detect the ancestral role of F. iinumae.

  16. A Phylogenetic Analysis of the Genus Fragaria (Strawberry) Using Intron-Containing Sequence from the ADH-1 Gene

    PubMed Central

    DiMeglio, Laura M.; Yu, Hongrun; Davis, Thomas M.

    2014-01-01

    The genus Fragaria encompasses species at ploidy levels ranging from diploid to decaploid. The cultivated strawberry, Fragaria×ananassa, and its two immediate progenitors, F. chiloensis and F. virginiana, are octoploids. To elucidate the ancestries of these octoploid species, we performed a phylogenetic analysis using intron-containing sequences of the nuclear ADH-1 gene from 39 germplasm accessions representing nineteen Fragaria species and one outgroup species, Dasiphora fruticosa. All trees from Maximum Parsimony and Maximum Likelihood analyses showed two major clades, Clade A and Clade B. Each of the sampled octoploids contributed alleles to both major clades. All octoploid-derived alleles in Clade A clustered with alleles of diploid F. vesca, with the exception of one octoploid allele that clustered with the alleles of diploid F. mandshurica. All octoploid-derived alleles in clade B clustered with the alleles of only one diploid species, F. iinumae. When gaps encoded as binary characters were included in the Maximum Parsimony analysis, tree resolution was improved with the addition of six nodes, and the bootstrap support was generally higher, rising above the 50% threshold for an additional nine branches. These results, coupled with the congruence of the sequence data and the coded gap data, validate and encourage the employment of sequence sets containing gaps for phylogenetic analysis. Our phylogenetic conclusions, based upon sequence data from the ADH-1 gene located on F. vesca linkage group II, complement and generally agree with those obtained from analyses of protein-encoding genes GBSSI-2 and DHAR located on F. vesca linkage groups V and VII, respectively, but differ from a previous study that utilized rDNA sequences and did not detect the ancestral role of F. iinumae. PMID:25078607

  17. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

    PubMed Central

    Willerslev, Eske; Gilbert, M Thomas P; Binladen, Jonas; Ho, Simon YW; Campos, Paula F; Ratan, Aakrosh; Tomsho, Lynn P; da Fonseca, Rute R; Sher, Andrei; Kuznetsova, Tatanya V; Nowak-Kemp, Malgosia; Roth, Terri L; Miller, Webb; Schuster, Stephan C

    2009-01-01

    Background The scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based) approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments. Results In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (Coelodonta antiquitatis), and the threatened Javan (Rhinoceros sondaicus), Sumatran (Dicerorhinus sumatrensis), and black (Diceros bicornis) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (Ceratotherium simum) and Indian (Rhinoceros unicornis) rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i) The black/white, (ii) the woolly/Sumatran, and (iii) the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse vs tapir) has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths. Conclusion Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, large-scale sequencing of complete mitochondrial

  18. A New Orchid Genus, Danxiaorchis, and Phylogenetic Analysis of the Tribe Calypsoeae

    PubMed Central

    Zhai, Jun-Wen; Zhang, Guo-Qiang; Chen, Li-Jun; Xiao, Xin-Ju; Liu, Ke-Wei; Tsai, Wen-Chieh; Hsiao, Yu-Yun; Tian, Huai-Zhen; Zhu, Jia-Qiang; Wang, Mei-Na; Wang, Fa-Guo; Xing, Fu-Wu; Liu, Zhong-Jian

    2013-01-01

    Background Orchids have numerous species, and their speciation rates are presumed to be exceptionally high, suggesting that orchids are continuously and actively evolving. The wide diversity of orchids has attracted the interest of evolutionary biologists. In this study, a new orchid was discovered on Danxia Mountain in Guangdong, China. However, the phylogenetic clarification of this new orchid requires further molecular, morphological, and phytogeographic analyses. Methodology/Principal Findings A new orchid possesses a labellum with a large Y-shaped callus and two sacs at the base, and cylindrical, fleshy seeds, which make it distinct from all known orchid genera. Phylogenetic methods were applied to a matrix of morphological and molecular characters based on the fragments of the nuclear internal transcribed spacer, chloroplast matK, and rbcL genes of Orchidaceae (74 genera) and Calypsoeae (13 genera). The strict consensus Bayesian inference phylogram strongly supports the division of the Calypsoeae alliance (not including Dactylostalix and Ephippianthus) into seven clades with 11 genera. The sequence data of each species and the morphological characters of each genus were combined into a single dataset. The inferred Bayesian phylogram supports the division of the 13 genera of Calypsoeae into four clades with 13 subclades (genera). Based on the results of our phylogenetic analyses, Calypsoeae, under which the new orchid is classified, represents an independent lineage in the Epidendroideae subfamily. Conclusions Analyses of the combined datasets using Bayesian methods revealed strong evidence that Calypsoeae is a monophyletic tribe consisting of eight well-supported clades with 13 subclades (genera), which are all in agreement with the phytogeography of Calypsoeae. The Danxia orchid represents an independent lineage under the tribe Calypsoeae of the subfamily Epidendroideae. This lineage should be treated as a new genus, which we have named Danxiaorchis, that is

  19. Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest

    PubMed Central

    Staggemeier, Vanessa Graziele; Diniz-Filho, José Alexandre Felizola; Forest, Félix; Lucas, Eve

    2015-01-01

    Background and Aims Myrcia section Aulomyrcia includes ∼120 species that are endemic to the Neotropics and disjunctly distributed in the moist Amazon and Atlantic coastal forests of Brazil. This paper presents the first comprehensive phylogenetic study of this group and this phylogeny is used as a basis to evaluate recent classification systems and to test alternative hypotheses associated with the history of this clade. Methods Fifty-three taxa were sampled out of the 120 species currently recognized, plus 40 outgroup taxa, for one nuclear marker (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, trnL-trnF, trnQ-rpS16 and ndhF). The relationships were reconstructed based on Bayesian and maximum likelihood analyses. Additionally, a likelihood approach, ‘geographic state speciation and extinction’, was used to estimate region- dependent rates of speciation, extinction and dispersal, comparing historically climatic stable areas (refugia) and unstable areas. Key Results Maximum likelihood and Bayesian inferences indicate that Myrcia and Marlierea are polyphyletic, and the internal groupings recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Amazonian and north-eastern species and between north-eastern and south-eastern species. Lower extinction rates within glacial refugia suggest that these areas were important in maintaining diversity in the Atlantic forest biodiversity hotspot. Conclusions This study provides a robust phylogenetic framework to address important ecological questions for Myrcia s.l. within an evolutionary context, and supports the need to unite taxonomically the two traditional genera Myrcia and Marlierea in an expanded Myrcia s.l. Furthermore, this study offers valuable insights into the diversification of plant species in the highly impacted Atlantic forest of South America; evidence is presented that the lowest extinction rates are found inside

  20. AFLP analysis of genetic diversity and phylogenetic relationships of Brassica oleracea in Ireland.

    PubMed

    El-Esawi, Mohamed A; Germaine, Kieran; Bourke, Paula; Malone, Renee

    2016-01-01

    Brassica oleracea L. is one of the most economically important vegetable crop species of the genus Brassica L. This species is threatened in Ireland, without any prior reported genetic studies. The use of this species is being very limited due to its imprecise phylogeny and uncompleted genetic characterisation. The main objective of this study was to assess the genetic diversity and phylogenetic relationships of a set of 25 Irish B. oleracea accessions using the powerful amplified fragment length polymorphism (AFLP) technique. A total of 471 fragments were scored across all the 11 AFLP primer sets used, out of which 423 (89.8%) were polymorphic and could differentiate the accessions analysed. The dendrogram showed that cauliflowers were more closely related to cabbages than kales were, and accessions of some cabbage types were distributed among different clusters within cabbage subgroups. Approximately 33.7% of the total genetic variation was found among accessions, and 66.3% of the variation resided within accessions. The total genetic diversity (HT) and the intra-accessional genetic diversity (HS) were 0.251 and 0.156, respectively. This high level of variation demonstrates that the Irish B. oleracea accessions studied should be managed and conserved for future utilisation and exploitation in food and agriculture. In conclusion, this study addressed important phylogenetic questions within this species, and provided a new insight into the inclusion of four accessions of cabbages and kales in future breeding programs for improving varieties. AFLP markers were efficient for assessing genetic diversity and phylogenetic relationships in Irish B. oleracea species.

  1. Phylogenetic analysis of the surface proteins of influenza A (H5N1) viruses isolated in Asian and African populations.

    PubMed

    Babakir-Mina, Muhammed; Ciccozzi, Massimo; Ciotti, Marco; Marcuccilli, Fabio; Balestra, Emanuela; Dimonte, Salvatore; Perno, Carlo Federico; Aquaro, Stefano

    2009-10-01

    Highly pathogenic H5N1 virus can infect a variety of animals and continually poses a threat to animal and human health. Here, phylogenetic analysis of the hemagglutinin and neuraminidase genes indicated that the hemagglutinin gene of all human isolates, although very similar to each other, fell within different clades corresponding to antigenically distinguishable variants. Likewise, the N1 neuraminidase gene forms a clade that is evolutionarily distinct from previously characterized N1 neuraminidases. So, although all H5N1 viruses were derived from ancestors circulating in south-east Asia more than ten years ago, since 2003 they have evolved into geographically distinct groups within each country.

  2. Phylogenetic analysis of the non-structural (NS) gene of influenza A viruses isolated from mallards in Northern Europe in 2005

    PubMed Central

    Zohari, Siamak; Gyarmati, Péter; Ejdersund, Anneli; Berglöf, Ulla; Thorén, Peter; Ehrenberg, Maria; Czifra, György; Belák, Sándor; Waldenström, Jonas; Olsen, Björn; Berg, Mikael

    2008-01-01

    Background Although the important role of the non-structural 1 (NS) gene of influenza A in virulence of the virus is well established, our knowledge about the extent of variation in the NS gene pool of influenza A viruses in their natural reservoirs in Europe is incomplete. In this study we determined the subtypes and prevalence of influenza A viruses present in mallards in Northern Europe and further analysed the NS gene of these isolates in order to obtain a more detailed knowledge about the genetic variation of NS gene of influenza A virus in their natural hosts. Results A total number of 45 influenza A viruses of different subtypes were studied. Eleven haemagglutinin- and nine neuraminidase subtypes in twelve combinations were found among the isolated viruses. Each NS gene reported here consisted of 890 nucleotides; there were no deletions or insertions. Phylogenetic analysis clearly shows that two distinct gene pools, corresponding to both NS allele A and B, were present at the same time in the same geographic location in the mallard populations in Northern Europe. A comparison of nucleotide sequences of isolated viruses revealed a substantial number of silent mutations, which results in high degree of homology in amino acid sequences. The degree of variation within the alleles is very low. In our study allele A viruses displays a maximum of 5% amino acid divergence while allele B viruses display only 2% amino acid divergence. All the viruses isolated from mallards in Northern Europe possessed the typical avian ESEV amino acid sequence at the C-terminal end of the NS1 protein. Conclusion Our finding indicates the existence of a large reservoir of different influenza A viruses in mallards population in Northern Europe. Although our phylogenetic analysis clearly shows that two distinct gene pools, corresponding to both NS allele A and B, were present in the mallards populations in Northern Europe, allele B viruses appear to be less common in natural host species

  3. A molecular analysis of the phylogenetic affinities of Saccoglossus cambrensis Brambell & Cole (Hemichordata).

    PubMed

    Holland, P W; Hacker, A M; Williams, N A

    1991-06-29

    Traditional approaches to phylogeny reconstruction have not allowed precise resolution of the evolutionary relationships between the major deuterostome phyla (chordates, hemichordates, echinoderms). Here we report the use of a molecular approach to investigate deuterostome phylogeny. We have used a polymerase chain reaction-based strategy to amplify, clone and sequence parts of the genes coding for 18S ribosomal RNA from Saccoglossus cambrensis (Hemichordata), Arbacia sp. (Echinodermata) and, for comparison, Mytilus edulis (Mollusca). We report the results of phylogenetic reconstructions using these, and homologous sequences from other eukaryotes. The results of our analyses are consistent with the hypothesis that S. cambrensis and vertebrates share a common ancestor not shared by echinoderms.

  4. Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage.

    PubMed

    Sardina, M T; Ballester, M; Marmi, J; Finocchiaro, R; van Kaam, J B C H M; Portolano, B; Folch, J M

    2006-08-01

    The mitochondrial hypervariable region 1 (HVR1) sequence of 67 goats belonging to the Girgentana, Maltese and Derivata di Siria breeds was partially sequenced in order to present the first phylogenetic characterization of Sicilian goat breeds. These sequences were compared with published sequences of Indian and Pakistani domestic goats and wild goats. Mitochondrial lineage A was observed in most of the Sicilian goats. However, three Girgentana haplotypes were highly divergent from the Capra hircus clade, indicating that a new mtDNA lineage in domestic goats was found.

  5. Phylogenetic analysis of the Mustela altaica (Carnivora: Mustelidae) based on complete mitochondrial genome.

    PubMed

    Huang, Jie; Yang, Bo; Yan, Chaochao; Yang, Chengzhong; Tu, Feiyun; Zhang, Xiuyue; Yue, Bisong

    2014-08-01

    The mountain weasel (Mustela altaica) belongs to family Mustelidae, which is the near threatened species in the IUCN Red List. In this study, the complete mitochondrial genome of M. altaica was sequenced and characterized. The genome is 16,521 bases in length (GenBank accession no. KC815122). The nucleotide sequence data of 12 heavy-strand protein-coding genes of M. altaica and other 20 Mustelidae species were used for phylogenetic analyses. Trees constructed by using Bayesian inference, maximum parsimony and maximum likelihood demonstrated that M. altaica was close to Mustela nivalis and they were sister to Mustela putorius and Mustela sibirica.

  6. Temporal shifts and temperature sensitivity of avian spring migratory phenology: a phylogenetic meta-analysis.

    PubMed

    Usui, Takuji; Butchart, Stuart H M; Phillimore, Albert B

    2017-03-01

    There are wide reports of advances in the timing of spring migration of birds over time and in relation to rising temperatures, though phenological responses vary substantially within and among species. An understanding of the ecological, life-history and geographic variables that predict this intra- and interspecific variation can guide our projections of how populations and species are likely to respond to future climate change. Here, we conduct phylogenetic meta-analyses addressing slope estimates of the timing of avian spring migration regressed on (i) year and (ii) temperature, representing a total of 413 species across five continents. We take into account slope estimation error and examine phylogenetic, ecological and geographic predictors of intra- and interspecific variation. We confirm earlier findings that on average birds have significantly advanced their spring migration time by 2·1 days per decade and 1·2 days °C(-1) . We find that over time and in response to warmer spring conditions, short-distance migrants have advanced spring migratory phenology by more than long-distance migrants. We also find that larger bodied species show greater advance over time compared to smaller bodied species. Our results did not reveal any evidence that interspecific variation in migration response is predictable on the basis of species' habitat or diet. We detected a substantial phylogenetic signal in migration time in response to both year and temperature, suggesting that some of the shifts in migratory phenological response to climate are predictable on the basis of phylogeny. However, we estimate high levels of species and spatial variance relative to phylogenetic variance, which is consistent with plasticity in response to climate evolving fairly rapidly and being more influenced by adaptation to current local climate than by common descent. On average, avian spring migration times have advanced over time and as spring has become warmer. While we are able to

  7. Phylogenetic analysis reveals that a dwarfing disease on different cereal crops in China is due to rice black streaked dwarf virus (RBSDV).

    PubMed

    Bai, Feng-Wei; Yan, Jian; Qu, Zhi-cai; Zhang, Hong-Wei; Xu, Jia; Ye, Ming-Ming; Shen, Da-leng

    2002-10-01

    A viral disease with dwarfing symptoms is associated with severe damage of different cereal crops including rice, maize, wheat and sorghum grown in China. It is believed that the pathogenic agent of the disease on rice and sorghum is rice black streaked dwarf virus (RBSDV), however, the cause of maize dwarf disease in China is still inconclusive. In this report, dsRNA was isolated from virus particles obtained from the diseased plants of rice, maize, wheat and sorghum from two Chinese provinces. Full-length cDNAs of genome segments 9 (S9) and 10 (S 10) were obtained through a RT-PCR approach. Sequence analysis showed that the S9 sequences of Chinese isolates and Japanese RBSDV isolate were very similar to each other (89.1-89.6% identity at the nucleotide level, 92.3-92.9% and 95.8-98.6% identity at the amino acid level for ORF1 and ORF2, respectively). In addition, the S10 sequences of Chinese isolates and Japanese RBSDV were very similar to each other (93.0-95.4% identical nucleotides and 96.2-97.0% identical amino acids, respectively). However, there were lower similarities for S9 and S10 sequences between Chinese isolates and an Italian Maize Rough Dwarf Virus (MRDV) isolate. Phylogenetic analysis indicates that Chinese viral isolates found to infect rice, maize, wheat and sorghum and leading to similar cereal dwarfing manifestations could be grouped to the same virus species, RBSDV.

  8. Piscine Reovirus: Genomic and Molecular Phylogenetic Analysis from Farmed and Wild Salmonids Collected on the Canada/US Pacific Coast

    PubMed Central

    Siah, Ahmed; Morrison, Diane B.; Fringuelli, Elena; Savage, Paul; Richmond, Zina; Johns, Robert; Purcell, Maureen K.; Johnson, Stewart C.; Saksida, Sonja M.

    2015-01-01

    Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period. PMID:26536673

  9. Phylogenetic analysis of basic helix-loop-helix transcription factors in the genome of a typical human-disease vector

    PubMed Central

    Chen, Meng-Yun; Dong, Ying; Chang, Rui-Xue; Ang, Qian-Qian; Zhang, Ran; Wu, Yan-Yan; Xu, Yi-Hui; Lu, Wen-Sheng; Zheng, Xiao-Dong

    2016-01-01

    Ixodes scapularis, the black-legged tick, is one of the most common human-disease vectors and transmits Borrelia species, such as B. burgdorferi, as well as Theileria microti, Anaplasma phagocytophilum, etc. As basic helix-loop-helix (bHLH) transcription factors have been recognized for many years as important regulators of various developmental processes, we performed phylogenetic analysis of the black-legged tick genome in order to identify the number and family of bHLH transcription factors. Because bHLH family members have been identified in many organisms, including silkworm and fruit fly, we were able to conduct this survey and identify 58 putative bHLH transcription factors. Phylogenetic analysis revealed that the black-legged tick has 26, 10, 9, 1, 9, and 1 member in groups A, B, C, D, E, and F, respectively, whereas two were orphan genes. This analysis also revealed that unlike silkworm and fruit fly, the black-legged tick has no Mesp, Mlx, or TF4 family members, but has one more MyoRb family member. The present study provides useful background information for future studies of the black-legged tick as a disease vector with the goal of prevention and treatment. PMID:27904685

  10. Piscine reovirus: Genomic and molecular phylogenetic analysis from farmed and wild salmonids collected on the Canada/US Pacific Coast

    USGS Publications Warehouse

    Siah, Ahmed; Morrison, Diane B.; Fringuelli, Elena; Savage, Paul S.; Richmond, Zina; Purcell, Maureen K.; Johns, Robert; Johnson, Stewart C.; Sakasida, Sonja M.

    2015-01-01

    Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

  11. Phylogenetic analysis of Xanthomonas based on partial rpoB gene sequences and species differentiation by PCR-RFLP.

    PubMed

    Ferreira-Tonin, Mariana; Rodrigues-Neto, Júlio; Harakava, Ricardo; Destéfano, Suzete Aparecida Lanza

    2012-06-01

    The rpoB gene was evaluated as an alternative molecular marker for the differentiation of Xanthomonas species and in order to understand better the phylogenetic relationships within the genus. PCR-RFLP experiments using HaeIII allowed differentiation of Xanthomonas species, particularly those that affect the same plant host such as Xanthomonas albilineans and X. sacchari, pathogenic to sugar cane, Xanthomonas cucurbitae and X. melonis, which cause disease in melon, and Xanthomonas gardneri, X. vesicatoria and X. euvesicatoria/X. perforans, pathogenic to tomato. Phylogenetic relationships within the genus Xanthomonas were also examined by comparing partial rpoB gene sequences (612 nt) and the Xanthomonas species were separated into two main groups. Group I, well supported by bootstrap values of 99 %, comprised X. euvesicatoria, X. perforans, X. alfalfae, X. citri, X. dyei, X. axonopodis, X. oryzae, X. hortorum, X. bromi, X. vasicola, X. cynarae, X. gardneri, X. campestris, X. fragariae, X. arboricola, X. cassavae, X. cucurbitae, X. pisi, X. vesicatoria, X. codiaei and X. melonis. Group II, again well supported by bootstrap values of 99 %, comprised X. albilineans, X. sacchari, X. theicola, X. translucens and X. hyacinthi. The rpoB gene sequence similarity observed among the species in this study ranged from 87.8 to 99.7 %. The results of PCR-RFLP of the rpoB gene indicated that this technique can be used for diagnosis and identification of most Xanthomonas strains, including closely related species within the genus. However, species that showed identical profiles could be differentiated clearly only by sequence analysis. The results obtained in our phylogenetic analysis suggested that the rpoB gene can be used as an alternative molecular marker for genetic relatedness in the genus Xanthomonas. The results of PCR-RFLP of the rpoB gene indicate that this technique can be used for diagnosis and identification of closely related species within the genus, representing

  12. Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway.

    PubMed

    Muñoz-Ramírez, Zilia Y; Mendez-Tenorio, Alfonso; Kato, Ikuko; Bravo, Maria M; Rizzato, Cosmeri; Thorell, Kaisa; Torres, Roberto; Aviles-Jimenez, Francisco; Camorlinga, Margarita; Canzian, Federico; Torres, Javier

    2017-01-01

    Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk.

  13. A multi-locus analysis of phylogenetic relationships within cheilostome bryozoans supports multiple origins of ascophoran frontal shields.

    PubMed

    Knight, Sarah; Gordon, Dennis P; Lavery, Shane D

    2011-11-01

    Phylogenetic relationships within the bryozoan order Cheilostomata are currently uncertain, with many morphological hypotheses proposed but scarcely tested by independent means of molecular analysis. This research uses DNA sequence data across five loci of both mitochondrial and nuclear origin from 91 species of cheilostome Bryozoa (34 species newly sequenced). This vastly improved the taxonomic coverage and number of loci used in a molecular analysis of this order and allowed a more in-depth look into the evolutionary history of Cheilostomata. Maximum likelihood and Bayesian analyses of individual loci were carried out along with a partitioned multi-locus approach, plus a range of topology tests based on morphological hypotheses. Together, these provide a comprehensive set of phylogenetic analyses of the order Cheilostomata. From these results inferences are made about the evolutionary history of this order and proposed morphological hypotheses are discussed in light of the independent evidence gained from the molecular data. Infraorder Ascophorina was demonstrated to be non-monophyletic, and there appears to be multiple origins of the ascus and associated structures involved in lophophore extension. This was further supported by the lack of monophyly within each of the four ascophoran grades (acanthostegomorph/spinocystal, hippothoomorph/gymnocystal, umbonulomorph/umbonuloid, lepraliomorph/lepralioid) defined by frontal-shield morphology. Chorizopora, currently classified in the ascophoran grade Hippothoomorpha, is phylogenetically distinct from Hippothoidae, providing strong evidence for multiple origins of the gymnocystal frontal shield type. Further evidence is produced to support the morphological hypothesis of multiple umbonuloid origins of lepralioid frontal shields, using a step-wise set of topological hypothesis tests combined with examination of multi-locus phylogenies.