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Sample records for mitochondrial coi sequence

  1. Genetic identification and phylogenetic relationships of Indian clariids based on mitochondrial COI sequences.

    PubMed

    Devassy, Aneesha; Kumar, Raj; Shajitha, P P; John, Reshma; Padmakumar, K G; Basheer, V S; Gopalakrishnan, A; Mathew, Linu

    2016-09-01

    Mitochondrial cytochrome C Oxidase I (COI) sequence variation among the clariid fishes of India (Clarias magur, C. dussumieri and C. gariepinus) and their relationship with other representative clariids was studied in this work. Three species were sampled and together with 23 COI sequences from GenBank were used to reconstruct phylogenetic relationships in the family Clariidae. The study revealed two clades: one consisting of the African species with C. dussumieri, and the other of Asian species suggesting the prevalence of intra-continental diversification of catfishes. This study further revealed that the genus Clarias is monophyletic. For the COI gene, the interspecies genetic divergence ranged from 0.056 to 0.182. The mean genetic difference between C. dussumieri and other selected African species in this study is 12.1%. It was also observed that the morphological similarity of C. dussumieri and C. magur was not replicated in the genetic level. Clarias dussumieri was more close to African catfish C. gariepinus thus indicating the utility of COI phylogeny to identify the well-known African-Asian relationships within catfishes. The results also showed that C. magur and C. batrachus are genetically distinct from each other. PMID:26358817

  2. Mitochondrial COI sequences in mites: evidence for variations in base composition.

    PubMed

    Navajas, M; Fournier, D; Lagnel, J; Gutierrez, J; Boursot, P

    1996-11-01

    Studies of mitochondrial DNA sequences in a variety of animals have shown important differences between phyla, including differences in the genetic codes used, and varying constraints on base composition. In that respect, little is known of mites, an important and diversified group. We sequenced a portion (340 nt) of the cytochrome oxidase subunit I (COI) encoding gene in twenty species of phytophagous mites belonging to nine genera of the two families Tetranychidae and Tenuipalpidae. The mitochondrial genetic code used in mites appeared to be the same as in insects. As is generally also the case in insects, the mite sequences were very rich in A + T (75% on average), especially at the third codon position (94%). However, important variations of base composition were observed among mite species, one of them showing as little as 69% A + T. Variations of base composition occur mostly through synonymous transitions, and do not have detectable effects on polypeptide evolution in this group. PMID:8933179

  3. The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters

    PubMed Central

    Arévalo, Elisabeth; Zhu, Yong; Carpenter, James M; Strassmann, Joan E

    2004-01-01

    Background Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae) have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera) using 69 species. Results Our phylogeny is largely concordant with previous phylogenies at higher levels, and is more resolved at the species level. Our results support the monophyly of the New World subgenera of Polistini, while the Old World subgenera are a paraphyletic group. All genera for which we had more than one exemplar were supported as monophyletic except Polybia which is not resolved, and may be paraphyletic. Conclusion The combination of DNA sequences from flanks of microsatellite repeats with mtCOI sequences and morphological characters proved to be useful characters establishing relationships among the different subgenera and species of the Polistini. This is the first detailed hypothesis for the species of this important group. PMID:15070433

  4. GLOBAL RELATIONSHIPS OF BEMISIA TABACI (HEMIPTERA: ALEYRODIDAE) REVEALED USING BAYESIAN ANALYSIS OF MITOCHONDRIAL COI DNA SEQUENCE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Global phylogenetic relationships of the major races of B. tabaci remain unresolved thus a Bayesian phylogenetic technique was utilized to elucidate affinities. All COI DNA sequence data available in Genbank for B. tabaci world-wide (369 specimens) were obtained and the first well resolved phylogen...

  5. Molecular Phylogenetic Relationships of Flightless Beetles Belonging to the Genus Mesechthistatus Breuning, (Coleoptera: Cerambycidae) Inferred from Mitochondrial COI Gene Sequences.

    PubMed Central

    Nakamine, Hiroshi; Takeda, Makio

    2008-01-01

    The longicorn beetles belonging to the genus MesechthistatusBreuning., 1950 (Coleoptera: Cerambycidae) cannot fly since their hindwings are atrophied. This slows down gene flow between local populations. Currently, it is considered that the genus contains four endemic species from the eastern Honshu Is., Japan, M. binodosus, M. furciferus, M. taniguchii and M. fujisanus, that are distributed parapatrically. Sequence analyses of the cytochrome oxidase subunit I gene suggests that lineages of mitochondrial haplotypes split approximately in the same era. However, this result is not consistent with the monophyly of morphological species. The estimated evolutionary rate of the COI gene in other insects suggests that mitochondrial haplotypes of Mesechthistatus differentiated at the end of the Pliocene epoch during the Tertiary era.

  6. Phylogenetic relationship of the Brazilian isolates of the rat lungworm Angiostrongylus cantonensis (Nematoda: Metastrongylidae) employing mitochondrial COI gene sequence data

    PubMed Central

    2012-01-01

    Background The rat lungworm Angiostrongylus cantonensis can cause eosinophilic meningoencephalitis in humans. This nematode’s main definitive hosts are rodents and its intermediate hosts are snails. This parasite was first described in China and currently is dispersed across several Pacific islands, Asia, Australia, Africa, some Caribbean islands and most recently in the Americas. Here, we report the genetic variability among A. cantonensis isolates from different geographical locations in Brazil using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Methods The isolates of A. cantonensis were obtained from distinct geographical locations of Brazil. Genomic DNAs were extracted, amplified by polymerase reaction, purified and sequenced. A partial sequence of COI gene was determined to assess their phylogenetic relationship. Results The sequences of A. cantonensis were monophyletic. We identified a distinct clade that included all isolates of A. cantonensis from Brazil and Asia based on eight distinct haplotypes (ac1, ac2, ac3, ac4, ac5, ac6, ac7 and ac8) from a previous study. Interestingly, the Brazilian haplotype ac5 is clustered with isolates from Japan, and the Brazilian haplotype ac8 from Rio de Janeiro, São Paulo, Pará and Pernambuco states formed a distinct clade. There is a divergent Brazilian haplotype, which we named ac9, closely related to Chinese haplotype ac6 and Japanese haplotype ac7. Conclusion The genetic variation observed among Brazilian isolates supports the hypothesis that the appearance of A. cantonensis in Brazil is likely a result of multiple introductions of parasite-carrying rats, transported on ships due to active commerce with Africa and Asia during the European colonization period. The rapid spread of the intermediate host, Achatina fulica, also seems to have contributed to the dispersion of this parasite and the infection of the definitive host in different Brazilian regions. PMID:23130987

  7. [Approach to Spodoptera (Lepidoptera: Noctuidae) phylogeny based on the sequence of the cytocrhome oxydase I (COI) mitochondrial gene].

    PubMed

    Saldamando, Clara Inés; Marquez, Edna Judith

    2012-09-01

    The genus Spodoptera includes 30 species of moths considered important pests worldwide, with a great representation in the Western Hemisphere. In general, Noctuidae species have morphological similarities that have caused some difficulties for assertive species identification by conventional methods. The purpose of this work was to generate an approach to the genus phylogeny from several species of the genus Spodoptera and the species Bombyx mori as an out group, with the use of molecular tools. For this, a total of 102 S. frugiperda larvae were obtained at random in corn, cotton, rice, grass and sorghum, during late 2006 and early 2009, from Colombia. We took ADN samples from the larval posterior part and we analyzed a fragment of 451 base pairs of the mitochondrial gene cytochrome oxydase I (COI), to produce a maximum likelihood (ML) tree by using 62 sequences (29 Colombian haplotypes were used). Our results showed a great genetic differentiation (K2 distances) amongst S. frugiperda haplotypes from Colombia and the United States, condition supported by the estimators obtained for haplotype diversity and polymorphism. The obtained ML tree clustered most of the species with bootstrapping values from 73-99% in the interior branches; with low values also observed in some of the branches. In addition, this tree clustered two species of the Eastern hemisphere (S littoralis and S. litura) and eight species of the Western hemisphere (S. androgea, S. dolichos, S. eridania, S. exigua, S. frugiperda, S. latifascia, S. ornithogalli and S. pulchella). In Colombia, S. frugiperda, S. ornithogalli and S. albula represent a group of species referred as "the Spodoptera complex" of cotton crops, and our work demonstrated that sequencing a fragment of the COI gene, allows researchers to differentiate the first two species, and thus it can be used as an alternative method to taxonomic keys based on morphology. Finally, the ML tree did not cluster S. frugiperda with S. ornithogalli

  8. Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence

    PubMed Central

    Falla, Ana Carolina; Brieva, Claudia; Bloor, Paul

    2015-01-01

    Prosthenorchis elegans is a member of the Phylum Acanthocephala and is an important parasite affecting New World Primates in the wild in South America and in captivity around the world. It is of significant management concern due to its pathogenicity and mode of transmission through intermediate hosts. Current diagnosis of P. elegans is based on the detection of eggs by coprological examination. However, this technique lacks both specificity and sensitivity, since eggs of most members of the genus are morphologically indistinguishable and shed intermittently, making differential diagnosis difficult, and coprological examinations are often negative in animals severely infected at death. We examined sequence variation in 633 bp of mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) sequence in 37 isolates of P. elegans from New World monkeys (Saguinus leucopus and Cebus albifrons) in Colombia held in rescue centers and from the wild. Intraspecific divergence ranged from 0.0 to 1.6% and was comparable with corresponding values within other species of acanthocephalans. Furthermore, comparisons of patterns of sequence divergence within the Acanthocephala suggest that Prosthenorchis represents a separate genus within the Oligacanthorhynchida. Six distinct haplotypes were identified within P. elegans which grouped into one of two well-supported mtDNA haplogroups. No association between haplogroup/haplotype, holding facility and species was found. This information will help pave the way to the development of molecular-based diagnostic tools for the detection of P. elegans as well as furthering research into the life cycle, intermediate hosts and epidemiological aspects of the species. PMID:26759793

  9. Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence.

    PubMed

    Falla, Ana Carolina; Brieva, Claudia; Bloor, Paul

    2015-12-01

    Prosthenorchis elegans is a member of the Phylum Acanthocephala and is an important parasite affecting New World Primates in the wild in South America and in captivity around the world. It is of significant management concern due to its pathogenicity and mode of transmission through intermediate hosts. Current diagnosis of P. elegans is based on the detection of eggs by coprological examination. However, this technique lacks both specificity and sensitivity, since eggs of most members of the genus are morphologically indistinguishable and shed intermittently, making differential diagnosis difficult, and coprological examinations are often negative in animals severely infected at death. We examined sequence variation in 633 bp of mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) sequence in 37 isolates of P. elegans from New World monkeys (Saguinus leucopus and Cebus albifrons) in Colombia held in rescue centers and from the wild. Intraspecific divergence ranged from 0.0 to 1.6% and was comparable with corresponding values within other species of acanthocephalans. Furthermore, comparisons of patterns of sequence divergence within the Acanthocephala suggest that Prosthenorchis represents a separate genus within the Oligacanthorhynchida. Six distinct haplotypes were identified within P. elegans which grouped into one of two well-supported mtDNA haplogroups. No association between haplogroup/haplotype, holding facility and species was found. This information will help pave the way to the development of molecular-based diagnostic tools for the detection of P. elegans as well as furthering research into the life cycle, intermediate hosts and epidemiological aspects of the species. PMID:26759793

  10. Carposina sasakii (Lepidoptera: Carposinidae) in its Native Range Consists of Two Sympatric Cryptic Lineages as Revealed by Mitochondrial COI Gene Sequences

    PubMed Central

    Wang, J.; Yu, Y.; Li, L.-L.; Guo, D.; Tao, Y.-L.; Chu, D.

    2015-01-01

    The genetic differentiation and genetic structure of the peach fruit moth, Carposina sasakii Matsumura (Lepidoptera: Carposinidae), was investigated in China, where the moth is native. The mitochondrial cytochrome c oxidase I (COI) gene of 180 individuals from 16 collections were sequenced and analyzed. The results showed that two sympatric and cryptic mtDNA lineages existed within C. sasakii in China. The genetic differentiation has significant correlation with the geographical distance, but has no evidence for host plant associations. Our results of haplotype distribution suggest that the C. sasakii individuals can naturally move between areas, while the movement of individuals between long-distance locations may be associated with human activities such as the transport of fruit. Finally, an mitochondrial COI gene PCR-RFLP method was developed to differentiate the two cryptic mtDNA lineages within C. sasakii, which provides rapid and reliable tool for the future research of the two lineages. PMID:26136498

  11. Genetic diversity and population structure of Eleutheronema rhadinum in the East and South China Seas revealed in mitochondrial COI sequences

    NASA Astrophysics Data System (ADS)

    Sun, Xinxu; Xu, Dongdong; Lou, Bao; Zhang, Tao; Xin, Jian; Guo, Yaoshi; Ma, Shilei

    2013-11-01

    Eleutheronema rhadinum is a potential commercial fisheries species and is subject to intense exploitation in China. Knowledge on the population structure of E. rhadinum in Chinese coastal waters, which is important for sustainable exploitation and proper resource management, is lacking. In the present study, the genetic diversity and population structure of E. rhadinum were evaluated using a 564-base pair fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 76 specimens were collected from three localities around the East (Qidong and Zhoushan) and South China Seas (Zhuhai). Among these individuals, nine polymorphic sites were detected and 11 distinct haplotypes were defined. High levels of haplotype diversity ( h =0.759±0.035) and low levels of nucleotide diversity ( π= 0.001 98±0.003 26) were observed in these populations. Hierarchical analysis of molecular variance (AMOVA) indicated that 96.72% of the genetic variation occurred within the populations, whereas 3.28% occurred among populations. No significant genealogical branches or clusters were recognized on the neighbor-joining tree. Intra-group variation among populations was significant ( φ st=0.032 85, P<0.01). These results suggest that E. rhadinum populations in the East and South China Seas have developed divergent genetic structures. Tests of neutral evolution and mismatch distribution suggest that E. rhadinum may have experienced a population expansion. The present study provides basic information for the conservation and sustainable exploitation of this species.

  12. Population genetic structure of the parasitic nematode Camallanus cotti inferred from DNA sequences of ITS1 rDNA and the mitochondrial COI gene.

    PubMed

    Wu, Shan G; Wang, Gui T; Xi, Bing W; Xiong, Fan; Liu, Tao; Nie, Pin

    2009-10-14

    The population genetic structure of fish parasitic nematode, Camallanus cotti, collected from the Yangtze River, Pearl River and Minjiang River in China was investigated. From these parasites, the approximately 730 bp of the first internal transcribed spacer of ribosomal DNA (ITS1 rDNA) and the 428bp of mitochondrial cytochrome c oxidase subunit I (COI) gene were sequenced. For the ITS1 rDNA data set, highly significant Fst values and low rates of migration were detected between the Pearl River group and both the Yangtze River (Fst=0.70, P<0.00001; Nm=0.21) and Minjiang River (Fst=0.73, P<0.00001; Nm=0.18) groups, while low Fst value (Fst=0.018, P>0.05) and high rate of migration (Nm=28.42) were found between the Minjiang and the Yangtze rivers. When different host/locality populations (subpopulations) within each river were considered, subpopulations between the Yangtze River and Minjiang River had low Fst values (3.72), while Pearl River subpopulations were significantly different from the Yangtze River and Minjiang River subpopulations (Fst>or=0.59; Nm<1). The COI gene data set revealed a similar genetic structure. Both phylogenetic analyses and a statistical parsimony network grouped the Pearl River haplotypes into one phylogroup, while the Yangtze River and Minjiang River haplotypes formed a second group. These results suggested that the Yangtze River and Minjiang River subpopulations constituted a single reproductive pool that was distinct from the Pearl River subpopulations. In addition, the present study did not find host-related genetic differentiation occurring in the same drainage. PMID:19632785

  13. A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&2) and mitochondrial (COI) DNA sequences.

    PubMed

    Wood, Ann R; Apte, Smita; MacAvoy, Elizabeth S; Gardner, Jonathan P A

    2007-08-01

    A molecular phylogeny is presented for marine mussels of the genus Perna, based on nuclear (ITS1,ITS2) and mitochondrial (COI) DNA sequence data. The three generally recognised species (Perna viridis, Perna perna and Perna canaliculus) and one putative species (Perna picta) were each sampled from several locations within their known geographic distributions. A range of phylogenetic analyses was used to investigate the current taxonomic assignments, evolutionary relationships and the biogeographical history of the genus. The different analyses produced similar, well supported topologies and verified the monophyly of the genus with respect to five mytilid outgroup species. P. perna (Atlantic), P. viridis (Indo-West Pacific), and P. canaliculus (New Zealand) each formed distinct clades, confirming their specific status. Putative P. picta from North Africa clustered within the P. perna clade and is not regarded as a separate species. P. perna and P. canaliculus were the most closely related of the three species. Possible biogeographic explanations for the present species distributions are evaluated. PMID:17292632

  14. Southeast Asian mouth-brooding Betta fighting fish (Teleostei: Perciformes) species and their phylogenetic relationships based on mitochondrial COI and nuclear ITS1 DNA sequences and analyses

    PubMed Central

    Panijpan, Bhinyo; Kowasupat, Chanon; Laosinchai, Parames; Ruenwongsa, Pintip; Phongdara, Amornrat; Senapin, Saengchan; Wanna, Warapond; Phiwsaiya, Kornsunee; Kühne, Jens; Fasquel, Frédéric

    2014-01-01

    Fighting fish species in the genus Betta are found in several Southeast Asian countries. Depending on the mode of paternal care for fertilized eggs and hatchlings, various species of the betta fish are classified as mouth brooders or nest builders whose members in turn have been grouped according to their similarities mainly in morphology. The mouth brooders as well as some nest builders involved in the present study include fishes discovered and identified subsequent to previous reports on species groupings and their positions on phylogenetic trees based on DNA sequences that differ from those used by us in this study. From the mitochondrial COI gene and nuclear ITS1 gene sequences and more accurate analyses we conclude that the following members of the mouth-brooding pairs, named differently previously, are virtually identical, viz the Betta prima–Betta pallida pair and Betta ferox–Betta apollon pair. The Betta simplex, hitherto believed to be one species, could possibly be genetically split into 2 distinct species. In addition, several other established type-locality fishes could harbor cryptic species as judged by genetic differences. Assignments of fish species to groups reported earlier may have to be altered somewhat by the present genetic findings. We propose here a new Betta fish phylogenetic tree which, albeit being similar to the previous ones, is clearly different from them. Our gene-based evidence also leads to assignments of some fishes to new species groups and alters the positions of some species on the new phylogenetic tree, thus implying different ancestral relationships. PMID:25606468

  15. Southeast Asian mouth-brooding Betta fighting fish (Teleostei: Perciformes) species and their phylogenetic relationships based on mitochondrial COI and nuclear ITS1 DNA sequences and analyses.

    PubMed

    Panijpan, Bhinyo; Kowasupat, Chanon; Laosinchai, Parames; Ruenwongsa, Pintip; Phongdara, Amornrat; Senapin, Saengchan; Wanna, Warapond; Phiwsaiya, Kornsunee; Kühne, Jens; Fasquel, Frédéric

    2014-12-01

    Fighting fish species in the genus Betta are found in several Southeast Asian countries. Depending on the mode of paternal care for fertilized eggs and hatchlings, various species of the betta fish are classified as mouth brooders or nest builders whose members in turn have been grouped according to their similarities mainly in morphology. The mouth brooders as well as some nest builders involved in the present study include fishes discovered and identified subsequent to previous reports on species groupings and their positions on phylogenetic trees based on DNA sequences that differ from those used by us in this study. From the mitochondrial COI gene and nuclear ITS1 gene sequences and more accurate analyses we conclude that the following members of the mouth-brooding pairs, named differently previously, are virtually identical, viz the Betta prima-Betta pallida pair and Betta ferox-Betta apollon pair. The Betta simplex, hitherto believed to be one species, could possibly be genetically split into 2 distinct species. In addition, several other established type-locality fishes could harbor cryptic species as judged by genetic differences. Assignments of fish species to groups reported earlier may have to be altered somewhat by the present genetic findings. We propose here a new Betta fish phylogenetic tree which, albeit being similar to the previous ones, is clearly different from them. Our gene-based evidence also leads to assignments of some fishes to new species groups and alters the positions of some species on the new phylogenetic tree, thus implying different ancestral relationships. PMID:25606468

  16. Biodiversity of the Betta smaragdina (Teleostei: Perciformes) in the northeast region of Thailand as determined by mitochondrial COI and nuclear ITS1 gene sequences.

    PubMed

    Kowasupat, Chanon; Panijpan, Bhinyo; Laosinchai, Parames; Ruenwongsa, Pintip; Phongdara, Amornrat; Wanna, Warapond; Senapin, Saengchan; Phiwsaiya, Kornsunee

    2014-12-01

    In Thailand, there are currently five recognized species members of the bubble-nesting Betta genus, namely Betta splendens, B. smaragdina, B. imbellis, B. mahachaiensis and B. siamorientalis. In 2010, we indicated the possibility, based on COI barcoding evidence, that there might be two additional species, albeit cryptic, related to the type-locality B. smaragdina in some provinces in the northeast of Thailand. In the present study, after a more extensive survey of the northeast, and phylogenetic analyses based on COI and ITS1 sequences, the B. smaragdina group may be composed of at least 3 cryptic species members. The phylogenetic positions of these B. smaragdina group members in the bubble-nesting bettas' tree together with those of their congeners have been consolidated by better DNA sequence quality and phylogenetic analyses. With a better supported tree, the species statuses of B. siamorientalis and the Cambodian B. smaragdina-like fish, B. stiktos, are also confirmed. PMID:25606392

  17. Identification of forensically important Sarcophaga species (Diptera: Sarcophagidae) using the mitochondrial COI gene.

    PubMed

    Jordaens, Kurt; Sonet, Gontran; Richet, René; Dupont, Erena; Braet, Yves; Desmyter, Stijn

    2013-03-01

    The identification of species of the forensically important genus Sarcophaga is very difficult and requires strong taxonomic expertise. In this study, we sequenced the mitochondrial cytochrome c oxidase subunit I (COI) gene of 126 specimens of 56 W European Sarcophaga species and added GenBank data to our database to yield a total dataset of 270 COI sequences from 99 Sarcophaga species to evaluate the COI gene as a molecular diagnostic tool for species identification in this genus. Using two simple criteria (Best Match, BM and Best Close Match, BCM), we showed that the identification success using a mini-barcode region of 127 bp was very low (80.7-82.5 %) and the use of this region is not recommended as a species identifier. In contrast, identification success was very high using the standard barcode region (658 bp) or using the entire COI region (1,535 bp) (98.2-99.3 %). Yet, there was a low interspecific sequence divergence (<2 %) in six species groups so that for 16 out of the 99 species (nine of which are of forensic importance), the use of COI barcodes as species identifier should be done with care. For these species, additional markers will be necessary to achieve a 100 % identification success. We further illustrate how such reference databases can improve local reference databases for forensic entomologists. PMID:22960880

  18. Pleistocene phylogeography and cryptic diversity of a tiger beetle, Calomera littoralis, in North-Eastern Mediterranean and Pontic regions inferred from mitochondrial COI gene sequences

    PubMed Central

    Rewicz, Tomasz; Płóciennik, Mateusz; Grabowski, Michał

    2016-01-01

    Background. Calomera littoralis is a Palearctic species, widely distributed in Europe; inhabiting predominantly its Atlantic, Mediterranean and Black Sea coastlines. Methods. Its phylogeography on the Balkan Peninsula and on the north-western Black Sea coast was inferred using a 697 bp long portion of the mitochondrial COI gene, amplified from 169 individuals collected on 43 localities. Results. The results revealed two genetically divergent groups/lineages, the southern one inhabiting both the Balkan Peninsula and the Pontic Region and the northern one found exclusively in the Pontic Region. Species delimitation based on DNA barcoding gap suggested an interspecific level of divergence between these groups. Multivariate analysis of eight male and female morphometric traits detected no difference between the groups, implying they may represent cryptic species. The Bayesian time-calibrated reconstruction of phylogeny suggested that the lineages diverged ca. 2.3 Ma, in early Pleistocene. Discussion. The presence of the two genetically divergent groups results most likely from contemporary isolation of the Pontic basin from the Mediterranean that broke the continuous strip of coastal habitats inhabited by C. littoralis. Demographic analyses indicated that both lineages have been in demographic and spatial expansion since ca. 0.15 Ma. It coincides with the terminal stage of MIS-6, i.e., Wartanian/Saalian glaciation, and beginning of MIS-5e, i.e., Eemian interglacial, during which, due to eustatic sea level rise, a wide connection between Mediterranean and the Pontic basin was re-established. This, along with re-appearance of coastal habitats could initiate north-east expansion of the southern lineage and its secondary contact with the northern one. The isolation of the Pontic basin from the Mediterranean during the Weichselian glaciation most likely did not have any effect on their phylogeography. PMID:27547517

  19. Pleistocene phylogeography and cryptic diversity of a tiger beetle, Calomera littoralis, in North-Eastern Mediterranean and Pontic regions inferred from mitochondrial COI gene sequences.

    PubMed

    Jaskuła, Radomir; Rewicz, Tomasz; Płóciennik, Mateusz; Grabowski, Michał

    2016-01-01

    Background. Calomera littoralis is a Palearctic species, widely distributed in Europe; inhabiting predominantly its Atlantic, Mediterranean and Black Sea coastlines. Methods. Its phylogeography on the Balkan Peninsula and on the north-western Black Sea coast was inferred using a 697 bp long portion of the mitochondrial COI gene, amplified from 169 individuals collected on 43 localities. Results. The results revealed two genetically divergent groups/lineages, the southern one inhabiting both the Balkan Peninsula and the Pontic Region and the northern one found exclusively in the Pontic Region. Species delimitation based on DNA barcoding gap suggested an interspecific level of divergence between these groups. Multivariate analysis of eight male and female morphometric traits detected no difference between the groups, implying they may represent cryptic species. The Bayesian time-calibrated reconstruction of phylogeny suggested that the lineages diverged ca. 2.3 Ma, in early Pleistocene. Discussion. The presence of the two genetically divergent groups results most likely from contemporary isolation of the Pontic basin from the Mediterranean that broke the continuous strip of coastal habitats inhabited by C. littoralis. Demographic analyses indicated that both lineages have been in demographic and spatial expansion since ca. 0.15 Ma. It coincides with the terminal stage of MIS-6, i.e., Wartanian/Saalian glaciation, and beginning of MIS-5e, i.e., Eemian interglacial, during which, due to eustatic sea level rise, a wide connection between Mediterranean and the Pontic basin was re-established. This, along with re-appearance of coastal habitats could initiate north-east expansion of the southern lineage and its secondary contact with the northern one. The isolation of the Pontic basin from the Mediterranean during the Weichselian glaciation most likely did not have any effect on their phylogeography. PMID:27547517

  20. Cytochrome Oxidase I (COI) sequence conservation and variation patterns in the yellowfin and longtail tunas.

    PubMed

    Kunal, Swaraj Priyaranjan; Kumar, Girish

    2013-01-01

    Tunas are commercially important fishery worldwide. There are at least 13 species of tuna belonging to three genera, out of which genus Thunnus has maximum eight species. On the basis of their availability, they can be characterised as oceanic such as Thunnus albacares (yellowfin tuna) or coastal such as Thunnus tonggol (longtail tuna). Although these two are different species, morphological differentiation can only be seen in mature individuals, hence misidentification may result in erroneous data set, which ultimately affect conservation strategies. The mitochondrial DNA cytochrome oxidase c subunit 1 (COI) gene is one of the most popular markers for population genetic and phylogeographic studies across the animal kingdom. The present study aims to study the sequence conservation and variation in mitochondrial Cytochrome Oxidase I (COI) between these two species of tuna. COI sequence analysis of yellowfin and longtail revealed the close relationship between them in Thunnus genera. The present study is the first direct comparison of mitochondrial COI sequences of these two tuna species. PMID:23649742

  1. Mitochondrial COI and nuclear RAG1 DNA sequences and analyses of specimens of the three morphologically established species in the genus Trichopsis (Perciformes: Osphronemidae) reveal new/cryptic species

    PubMed Central

    Panijpan, Bhinyo; Laosinchai, Parames; Senapin, Saengchan; Kowasupat, Chanon; Ruenwongsa, Pintip; Kühne, Jens; Phiwsaiya, Kornsunee

    2015-01-01

    Air-breathing fish species of the genus Trichopsis have been reported in Cambodia, Lao PDR, Indonesia, Malaysia, Singapore, Thailand and Vietnam. It is only in Thailand that all three recognized species (Trichopsis vittata, Trichopsis schalleri and Trichopsis pumila), as judged by distinct external features, are found. Cambodia and Lao PDR harbor two species each. The present work involves first-time DNA sequencing and analysis based on mitochondrial (COI) and nuclear (RAG1) DNA of numerous specimens of these species and specimens of a controversial Phetchaburi (Thailand) fish population with a mixed outward appearance. In addition to confirming the morphologically clear-cut taxonomic division of the three fish species, our DNA results show that whereas the T. pumila populations form one single species, there are cryptic species in the T. vittata and T. schalleri populations and possibly a new one in the latter. Members of the putative Phetchaburi fish population have been proven to be hybrids between T. pumila and T. vittata. In addition, a new the phylogenetic tree indicating ancestral relationships is also presented. This study should generate further research to find new/cryptic species of the genus Trichopsis in all countries harboring the fish. PMID:25853058

  2. Mitochondrial COI and nuclear RAG1 DNA sequences and analyses of specimens of the three morphologically established species in the genus Trichopsis (Perciformes: Osphronemidae) reveal new/cryptic species.

    PubMed

    Panijpan, Bhinyo; Laosinchai, Parames; Senapin, Saengchan; Kowasupat, Chanon; Ruenwongsa, Pintip; Kühne, Jens; Phiwsaiya, Kornsunee

    2015-06-01

    Air-breathing fish species of the genus Trichopsis have been reported in Cambodia, Lao PDR, Indonesia, Malaysia, Singapore, Thailand and Vietnam. It is only in Thailand that all three recognized species (Trichopsis vittata, Trichopsis schalleri and Trichopsis pumila), as judged by distinct external features, are found. Cambodia and Lao PDR harbor two species each. The present work involves first-time DNA sequencing and analysis based on mitochondrial (COI) and nuclear (RAG1) DNA of numerous specimens of these species and specimens of a controversial Phetchaburi (Thailand) fish population with a mixed outward appearance. In addition to confirming the morphologically clear-cut taxonomic division of the three fish species, our DNA results show that whereas the T. pumila populations form one single species, there are cryptic species in the T. vittata and T. schalleri populations and possibly a new one in the latter. Members of the putative Phetchaburi fish population have been proven to be hybrids between T. pumila and T. vittata. In addition, a new the phylogenetic tree indicating ancestral relationships is also presented. This study should generate further research to find new/cryptic species of the genus Trichopsis in all countries harboring the fish. PMID:25853058

  3. A diagnostic molecular marker for zebra mussels (Dreissena polymorpha) and potentially co-occurring bivalves: mitochondrial COI.

    PubMed

    Baldwin, B S; Black, M; Sanjur, O; Gustafson, R; Lutz, R A; Vrijenhoek, R C

    1996-03-01

    We report diagnostic differences in the nucleotide sequences of a 710-bp fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) from the zebra mussel (Dreissena polymorpha) and potentially co-occurring bivalves: the quagga mussel (Dreissena bugensis); the Asiatic clam (Corbicula fluminea), the dark false mussel (Mytilopsis leucophaeata), and the wedge clam (Rangia cuneata). The COI sequence of the deep-water "profunda" phenotype of the quagga mussel was nearly identical to that of shallow-water quagga mussels. Restriction fragment length polymorphisms (RFLPs) in this portion of COI produced species-specific differences in fragment numbers and sizes that could be used as diagnostic markers to distinguish the free-living larvae produced by these bivalves. PMID:8869514

  4. Molecular Identification of Paramecium bursaria Syngens and Studies on Geographic Distribution using Mitochondrial Cytochrome C Oxidase Subunit I (COI).

    PubMed

    Zagata, Patrycja; Greczek-Stachura, Magdalena; Tarcz, Sebastian; Rautian, Maria

    2015-01-01

    Paramecium bursaria is composed of five syngens that are morphologically indistinguishable but sexually isolated. The aim of the present study was to confirm by molecular methods (analyses of mitochondrial COI) the identification of P. bursaria syngens originating from different geographical locations. Phylograms constructed using both the neighbor-joining and maximum-likelihood methods based on a comparison of 34 sequences of P. bursaria strains and P. multimicronucleatum, P. caudatum and P.calkinsi strains used as outgroups revealed five clusters which correspond to results obtained previously by mating reaction. Our analysis shows the existence of 24 haplotypes for the COI gene sequence in the studied strains. The interspecies haplotype diversity was Hd = 0.967. We confirmed genetic differentiation between strains of P. bursaria and the occurrence of a correlation between geographical distribution and the correspondent syngen. PMID:26103689

  5. The Mycetophila ruficollis Meigen (Diptera, Mycetophilidae) group in Europe: elucidating species delimitation with COI and ITS2 sequence data

    PubMed Central

    Jürgenstein, Siiri; Kurina, Olavi; Põldmaa, Kadri

    2015-01-01

    Abstract European species of the Mycetophila ruficollis group are compared on the basis of morphology and sequences of mitochondrial cytochrome oxidase subunit one (COI) and the ITS2 region of nuclear ribosomal DNA. The study represents the first evaluation of morphology-based species delimitation of closely related fungus gnat species by applying molecular information. Detailed descriptions and illustrations of the male terminalia are presented along with a key for the identification of all nine European species of the group. Phylogenetic analyses of molecular data generally supported the morphological species discrimination. The barcoding region of COI superseded ITS2 rDNA in resolving species. In the COI barcoding region interspecific differences ranged from 2.9 to 10.6% and the intraspecific distance from 0.08 to 0.8%. Only COI data distinguished between the similar and closely related Mycetophila ichneumonea and Mycetophila uninotata of which the latter was observed to include cryptic species. The host range of some species is suggested to be narrower than previously considered and to depend on the forest type. Presented evidence indicates the importance of analysing sequence data of morphologically very similar mycetophages reared from identified host fungi for elucidating species delimitation as well as their geographic and host ranges. New country records, viz. Estonia for Mycetophila evanida, Georgia for Mycetophila ichneumonea, Mycetophila idonea and Mycetophila ruficollis, and Norway for Mycetophila strobli, widen the known distribution ranges of these species. PMID:26167119

  6. Twin Mitochondrial Sequence Analysis.

    PubMed

    Bouhlal, Yosr; Martinez, Selena; Gong, Henry; Dumas, Kevin; Shieh, Joseph T C

    2013-09-01

    When applying genome-wide sequencing technologies to disease investigation, it is increasingly important to resolve sequence variation in regions of the genome that may have homologous sequences. The human mitochondrial genome challenges interpretation given the potential for heteroplasmy, somatic variation, and homologous nuclear mitochondrial sequences (numts). Identical twins share the same mitochondrial DNA (mtDNA) from early life, but whether the mitochondrial sequence remains similar is unclear. We compared an adult monozygotic twin pair using high throughput-sequencing and evaluated variants with primer extension and mitochondrial pre-enrichment. Thirty-seven variants were shared between the twin individuals, and the variants were verified on the original genomic DNA. These studies support highly identical genetic sequence in this case. Certain low-level variant calls were of high quality and homology to the mitochondrial DNA, and they were further evaluated. When we assessed calls in pre-enriched mitochondrial DNA templates, we found that these may represent numts, which can be differentiated from mtDNA variation. We conclude that twin identity extends to mitochondrial DNA, and it is critical to differentiate between numts and mtDNA in genome sequencing, particularly since significant heteroplasmy could influence genome interpretation. Further studies on mtDNA and numts will aid in understanding how variation occurs and persists. PMID:24040623

  7. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

    PubMed Central

    2013-01-01

    Introduction The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile (“universal”) COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results We first design a new PCR primer within the highly variable mitochondrial COI region, the “mlCOIintF” primer. We then show that this newly designed forward primer combined with the “jgHCO2198” reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a

  8. Molecular characterization of Opisthorchis noverca (Digenea: Opisthorchiidae) based on nuclear ribosomal ITS2 and mitochondrial COI genes.

    PubMed

    Sahu, R; Biswal, D K; Roy, B; Tandon, V

    2016-09-01

    Opisthorchiasis is a public health problem in South-East Asian countries and Eastern Europe. The infection implicates mainly two species of Opisthorchis, namely O. viverrini and O. felineus, that occur mostly in fish-eating mammals and humans, although there are rare reports of human cases involving two other species, O. noverca and O. guayaquilensis. Opisthorchis noverca has been reported frequently in dogs and pigs from the Indian subcontinent, with rare reports from cattle and human subjects. With a view to supplementing morphology-based identification of this species, the present study aimed to provide molecular characterization of O. noverca, using rDNA internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome oxidase I (mt COI) markers so as to determine its genetic correlation with other species of Opisthorchiidae, and also to generate a taxon-specific molecular marker based on the ITS2 region. The phylogenetic relationship between O. noverca and other species of the genus was determined using molecular sequence data. To strengthen the result, secondary structure sequence analyses of ITS2 with hemi-compensatory base changes (hCBCs), and amino acid sequence analyses, were also evaluated. Our results confirm that O. noverca is a distinct and valid species. PMID:26467395

  9. Mitochondrial COI and morphological evidence for host specificity of the black cherry aphids Myzus cerasi (Fabricius, 1775) collected from different cherry tree species in Europe (Hemiptera, Aphididae).

    PubMed

    Rakauskas, Rimantas; Havelka, Jekaterina; Zaremba, Audrius; Bernotienė, Rasa

    2014-01-01

    Partial sequences of the mitochondrial COI gene of forty eight European and two Turkish population samples of Myzus cerasi from different winter hosts (Prunus spp.) were subjected to phylogenetic analyses. The analysed M. cerasi samples emerged as paraphyletic relative to a Myzus borealis sample used as an out-group, and formed two major clades in neighbor joining, maximum parsimony, maximum likelihood and Bayesian inference trees, corresponding to subspecies living specifically on Prunus avium and P. cerasus. Multivariate discriminant analysis (method of canonical variates) was applied to find out if morphological variation of samples correlated with mitochondrial COI and host plant information. Mean scores on the first two canonical variables clustered samples fully in accordance with their COI haplotypes and host plants confirming the existence of two morphologically similar winter host - specific subspecies of M. cerasi in Europe. No single morphological character enabled satisfactory discrimination between apterous viviparous females of the two subspecies. A three-character linear discriminant function enabled 92.37% correct identification of apterous viviparous females of M. cerasi cerasi (n = 118) and 93.64% of M. cerasi pruniavium (n = 110). A key for the morphological identification of the two subspecies is presented and their taxonomic status is discussed. PMID:24715766

  10. Population genetic structure of Cheyletus malaccensis (Acari: Cheyletidae) in China based on mitochondrial COI and 12S rRNA genes.

    PubMed

    Yang, Xiaoqiang; Ye, Qingtian; Xin, Tianrong; Zou, Zhiwen; Xia, Bin

    2016-06-01

    Cheyletus malaccensis is a predatory mite widely distributed in grain storages. It has been regarded as an important biological control agent for pest mites. In this study, we investigated the population genetic structure of C. malaccensis distributed in China based on the partial regions of mitochondrial COI and 12S rRNA genes. We collected 256 individuals of C. malaccensis from stored grain in 34 sites of China. We detected 50 COI gene haplotypes and nine 12S rRNA gene haplotypes. There were three clades in the haplotype network and Bayesian and maximum parsimony phylogenetic trees based on COI sequences, and two based on 12S rRNA sequences. The clustering of haplotypes was not correlated with their geographical distributions. The analysis of molecular variance, AMOVA, indicated that the genetic differentiation between populations was relatively weak. The major genetic differentiation was found within populations. We suggest that the genetic structure of C. malaccensis observed in this study may be the result of long-term climate fluctuations and recent human disturbances. PMID:26947027

  11. Distinct genetic lineages of Bactrocera caudata (Insecta: Tephritidae) revealed by COI and 16S DNA sequences.

    PubMed

    Lim, Phaik-Eem; Tan, Ji; Suana, I Wayan; Eamsobhana, Praphathip; Yong, Hoi Sen

    2012-01-01

    The fruit fly Bactrocera caudata is a pest species of economic importance in Asia. Its larvae feed on the flowers of Cucurbitaceae such as Cucurbita moschata. To-date it is distinguished from related species based on morphological characters. Specimens of B. caudata from Peninsular Malaysia and Indonesia (Bali and Lombok) were analysed using the partial DNA sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA genes. Both gene sequences revealed that B. caudata from Peninsular Malaysia was distinctly different from B. caudata of Bali and Lombok, without common haplotype between them. Phylogenetic analysis revealed two distinct clades, indicating distinct genetic lineage. The uncorrected 'p' distance for COI sequences between B. caudata of Malaysia-Thailand-China and B. caudata of Bali-Lombok was 5.65%, for 16S sequences from 2.76 to 2.99%, and for combined COI and 16S sequences 4.45 to 4.46%. The 'p' values are distinctly different from intraspecific 'p' distance (0-0.23%). Both the B. caudata lineages are distinctly separated from related species in the subgenus Zeugodacus - B. ascita, B. scutellata, B. ishigakiensis, B. diaphora, B. tau, B. cucurbitae, and B. depressa. Molecular phylogenetic analysis indicates that the B. caudata lineages are closely related to B. ascita sp. B, and form a clade with B. scutellata, B. ishigakiensis, B. diaphora and B. ascita sp. A. This study provides additional baseline for the phylogenetic relationships of Bactrocera fruit flies of the subgenus Zeugodacus. Both the COI and 16S genes could be useful markers for the molecular differentiation and phylogenetic analysis of tephritid fruit flies. PMID:22615962

  12. Distinct Genetic Lineages of Bactrocera caudata (Insecta: Tephritidae) Revealed by COI and 16S DNA Sequences

    PubMed Central

    Lim, Phaik-Eem; Tan, Ji; Suana, I. Wayan; Eamsobhana, Praphathip; Yong, Hoi Sen

    2012-01-01

    The fruit fly Bactrocera caudata is a pest species of economic importance in Asia. Its larvae feed on the flowers of Cucurbitaceae such as Cucurbita moschata. To-date it is distinguished from related species based on morphological characters. Specimens of B. caudata from Peninsular Malaysia and Indonesia (Bali and Lombok) were analysed using the partial DNA sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA genes. Both gene sequences revealed that B. caudata from Peninsular Malaysia was distinctly different from B. caudata of Bali and Lombok, without common haplotype between them. Phylogenetic analysis revealed two distinct clades, indicating distinct genetic lineage. The uncorrected ‘p’ distance for COI sequences between B. caudata of Malaysia-Thailand-China and B. caudata of Bali-Lombok was 5.65%, for 16S sequences from 2.76 to 2.99%, and for combined COI and 16S sequences 4.45 to 4.46%. The ‘p’ values are distinctly different from intraspecific ‘p’ distance (0–0.23%). Both the B. caudata lineages are distinctly separated from related species in the subgenus Zeugodacus – B. ascita, B. scutellata, B. ishigakiensis, B. diaphora, B. tau, B. cucurbitae, and B. depressa. Molecular phylogenetic analysis indicates that the B. caudata lineages are closely related to B. ascita sp. B, and form a clade with B. scutellata, B. ishigakiensis, B. diaphora and B. ascita sp. A. This study provides additional baseline for the phylogenetic relationships of Bactrocera fruit flies of the subgenus Zeugodacus. Both the COI and 16S genes could be useful markers for the molecular differentiation and phylogenetic analysis of tephritid fruit flies. PMID:22615962

  13. Progress on resolving the Gonatocerus tuberculifemur complex: neither COI nor ITS2 sequence data alone can discriminate all the species within the complex, whereas, ISSR-PCR DNA fingerprinting can

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We utilized two molecular methods to aid in resolving the Gonatocerus tuberculifemur complex, potential glassy-winged sharpshooter (GWSS) biological control candidate agents from South America. The two methods used were DNA sequencing of both the mitochondrial cytochrome oxidase subunit 1 gene (COI...

  14. Application of COI barcode sequence for the identification of snake medicine (Zaocys).

    PubMed

    Cao, Shuping; Guo, Linong; Luo, Huiming; Yuan, Hang; Chen, Shuyun; Zheng, Jian; Lin, Ruichao

    2016-01-01

    Counterfeits in the medicine market make the authentication of snakes used for Chinese medicine a challenge to Chinese drug regulatory control agencies. This paper explores existing methods that can be used to quickly and accurately distinguish Zaocys (Z. dhumnades) from its counterfeits for routine identification of snake meats in food and drug control laboratories. In this research, the Cytochrome Oxidase I (COI) fragments of 51 samples from 17 species of snakes were amplified using Polymerase Chain Reaction (PCR) and sequenced. The inter- and intra-specific variations of COI sequences were analyzed and compared based on Kimura-2-parameter (K-2P) distances; the minimal interspecific K-2P distance was 0.0934, which was bigger than the maximum intraspecific K-2P distance in Z. dhumnades (0.0523), indicating that Zaocys can be separated from its counterfeits. The Neighbor-Joining (N-J) tree of the snakes was constructed and the results show that snakes of the same species cluster with 100% bootstrap values. Since the Zaocys and its counterfeits are of different species, they can be distinguished using the N-J tree method. Another 10 samples of Zaocys from markets and drug stores were identified at the species level, among which 5 samples were proven to be the counterfeits--Ptyas korros. PMID:24857374

  15. Phylogenetic relationship of Turkish Apis mellifera subspecies based on sequencing of mitochondrial cytochrome C oxidase I region.

    PubMed

    Özdil, F; İlhan, F

    2012-01-01

    Mitochondrial DNA sequence variation can be used to infer honey bee evolutionary relationships. We examined DNA sequence diversity in the cytochrome C oxidase I (COI or Cox1) gene segment of the mitochondrial genome in 112 samples of Apis mellifera from 15 different populations in Turkey. Six novel haplotypes were found for the COI gene segment. There were eight variable sites in the COI gene, although only three were parsimony-informative sites. The mean pairwise genetic distance was 0.3% for the COI gene segment. Neighbor-joining (NJ) trees of the COI gene segment were constructed with the published sequences of A. mellifera haplotypes that are available in GenBank; the genetic variation was compared among the different honeybee haplotypes. The NJ dendogram based on the COI sequences available in GenBank showed that Eastern European races were clustered together, whereas the Mellifera and Iberian haplotypes were clustered far apart. The haplotypes found in this study were clustered together with A. mellifera ligustica and some of the Greek honey bees (accession Nos. GU056169 and GU056170) found in NCBI GenBank database. This study expands the knowledge about the mitochondrial COI region and presents the first comprehensive sequence analysis of this region in Turkish honeybees. PMID:22614282

  16. Identification of cephalopod species from the North and Baltic Seas using morphology, COI and 18S rDNA sequences

    NASA Astrophysics Data System (ADS)

    Gebhardt, Katharina; Knebelsberger, Thomas

    2015-09-01

    We morphologically analyzed 79 cephalopod specimens from the North and Baltic Seas belonging to 13 separate species. Another 29 specimens showed morphological features of either Alloteuthis mediaor Alloteuthis subulata or were found to be in between. Reliable identification features to distinguish between A. media and A. subulata are currently not available. The analysis of the DNA barcoding region of the COI gene revealed intraspecific distances (uncorrected p) ranging from 0 to 2.13 % (average 0.1 %) and interspecific distances between 3.31 and 22 % (average 15.52 %). All species formed monophyletic clusters in a neighbor-joining analysis and were supported by bootstrap values of ≥99 %. All COI haplotypes belonging to the 29 Alloteuthis specimens were grouped in one cluster. Neither COI nor 18S rDNA sequences helped to distinguish between the different Alloteuthis morphotypes. For species identification purposes, we recommend the use of COI, as it showed higher bootstrap support of species clusters and less amplification and sequencing failure compared to 18S. Our data strongly support the assumption that the genus Alloteuthis is only represented by a single species, at least in the North Sea. It remained unclear whether this species is A. subulata or A. media. All COI sequences including important metadata were uploaded to the Barcode of Life Data Systems and can be used as reference library for the molecular identification of more than 50 % of the cephalopod fauna known from the North and Baltic Seas.

  17. The complete mitochondrial genome sequence of Beaufortia szechuanensis (Cypriniformes, Balitoridae).

    PubMed

    Wu, Jiayun; He, Yuxiao; Ren, Hongmei; Zhang, Yi; Du, Zongjun; Xie, Meng; Zhu, Guangxiang; Wang, Qin; Jiang, Yanzhi; He, Tao; Wen, Anxiang

    2016-07-01

    The Beaufortia szechuanensis is endemic to the upper reaches of Yangtze River in China. In this study, we successfully sequenced the mitochondrial genome of the B. szechuanensis, collected from the Qingyi River. The complete mitochondrial genome of B. szechuanensis was a circular molecule of 16,559 bp in length, containing 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, an origin of light-strand replication (OL) and a control region (D-loop). It is the first complete mitochondrial DNA data in the genus Beaufortia. The cytochrome c oxidase subunit I (COI) sequence of 14 species in Balitoridae was used for phylogenetic analysis. The topology demonstrated that the Balitoridae can be classified into two subfamilies, and the B. szechuanensis belongs to the subfamily Gastromyzoninae. PMID:25922961

  18. Genetic diversity in two Japanese flounder populations from China seas inferred using microsatellite markers and COI sequences

    NASA Astrophysics Data System (ADS)

    Xu, Dongdong; Li, Sanlei; Lou, Bao; Zhang, Yurong; Zhan, Wei; Shi, Huilai

    2012-07-01

    Japanese flounder is one of the most important commercial species in China; however, information on the genetic background of natural populations in China seas is scarce. The lack of genetic data has hampered fishery management and aquaculture development programs for this species. In the present study, we have analyzed the genetic diversity in natural populations of Japanese flounder sampled from the Yellow Sea (Qingdao population, QD) and East China Sea (Zhoushan population, ZS) using 10 polymorphic microsatellite loci and cytochrome c oxidase subunit I (COI) sequencing data. A total of 68 different alleles were observed over 10 microsatellite loci. The total number of alleles per locus ranged from 2 to 9, and the number of genotypes per locus ranged from 3 to 45. The observed heterozygosity and expected heterozygosity in QD were 0.733 and 0.779, respectively, and in ZS the heterozygosity values were 0.708 and 0.783, respectively. Significant departures from Hardy-Weinberg equilibrium were observed in 7 of the 10 microsatellite loci in each of the two populations. The COI sequencing analysis revealed 25 polymorphic sites and 15 haplotypes in the two populations. The haplotype diversity and nucleotide diversity in the QD population were 0.746±0.072 8 and 0.003 34±0.001 03 respectively, and in ZS population the genetic diversity values were 0.712±0.047 0 and 0.003 18±0.000 49, respectively. The microsatellite data ( F st =0.048 7, P <0.001) and mitochondrial DNA data ( F st =0.128, P <0.001) both revealed significant genetic differentiation between the two populations. The information on the genetic variation and differentiation in Japanese flounder obtained in this study could be used to set up suitable guidelines for the management and conservation of this species, as well as for managing artificial selection programs. In future studies, more geographically diverse stocks should be used to obtain a deeper understanding of the population structure of Japanese

  19. Simultaneous identification and DNA barcoding of six Eimeria species infecting turkeys using PCR primers targeting the mitochondrial cytochrome c oxidase subunit I (mtCOI) locus.

    PubMed

    Hafeez, Mian A; Shivaramaiah, Srichaitanya; Dorsey, Kristi Moore; Ogedengbe, Mosun E; El-Sherry, Shiem; Whale, Julia; Cobean, Julie; Barta, John R

    2015-05-01

    Species-specific PCR primers targeting the mitochondrial cytochrome c oxidase subunit I (mtCOI) locus were generated that allow for the specific identification of the most common Eimeria species infecting turkeys (i.e., Eimeria adenoeides, Eimeria meleagrimitis, Eimeria gallopavonis, Eimeria meleagridis, Eimeria dispersa, and Eimeria innocua). PCR reaction chemistries were optimized with respect to divalent cation (MgCl2) and dNTP concentrations, as well as PCR cycling conditions (particularly anneal temperature for primers). Genomic DNA samples from single oocyst-derived lines of six Eimeria species were tested to establish specificity and sensitivity of these newly designed primer pairs. A mixed 60-ng total DNA sample containing 10 ng of each of the six Eimeria species was used as DNA template to demonstrate specific amplification of the correct product using each of the species-specific primer pairs. Ten nanograms of each of the five non-target Eimeria species was pooled to provide a non-target, control DNA sample suitable to test the specificity of each primer pair. The amplifications of the COI region with species-specific primer pairs from pooled samples yielded products of expected sizes (209 to 1,012 bp) and no amplification of non-target Eimeria sp. DNA was detected using the non-target, control DNA samples. These primer pairs specific for Eimeria spp. of turkeys did not amplify any of the seven Eimeria species infecting chickens. The newly developed PCR primers can be used as a diagnostic tool capable of specifically identifying six turkey Eimeria species; additionally, sequencing of the PCR amplification products yields sequence-based genotyping data suitable for identification and molecular phylogenetics. PMID:25678350

  20. Phylogenetic affinities of Diplonema within the Euglenozoa as inferred from the SSU rRNA gene and partial COI protein sequences.

    PubMed

    Maslov, D A; Yasuhira, S; Simpson, L

    1999-03-01

    In order to shed light on the phylogenetic position of diplonemids within the phylum Euglenozoa, we have sequenced small subunit rRNA (SSU rRNA) genes from Diplonema (syn. Isonema) papillatum and Diplonema sp. We have also analyzed a partial sequence of the mitochondrial gene for cytochrome c oxidase subunit I from D. papillatum. With both markers, the maximum likelihood method favored a closer grouping of diplonemids with kinetoplastids, while the parsimony and distance suggested a closer relationship of diplonemids with euglenoids. In each case, the differences between the best tree and the alternative trees were small. The frequency of codon usage in the partial D. papillatum COI was different from both related groups; however, as is the case in kinetoplastids but not in Euglena, both the non-canonical UGA codon and the canonical UGG codon were used to encode tryptophan in Diplonema. PMID:10724517

  1. Evolutionary history and phylogenetic relationship between Auxis thazard and Auxis rochei inferred from COI sequences of mtDNA.

    PubMed

    Kumar, Girish; Kunal, Swaraj Priyaranjan; Shyama, S K

    2013-01-01

    Tunas of the genus Auxis are cosmopolitan species and the smallest members of the tribe Thunnini, the true tunas. In the present study, COI sequences of mtDNA were employed to examine the evolutionary history and phylogenetic relationship between A. thazard and A. rochei. A total of 29 COI sequences were retrieved from NCBI. Historic demographic analyses of sequence data showed that A. thazard has undergone sudden population expansion in the past while population size of A. rochei has been remain constant for long period. Non-significant value of Tajimas's D (P = 0.22400) and Fu's FS (P = 0.21400) test fail to reject the null hypothesis of neutral evolution for A. rochei. Phylogenetic analyses of nucleotide sequences demonstrated separate clusters for both species and are strongly supported by 98% bootstrap value. The results of the present study suggest the recent founding of A. thazard in world ocean while A. rochei represents the ancestral species. PMID:24084241

  2. Unraveling the sequence information in COI barcode to achieve higher taxon assignment based on Indian freshwater fishes.

    PubMed

    Chakraborty, Mohua; Ghosh, Sankar Kumar

    2015-04-01

    Efficacy of cytochrome c oxidase subunit I (COI) DNA barcode in higher taxon assignment is still under debate in spite of several attempts, using the conventional DNA barcoding methods, to assign higher taxa. Here we try to understand whether nucleotide and amino acid sequence in COI gene carry sufficient information to assign species to their higher taxonomic rank, using 160 species of Indian freshwater fishes. Our results reveal that with increase in the taxonomic rank, sequence conservation decreases for both nucleotides and amino acids. Order level exhibits lowest conservation with 50% of the nucleotides and amino acids being conserved. Among the variable sites, 30-50% were found to carry high information content within an order, while it was 70-80% within a family and 80-99% within a genus. High information content shows sites with almost conserved sequence but varying at one or two locations, which can be due to variations at species or population level. Thus, the potential of COI gene in higher taxon assignment is revealed with validation of ample inherent signals latent in the gene. PMID:24409929

  3. Unusually high genetic diversity in COI sequences of Chimarra obscura (Trichoptera: Philopotamidae)

    EPA Science Inventory

    Chimarra obscura (Walker 1852) is a philopotamid caddisfly found throughout much of North America. Using the COI DNA barcode locus, we have found unexpectedly high amounts of genetic diversity and distances within C. obscura. Of the approximately 150 specimens sampled, we have fo...

  4. Identification of a group of cryptic marine limpet species, Cellana karachiensis (Mollusca: Patellogastropoda) off Veraval coast, India, using mtDNA COI sequencing.

    PubMed

    Joseph, Sneha; Poriya, Paresh; Vakani, Bhavik; Singh, S P; Kundu, Rahul

    2016-01-01

    Present communication reports the phylogenetic relationship between three groups of a marine limpet having different color banding patterns using COI sequencing. Samples were sequenced for mtDNA COI gene using universal primer. Comparative BLAST revealed that all three types were around 99.59% identical with Cellana karachiensis, first record of this species from Indian coasts. Apart from the morphological variations, the mtDNA COI gene analysis revealed around 1% nucleotide variations between these three types. The observed dissimilarity in COI sequences was possibly too little to consider these types as three different species. The derivation of amino acid positions indicated that these types could possibly be a complex of three cryptic species of C. karachiensis. The study proposes that the Oman and Indian populations of C. karachiensis might have derived by allopatric speciation due to geographical isolation. The group of these three cryptic species, sharing same habitat between themselves, possibly showed sympatric speciation. PMID:25109628

  5. Determination of Opiinae parasitoids (Hymenoptera: Braconidae) associated with crop infesting Bactrocera spp. (Diptera: Tephritidae) using COI and Cyt b sequences

    NASA Astrophysics Data System (ADS)

    Shariff, Safiah; Yaakop, Salmah; Zain, Badrul Munir Md.

    2013-11-01

    Members of the Opiinae subfamily (Hymenoptera: Braconidae) are well known as important parasitoids of fruit fly larvae (Diptera: Tephritidae). They are widely used as biological control agents of fruit flies, especially the Bactrocera Macquart species that infest fruits. In this study, the larvae of fruit flies were collected from infested crops including star fruit, guava, wax apple and ridge gourd. The parasitized larvae were then reared under laboratory conditions until emergence of the adult parasitoids. Additionally, Malaise trap also was used to collect parasitoid species. The general concept of the multiplex PCR has been performed is to amplify two mitochondrial DNA markers, namely cytochrome oxidase subunit I (COI) and cytochrome b (Cyt b) simultaneously. Therefore, the lengthy process of reaction will be reduced. The status of the fruit fly species has also been confirmed by using COI marker on the early stage of the larvae. Maximum parsimony (MP) and Bayesian Inference (BI) were implemented to help and support the identification of Opiinae species. The result obtained from this study showed three parasitoid genera of the Opiinae viz. Fopius Wharton, Psyttalia Walker and Diachasmimorpha Viereck. Each genus has been determined by clustering together in a similar clade according to their infested crops. Therefore, accurate determination of parasitoids and the fruit fries species was highly useful and necessary for successful biological control of Bactrocera species.

  6. Genetic Population Structure of Thunnus albacares in the Central Pacific Ocean Based on mtDNA COI Gene Sequences.

    PubMed

    Li, Weiwen; Chen, Xinjun; Xu, Qianghua; Zhu, Jiangfeng; Dai, Xiaojie; Xu, Liuxiong

    2015-04-01

    Thunnus albacares is an important fishery species throughout the world. Polymorphisms of sequence variations in mtDNA COI genes were assessed to explore the genetic differentiations among 11 populations of T. albacares sampled from the central Pacific Ocean. Sixty-one mtDNA haplotypes and 38 variable sites were detected. Analysis of mtDNA COI sequences revealed that tuna from the 11 localities were characterized by moderately high haplotype diversity (h = 0.650 ± 0.040), while sequence divergence between haplotypes was relatively low (π = 0.00364 ± 0.00044). Analyses of molecular variance and FST analysis supported that significant genetic differentiations existed between some of the sampled populations. Tests of neutral evolution and mismatch distribution analysis suggested that T. albacares might have experienced a population expansion, which possibly occurred within the last 0.82 million years. Our study unraveled the genetic structure of the extant population of T. albacares and addressed the related fishery management issues including fishery stock identification and management. PMID:25854852

  7. Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea.

    PubMed

    Al-Rshaidat, Mamoon M D; Snider, Allison; Rosebraugh, Sydney; Devine, Amanda M; Devine, Thomas D; Plaisance, Laetitia; Knowlton, Nancy; Leray, Matthieu

    2016-09-01

    High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales. PMID:27584940

  8. Genetic divergence analysis of the Common Barn Owl Tyto alba (Scopoli, 1769) and the Short-eared Owl Asio flammeus (Pontoppidan, 1763) from southern Chile using COI sequence

    PubMed Central

    Colihueque, Nelson; Gantz, Alberto; Rau, Jaime Ricardo; Parraguez, Margarita

    2015-01-01

    Abstract In this paper new mitochondrial COI sequences of Common Barn Owl Tyto alba (Scopoli, 1769) and Short-eared Owl Asio flammeus (Pontoppidan, 1763) from southern Chile are reported and compared with sequences from other parts of the World. The intraspecific genetic divergence (mean p-distance) was 4.6 to 5.5% for the Common Barn Owl in comparison with specimens from northern Europe and Australasia and 3.1% for the Short-eared Owl with respect to samples from north America, northern Europe and northern Asia. Phylogenetic analyses revealed three distinctive groups for the Common Barn Owl: (i) South America (Chile and Argentina) plus Central and North America, (ii) northern Europe and (iii) Australasia, and two distinctive groups for the Short-eared Owl: (i) South America (Chile and Argentina) and (ii) north America plus northern Europe and northern Asia. The level of genetic divergence observed in both species exceeds the upper limit of intraspecific comparisons reported previously for Strigiformes. Therefore, this suggests that further research is needed to assess the taxonomic status, particularly for the Chilean populations that, to date, have been identified as belonging to these species through traditional taxonomy. PMID:26668551

  9. Genetic divergence analysis of the Common Barn Owl Tyto alba (Scopoli, 1769) and the Short-eared Owl Asio flammeus (Pontoppidan, 1763) from southern Chile using COI sequence.

    PubMed

    Colihueque, Nelson; Gantz, Alberto; Rau, Jaime Ricardo; Parraguez, Margarita

    2015-01-01

    In this paper new mitochondrial COI sequences of Common Barn Owl Tyto alba (Scopoli, 1769) and Short-eared Owl Asio flammeus (Pontoppidan, 1763) from southern Chile are reported and compared with sequences from other parts of the World. The intraspecific genetic divergence (mean p-distance) was 4.6 to 5.5% for the Common Barn Owl in comparison with specimens from northern Europe and Australasia and 3.1% for the Short-eared Owl with respect to samples from north America, northern Europe and northern Asia. Phylogenetic analyses revealed three distinctive groups for the Common Barn Owl: (i) South America (Chile and Argentina) plus Central and North America, (ii) northern Europe and (iii) Australasia, and two distinctive groups for the Short-eared Owl: (i) South America (Chile and Argentina) and (ii) north America plus northern Europe and northern Asia. The level of genetic divergence observed in both species exceeds the upper limit of intraspecific comparisons reported previously for Strigiformes. Therefore, this suggests that further research is needed to assess the taxonomic status, particularly for the Chilean populations that, to date, have been identified as belonging to these species through traditional taxonomy. PMID:26668551

  10. Biodiversity of the Betta smaragdina (Teleostei: Perciformes) in the northeast region of Thailand as determined by mitochondrial COI and nuclear ITS1 gene sequences☆

    PubMed Central

    Kowasupat, Chanon; Panijpan, Bhinyo; Laosinchai, Parames; Ruenwongsa, Pintip; Phongdara, Amornrat; Wanna, Warapond; Senapin, Saengchan; Phiwsaiya, Kornsunee

    2014-01-01

    In Thailand, there are currently five recognized species members of the bubble-nesting Betta genus, namely Betta splendens, B. smaragdina, B. imbellis, B. mahachaiensis and B. siamorientalis. In 2010, we indicated the possibility, based on COI barcoding evidence, that there might be two additional species, albeit cryptic, related to the type-locality B. smaragdina in some provinces in the northeast of Thailand. In the present study, after a more extensive survey of the northeast, and phylogenetic analyses based on COI and ITS1 sequences, the B. smaragdina group may be composed of at least 3 cryptic species members. The phylogenetic positions of these B. smaragdina group members in the bubble-nesting bettas' tree together with those of their congeners have been consolidated by better DNA sequence quality and phylogenetic analyses. With a better supported tree, the species statuses of B. siamorientalis and the Cambodian B. smaragdina-like fish, B. stiktos, are also confirmed. PMID:25606392

  11. Molecular differences in the mitochondrial cytochrome oxidase I (mtCOI) gene and development of a species-specific marker for onion thrips, Thrips tabaci Lindeman, and melon thrips, T. palmi Karny (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae).

    PubMed

    Asokan, R; Krishna Kumar, N K; Kumar, Vikas; Ranganath, H R

    2007-10-01

    A quick and developmental-stage non-limiting method of the identification of vectors of tospoviruses, such as Thrips tabaci and T. palmi, is important in the study of vector transmission, insecticide resistance, biological control, etc. Morphological identification of these thrips vectors is often a stumbling block in the absence of a specialist and limited by polymorphism, sex, stage of development, etc. Molecular identification, on the other hand, is not hampered by the above factors and can easily be followed by a non-specialist with a little training. The mitochondrial cytochrome oxidase I (mtCOI) exhibits reliable inter-species variations as compared to the other markers. In this communication, we present the differences in the mtCOI partial sequence of morphologically identified specimens of T. tabaci and T. palmi collected from onion and watermelon, respectively. Species-specific markers, identified in this study, could successfully determine T. tabaci and T. palmi, which corroborated the morphological identification. Phylogenetic analyses showed that both T. tabaci and T. palmi formed different clades as compared to the other NCBI accessions. The implication of these variations in vector efficiency has to be investigated further. The result of this investigation is useful in the quick identification of T. tabaci and T. palmi, a critical factor in understanding the epidemiology of the tospoviruses, their management and also in quarantine. PMID:17916265

  12. Discrimination of two natural biocontrol agents in the Mediterranean region based on mitochondrial DNA sequencing data.

    PubMed

    Evangelou, V I; Bouga, M; Emmanouel, N G; Perdikis, D Ch; Papadoulis, G Th

    2013-12-01

    Macrolophus pygmaeus and M. melanotoma (Hemiptera: Miridae) are biological control agents used in greenhouse crops, the former preferring plants of the Solanaceae family and the latter the aster Dittrichia viscosa. The discrimination of these species is of high significance for effective biological pest control, but identification based on morphological characters of the host plant is not always reliable. In this study, sequencing analysis of mitochondrial gene segments 12S rDNA and COI has been combined with crossing experiments and morphological observations to develop new markers for Macrolophus spp. discrimination and to provide new data on their genetic variability. This is the first comprehensive research in Greece on M. pygmaeus and M. melanotoma genetic variability based on sequencing data from 12S rDNA and COI gene segments. The relationship of this variability to host plant preference must be investigated in an agricultural ecosystem. PMID:23839086

  13. The sequence and organization of complete mitochondrial genome of the yellowfin tuna, Thunnus albacares (Bonnaterre, 1788).

    PubMed

    Pang, Jiaohui; Cheng, Qiqun; Sun, Dandan; Zhang, Heng; Jin, Shaofei

    2016-09-01

    Yellowfin tuna (Thunnus albacares) is one of the most important economic fishes around the world. In the present study, we determined the complete mitochondrial DNA sequence and organization of T. albacares. The entire mitochondrial genome is a circular-molecule of 16,528 bp in length, which encodes 37 genes in all. These genes comprise 13 protein-coding genes (ATP6 and 8, COI-III, Cytb, ND1-6 and 4 L), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (12S and 16S rRNAs). The complete mitochondrial genome sequence of T. albacares can provide basic information for the studies on molecular taxonomy and conservation genetics of teleost fishes. PMID:25707413

  14. First report on the occurrence of the comb pen shell, Atrina pectinata (Linnaeus, 1767) (Bivalvia: Pinnidae) in Ulleungdo Island in the East Sea: Ecology and molecular identification of the species using COI gene sequence

    NASA Astrophysics Data System (ADS)

    Yang, Hyun-Sung; Kang, Hyun-Sil; Park, Heung-Sik; Noh, Choong Hwan; Jeong, Eui-Young; Choi, Kwang-Sik

    2015-12-01

    Pen shell is one of the largest marine bivalves inhabiting shallow subtidal soft bottoms in the west Pacific and Indian Oceans. In Korea, the comb pen shell Atrina pectinata fisheries has been established on the south and west coasts. Recently, a pen shell population has been discovered from a subtidal sand flat (25-30 m depth) in Ulleungdo Island located in the East Sea of Korea, suggesting a potential shellfish resource in this area. In the present study, we first surveyed the population density and size of the unique pen shell using SCUBA, and identified the pen shell to species level using mitochondrial cytochrome oxidase I gene (COI) sequence. An underwater survey carried out from July to September 2013 revealed that populations of pen shell patched on subtidal sand flat at a depth of 20-25 m. Grain size analysis indicated that sand particles accounted for 99% of the 600 × 700 m sand flat. The underwater survey also indicated that density of the pen shell ranged between 6-19 ind/m2, with a mean of 11 ind/m2. Shell height (i.e. longest axis of the shell) of the pen shell on the sand flat varied between 17.2 cm to 28.8 cm, with a mean of 25.1 cm, and the age was estimated to range between 1.5-7.5 yrs, with a mean of 5 yr. COI DNA sequence obtained from the pen shell in this study showed 98.9-99.2% similarity to Atrina pectinata (Linnaeus 1767) reported from Japan. In the cluster analysis, the COI DNA sequence of the pen shells from Ulleungdo Island was grouped with A. pectinata reported from Japan and China, indicating that the pen shell discovered in this study was A. pectinata, commonly distributed on the west and south coasts of Korea.

  15. A preliminary phylogenetic analysis of Luidia (Paxillosida: Luidiidae) from Chinese waters with cytochrome oxidase subunit I (COI) sequences

    NASA Astrophysics Data System (ADS)

    Xiao, Ning; Liu, Ruiyu; Yuan, Shuai; Sha, Zhongli

    2013-09-01

    Luidia Forbes (Paxillosida: Luidiidae) are common soft bottom sea stars with 49 described species. Because of substantial morphological diversity, the taxonomy of the genus is complex and hasn't been resolved definitely. In order to resolve general taxonomic issues, and determine species boundaries and phylogenetic relationships within the genus Luidia, the sequences of cytochrome oxidase subunit I (COI) gene from 24 specimens of Luidia, belonging to eight taxa in Chinese waters, were studied. Three sequences of two species in genus Luidia from GenBank were used to analyze the phylogenetic relationships. The molecular phylogeny exhibited three main clades, each with strong bootstrap support: Clade A including Luidia quinaria from the Sea of Japan; Clade B including seven nominal species ( L. quinaria von Martens, L. yesoensis Goto, L. changi Liu, Liao and Li, L. orientalis Fisher, L. avicularia Fisher, L. longispina Sladen and L. hardwicki Gray) from Chinese waters; and Clade C including L. maculata Müller & Troschel from Chinese waters. Our molecular phylogeny results support the morphological Quinaria-Group and Alternata-Group assigned by Döderlein. Seven nominal species we sampled do not exhibit genetic distances that are large enough to recognize them as separate species. Cryptic species may exist in' Luidia quinaria' from the Yellow Sea and the Sea of Japan. Meaningful morphological characters need further investigation in Luidia.

  16. Universal COI primers for DNA barcoding amphibians.

    PubMed

    Che, Jing; Chen, Hong-Man; Yang, Jun-Xiao; Jin, Jie-Qiong; Jiang, Ke; Yuan, Zhi-Yong; Murphy, Robert W; Zhang, Ya-Ping

    2012-03-01

    DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians. PMID:22145866

  17. Comparing COI and ITS as DNA Barcode Markers for Mushrooms and Allies (Agaricomycotina)

    PubMed Central

    Dentinger, Bryn T. M.; Didukh, Maryna Y.; Moncalvo, Jean-Marc

    2011-01-01

    DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (∼450 bp) representing ∼100 morphospecies from ∼650 collections of Agaricomycotina using several sets of new primers. Large introns (∼1500 bp) at variable locations were detected in ∼5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (∼30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms. PMID:21966418

  18. A pilot study on the molecular phylogeny of Drepanoidea (Insecta: Lepidoptera) inferred from the nuclear gene EF-1alpha and the mitochondrial gene COI.

    PubMed

    Wu, C G; Han, H X; Xue, D Y

    2010-04-01

    A molecular phylogenetic study of the Drepanoidea based on the EF-1alpha sequences and combined EF-1alpha and COI sequences was carried out in order to infer higher classification at and above the subfamily level. The sample contained 14 taxa representing 13 genera recognized in the Drepanoidea. The results revealed that the Drepaninae, Thyatirinae and Cyclidiinae respectively form monophyletic groups. The sister relationship between the Drepaninae and the Thyatirinae was validated. The monophyly of the Cyclidiinae with the Drepaninae+Thyatirinae was supported robustly. Hypsomadius insignis and Oreta vatama within the traditional definition of the Drepaninae formed an individual clade with robust support (100%) and constitutes a sister relationship to a clade containing the rest of the Drepaninae in all the topologies, which means that the subfamily Oretinae of the Drepanidae should be restored. The family Drepanidae is divided into four subfamilies: Drepaninae, Oretinae, Thyatirinae and Cyclidiinae in this work. The family Epicopeiidae formed a monophyly with high bootstrap values. The result of combined analysis of EF-1alpha and COI showed that the Epicopeiidae have a closer phylogenetic relationship with the Geometridae than with the Drepanidae and belong to neither the Drepanoidea nor the Geometroidea. PMID:19580687

  19. The complete mitochondrial genome sequence of Pterophyllum scalare (Cichliformes: Cichlidae).

    PubMed

    Wang, Guang-Peng; Min, Qiao; Si, Gui-Cai

    2016-07-01

    Pterophyllum scalare belongs in the family Cichlidae of Cichliformes. This species and its congeners are characterized by a compressed and disc-shaped body with dorsal and anal spiny rays increasing in length from anterior to posterior part of the fin. In this study, we determine and describe the complete mitogenome sequence of Pterophyllum scalare for the first time, which is 16,494 bp in length, and contains 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 origin of replication on the light-strand (OL) and a putative control region. The overall base composition is 27.5% A, 26.8% T, 30.1% C and 15.6% G, with a slight AT bias (54.3%). All protein-coding genes share the start codon ATG, except for COI that begins with GTG. These results are expected to provide useful molecular data for phylogenetic studies of Cichlidae and Cichliformes. Maximum Likelihood (ML) tree and Bayesian analyses based on partitioned nucleotide sequences of 12 mitochondrial protein-coding genes were constructed and both yielded trees with identical topologies. PMID:26017040

  20. Targeted exome sequencing of suspected mitochondrial disorders

    PubMed Central

    Lieber, Daniel S.; Calvo, Sarah E.; Shanahan, Kristy; Slate, Nancy G.; Liu, Shangtao; Hershman, Steven G.; Gold, Nina B.; Chapman, Brad A.; Thorburn, David R.; Berry, Gerard T.; Schmahmann, Jeremy D.; Borowsky, Mark L.; Mueller, David M.; Sims, Katherine B.

    2013-01-01

    Objective: To evaluate the utility of targeted exome sequencing for the molecular diagnosis of mitochondrial disorders, which exhibit marked phenotypic and genetic heterogeneity. Methods: We considered a diverse set of 102 patients with suspected mitochondrial disorders based on clinical, biochemical, and/or molecular findings, and whose disease ranged from mild to severe, with varying age at onset. We sequenced the mitochondrial genome (mtDNA) and the exons of 1,598 nuclear-encoded genes implicated in mitochondrial biology, mitochondrial disease, or monogenic disorders with phenotypic overlap. We prioritized variants likely to underlie disease and established molecular diagnoses in accordance with current clinical genetic guidelines. Results: Targeted exome sequencing yielded molecular diagnoses in established disease loci in 22% of cases, including 17 of 18 (94%) with prior molecular diagnoses and 5 of 84 (6%) without. The 5 new diagnoses implicated 2 genes associated with canonical mitochondrial disorders (NDUFV1, POLG2), and 3 genes known to underlie other neurologic disorders (DPYD, KARS, WFS1), underscoring the phenotypic and biochemical overlap with other inborn errors. We prioritized variants in an additional 26 patients, including recessive, X-linked, and mtDNA variants that were enriched 2-fold over background and await further support of pathogenicity. In one case, we modeled patient mutations in yeast to provide evidence that recessive mutations in ATP5A1 can underlie combined respiratory chain deficiency. Conclusion: The results demonstrate that targeted exome sequencing is an effective alternative to the sequential testing of mtDNA and individual nuclear genes as part of the investigation of mitochondrial disease. Our study underscores the ongoing challenge of variant interpretation in the clinical setting. PMID:23596069

  1. Next-generation sequencing for mitochondrial disorders

    PubMed Central

    Carroll, C J; Brilhante, V; Suomalainen, A

    2014-01-01

    A great deal of our understanding of mitochondrial function has come from studies of inherited mitochondrial diseases, but still majority of the patients lack molecular diagnosis. Furthermore, effective treatments for mitochondrial disorders do not exist. Development of therapies has been complicated by the fact that the diseases are extremely heterogeneous, and collecting large enough cohorts of similarly affected individuals to assess new therapies properly has been difficult. Next-generation sequencing technologies have in the last few years been shown to be an effective method for the genetic diagnosis of inherited mitochondrial diseases. Here we review the strategies and findings from studies applying next-generation sequencing methods for the genetic diagnosis of mitochondrial disorders. Detailed knowledge of molecular causes also enables collection of homogenous cohorts of patients for therapy trials, and therefore boosts development of intervention. Linked Articles This article is part of a themed issue on Mitochondrial Pharmacology: Energy, Injury & Beyond. To view the other articles in this issue visit http://dx.doi.org/10.1111/bph.2014.171.issue-8 PMID:24138576

  2. Distribution of Mosquitoes in the South East of Argentina and First Report on the Analysis Based on 18S rDNA and COI Sequences

    PubMed Central

    Díaz-Nieto, Leonardo M.; Maciá, Arnaldo; Parisi, Gustavo; Farina, Juan L.; Vidal-Domínguez, María E.; Perotti, M. Alejandra; Berón, Corina M.

    2013-01-01

    Although Mar del Plata is the most important city on the Atlantic coast of Argentina, mosquitoes inhabiting such area are almost uncharacterized. To increase our knowledge in their distribution, we sampled specimens of natural populations. After the morphological identification based on taxonomic keys, sequences of DNA from small ribosomal subunit (18S rDNA) and cytochrome c oxidase I (COI) genes were obtained from native species and the phylogenetic analysis of these sequences were done. Fourteen species from the genera Uranotaenia, Culex, Ochlerotatus and Psorophora were found and identified. Our 18S rDNA and COI-based analysis indicates the relationships among groups at the supra-species level in concordance with mosquito taxonomy. The introduction and spread of vectors and diseases carried by them are not known in Mar del Plata, but some of the species found in this study were reported as pathogen vectors. PMID:24098700

  3. EST and mitochondrial DNA sequences support a distinct Pacific form of salmon louse, Lepeophtheirus salmonis.

    PubMed

    Yazawa, Ryosuke; Yasuike, Motoshige; Leong, Jong; von Schalburg, Kristian R; Cooper, Glenn A; Beetz-Sargent, Marianne; Robb, Adrienne; Davidson, William S; Jones, Simon R M; Koop, Ben F

    2008-01-01

    Nuclear deoxyribonucleic acid sequences from approximately 15,000 salmon louse expressed sequence tags (ESTs), the complete mitochondrial genome (16,148bp) of salmon louse, and 16S ribosomal ribonucleic acid (rRNA) and cytochrome oxidase subunit I (COI) genes from 68 salmon lice collected from Japan, Alaska, and western Canada support a Pacific lineage of Lepeophtheirus salmonis that is distinct from that occurring in the Atlantic Ocean. On average, nuclear genes are 3.2% different, the complete mitochondrial genome is 7.1% different, and 16S rRNA and COI genes are 4.2% and 6.1% different, respectively. Reduced genetic diversity within the Pacific form of L. salmonis is consistent with an introduction into the Pacific from the Atlantic Ocean. The level of divergence is consistent with the hypothesis that the Pacific form of L. salmonis coevolved with Pacific salmon (Onchorhynchus spp.) and the Atlantic form coevolved with Atlantic salmonids (Salmo spp.) independently for the last 2.5-11 million years. The level of genetic divergence coincides with the opportunity for migration of fish between the Atlantic and Pacific Ocean basins via the Arctic Ocean with the opening of the Bering Strait, approximately 5 million years ago. The genetic differences may help explain apparent differences in pathogenicity and environmental sensitivity documented for the Atlantic and Pacific forms of L. salmonis. PMID:18574633

  4. BAYESIAN PHYLOGENETIC ANALYSIS OF MITOCHONDRIAL COI DNA SEQUENCE FROM GLOBAL SAMPLES OF BEMISIA TABACI (HEMIPTERA: ALEYRODIDAE)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bemisia tabaci (Gen.)(Hemiptera: Aleyrodidae) is one of the most devastating agricultural pests worldwide and affects the yield of a broad range of agricultural, fiber, vegetable and ornamental crops. Global phylogenetic relationships of the major races of B. tabaci remain unresolved thus a Bayesi...

  5. Global relationships of Bemisia tabaci (Hemiptera: Aleyrodidae) revealed using Bayesian analysis of mitochondrial COI DNA sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bemisia tabaci (Gen.)(Hemiptera: Aleyrodidae) is a species complex that is one of the most devastating agricultural pests worldwide and affects a broad range of food, fiber and ornamental crops. Unfortunately, using parsimony and neighbor joining methods, global phylogenetic relationships of the ma...

  6. Mitochondrial DNA sequence variation in Drosophilid species (Diptera: Drosophilidae) along altitudinal gradient from Central Himalayan region of India.

    PubMed

    Sarswat, Manisha; Dewan, Saurabh; Fartyal, Rajendra Singh

    2016-06-01

    Central Himalayan region of India encompasses varied ecological habitats ranging from near tropics to the mid-elevation forests dominated by cool-temperate taxa. In past, we have reported several new records and novel species from Uttarakhand state of India. Here, we assessed genetic variations in three mitochondrial genes, namely, 16S rRNA, cytochrome c oxidase subunit I and cytochrome c oxidase subunit II (COI and COII) in 26 drosophilid species collected along altitudinal transect from 550 to 2700 m above mean sea level. In the present study, overall 543 sequences were generated, 82 for 16S rRNA, 238 for COI, 223 for COII with 21, 47 and 45 mitochondrial haplotypes for 16S rRNA, COI and COII genes, respectively. Almost all species were represented by 2-3 unique mitochondrial haplotypes, depicting a significant impact of environmental heterogeneity along altitudinal gradient on genetic diversity. Also for the first time, molecular data of some rare species like Drosophila mukteshwarensis, Liodrosophila nitida, Lordiphosa parantillaria, Lordiphosa ayarpathaensis, Scaptomyza himalayana, Scaptomyza tistai, Zaprionus grandis and Stegana minuta are provided to public domains through this study. PMID:27350680

  7. Sequencing and comparing whole mitochondrial genomes ofanimals

    SciTech Connect

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  8. Mitochondrial genome sequencing in atherosclerosis: what's next?

    PubMed

    Sazonova, Margarita A; Shkurat, Tatiana P; Demakova, Natalya A; Zhelankin, Andrey V; Barinova, Valeria A; Sobenin, Igor A; Orekhov, Alexander N

    2016-01-01

    Cardiovascular diseases are currently a basic cause of mortality in highly developed countries. The major reason for genesis and development of cardiovascular diseases is atherosclerosis. At the present time high technology methods of molecular genetic diagnostics can significantly simplify early presymptomatic recognition of patients with atherosclerosis, to detect risk groups and to perform a family analysis of this pathology. A Next-Generation Sequencing (NGS) technology can be characterized by high productivity and cheapness of full genome analysis of each DNA sample. We suppose that in the nearest future NGS methods will be widely used for scientific and diagnostic purposes, including personalized medicine. In the present review article literature data on using NGS technology were described in studying mitochondrial genome mutations associated with atherosclerosis and its risk factors, such as mitochondrial diabetes, mitochondrial cardiomyopathy, diabetic nephropathy and left ventricular hypertrophy. With the use of the NGS technology it proved to be possible to detect a range of homoplasmic and heteroplasmic mutations and mitochondrial genome haplogroups which are associated with these pathologies. Meanwhile some mutations and haplogroups were detected both in atherosclerosis and in its risk factors. It conveys the suggestion that there are common pathogenetic mechanisms causing these pathologies. What comes next? New paradigm of crosstalk between non-pharmaceutical (including molecular genetic) and true pharmaceutical approaches may be developed to fill the niche of effective and pathogenically targeted pretreatment and treatment of preclinical and subclinical atherosclerosis to avoid the development of chronic life-threatening disease. PMID:26561059

  9. Phylogeny of Thaumastodermatidae (Gastrotricha: Macrodasyida) Inferred from Nuclear and Mitochondrial Sequence Data

    PubMed Central

    Todaro, M. Antonio; Kånneby, Tobias; Dal Zotto, Matteo; Jondelius, Ulf

    2011-01-01

    Background Phylogenetic relationships within Gastrotricha are poorly known. Attempts to shed light on this subject using morphological traits have led to hypotheses lacking satisfactory statistical support; it seemed therefore that a different approach was needed. Methodology/Principal Findings In this paper we attempt to elucidate the relationships within the taxonomically vast family Thaumastodermatidae (Macrodasyida) using molecular sequence data. The study includes representatives of all the extant genera of the family and for the first time uses a multi-gene approach to infer evolutionary liaisons within Gastrotricha. The final data set comprises sequences of three genes (18S, 28S rDNA and COI mtDNA) from 41 species, including 29 thaumastodermatids, 11 non-thaumastodermatid macrodasyidans and a single chaetonotidan. Molecular data was analyzed as a combined set of 3 genes and as individual genes, using Bayesian and maximum likelihood approaches. Two different outgroups were used: Xenotrichula intermedia (Chaetonotida) and members of the putative basal Dactylopodola (Macrodasyida). Thaumastodermatidae and all other sampled macrodasyidan families were found monophyletic except for Cephalodasyidae. Within Thaumastodermatidae Diplodasyinae and Thaumastodermatinae are monophyletic and so are most genera. Oregodasys turns out to be the most basal group within Thaumastodermatinae in analyses of the concatenated data set as well as in analyses of the nuclear genes. Thaumastoderma appears as the sister taxon to the remaining species. Surprisingly, Tetranchyroderma is non-monophyletic in our analyses as one group of species clusters with Ptychostomella while another appears as the sister group of Pseudostomella. Conclusions/Significance Results in general agree with the current classification; however, a revision of the more derived thaumastodermatid taxa seems necessary. We also found that the ostensible COI sequences from several species do not conform to the general

  10. A COI Nonsynonymous Mutation as Diagnostic Tool for Intraspecific Discrimination in the European Anchovy Engraulis encrasicolus (Linnaeus)

    PubMed Central

    Pappalardo, Anna Maria; Federico, Concetta; Sabella, Giorgio; Saccone, Salvatore; Ferrito, Venera

    2015-01-01

    The European anchovy, Engraulis encrasicolus, is currently one of the principal target species for commercial fisheries in Europe. In this study, the mitochondrial Control Region (CR) and the Cytochrome Oxidase I (COI) mitochondrial gene were analyzed in 74 specimens of E. encrasicolus from four localities in the central Mediterranean. In both populations, the two markers revealed the presence of two main haplogroups, A and B, already detected in previous investigations of different classes of molecular markers. Both CR and COI markers consistently identified two haplogroups. The COI sequence analysis identified a non-synonymous transversion (T to G) at position 116 of the translated sequence, resulting in an amino acid change. All COI sequences of haplogroup A had an amino acid sequence with alanine in this position, while serine was present in the same position in haplogroup B. The two haplogroups A and B were also discriminated by the variable number of TACA elements at the 5’-end of the mitochondrial CR. The selection tests applied to the COI dataset revealed that codon 116 was not under positive selection, that seven amino acid changes were under purifying selection, and that two amino acids were under episodic positive selection. PMID:26599908

  11. Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

    PubMed Central

    Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

    2014-01-01

    Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

  12. Genetic variation and population structure of hair crab (Erimacrus isenbeckii ) in Japan inferred from mitochondrial DNA sequence analysis.

    PubMed

    Azuma, Noriko; Kunihiro, Yasushi; Sasaki, Jun; Mihara, Eiji; Mihara, Yukio; Yasunaga, Tomoaki; Jin, Deuk-Hee; Abe, Syuiti

    2008-01-01

    Genetic variation and population structure of hair crab (Erimacrus isenbeckii) were examined using nucleotide sequence analysis of 580 base pairs (bp) in the 3' portion of the mitochondrial cytochrome c oxidase subunit I gene (COI) of 20 samples collected from 16 locales in Japan (the Hokkaido and Honshu Islands) and one in Korea. A total of 27 haplotypes was defined by 23 variable nucleotide sites in the examined COI region. Pairwise population F (ST) estimates and neighbor-joining tree inferred distinct genetic differentiation between the representative samples from the Pacific Ocean off the Eastern Hokkaido Island and the Sea of Japan, while others were intermediate between these two groups. AMOVA also showed a weak but significant differentiation among these three groups. The present results suggest a moderate population structure of hair crab, probably influenced by high gene flow between regional populations due to sea current dependent larval dispersal of this species. PMID:17955293

  13. Molecular phylogenetic analysis of Acridoidea (Orthoptera: Caelifera) based on mitochondrial cytochrome oxidase subunit sequences.

    PubMed

    Dong, Lijun; Shi, Jianping; Zhang, Xiaohong; Zhang, Yulong; Li, Xinjiang; Yin, Hong

    2015-01-01

    Phylogenetic relationships of Acridoidea were examined using mitochondrial cytochrome oxidase subunit sequences (COI, COII and COIII, total 2970bp). Fourteen grasshopper species of thirteen genera from seven families were sequenced to obtain mitochondrial genes data, along with twenty-two grasshopper species were obtained from the GenBank nucleotide database. The purpose of this study is to infer the phylogenetic relationships among families within Acridoidea and testing the monophyly of Acridoidea and each families of it. Phylogenic trees were reconstructed using Maximum Likelihood (ML) and Maximum Parsimony (MP) methods with Tettigonioidea and Gryllotalpoidea as outgroups. The putative initiation codon for COI is CCG in thirteen studied species and ATC in Bryodema luctuosum luctuosum. The 2970 bp concatenated sequences included 1431 conserved sites, 1539 variable sites, and 1216 parsimony-informative sites, the nucleotide compositions were significantly biased toward A and T (68.8%). The resulted phylogenetic trees supported the monophyly of Acridoidea, but did not entirely agree with the traditional morphology-based taxonomic system of grasshoppers within Acridoidea. The monophyly of three families of Acrididae, Catantopidae and Arcypteridae were not supported; Gomphoceridae and Arcypteridae were recovered together as a monophyletic group because of closer phylogenetic relationships; Pyrgomorphidae and Chrotogonidae have the same closer relationships; Pneumoridae, Pyrgomorphidae and Chrotogonidae were the most basal groups; while the taxonomic status of Pamphagidae, which was revealed as a monophyletic group, was not clear in this analysis. Moreover, the results indicate that a phylogeny inferred from the combination of several genes is more reliable than that from only a single gene sequence, and the third codon positions of protein coding genes can improve the topology and node supports of the phylogenetic trees. PMID:26624048

  14. Mitochondrial COI and 16sRNA evidence for a single species hypothesis of E. vitis, J. formosana and E. onukii in East Asia.

    PubMed

    Fu, Jian-Yu; Han, Bao-Yu; Xiao, Qiang

    2014-01-01

    Tea green leafhopper is one of the most damaging tea pests in main tea production regions of East Asia. For lack of recognized morphological characters, the dominant species of tea green leafhoppers in Mainland China, Taiwan and Japan have always been named as Empoasca vitis Göthe, Jacobiasca formosana Paoli and Empoasca onukii MATSUDA, respectively. Furthermore, nothing is known about the genetic relationships among them. In this study, we collected six populations from Mainland China, four populations from Japan and one population from Taiwan, and examined the genetic distances in the COI and 16sRNA regions of mtDNA among them. The results showed that the genetic distances based on single gene or the combined sequences among eleven leafhopper populations were 0.3-1.2%, which were all less than the species boundary of 2%. Moreover, there were at least two haplotypes shared by two distinct populations from different regions. The phylogenetic analysis based on single gene or combined sets also supported that tea green leafhoppers from Mainland China, Taiwan and Japan were closely related to each other, and there were at least two specimens from different regions clustered ahead of those from the same region. Therefore, we propose that the view of recognizing the dominant species of tea green leafhoppers in three adjacent tea production regions of East Asia as different species is unreliable or questionable and suggest that they are a single species. PMID:25506929

  15. Mitochondrial COI and 16sRNA Evidence for a Single Species Hypothesis of E. vitis, J. formosana and E. onukii in East Asia

    PubMed Central

    Fu, Jian-Yu; Han, Bao-Yu; Xiao, Qiang

    2014-01-01

    Tea green leafhopper is one of the most damaging tea pests in main tea production regions of East Asia. For lack of recognized morphological characters, the dominant species of tea green leafhoppers in Mainland China, Taiwan and Japan have always been named as Empoasca vitis Göthe, Jacobiasca formosana Paoli and Empoasca onukii MATSUDA, respectively. Furthermore, nothing is known about the genetic relationships among them. In this study, we collected six populations from Mainland China, four populations from Japan and one population from Taiwan, and examined the genetic distances in the COI and 16sRNA regions of mtDNA among them. The results showed that the genetic distances based on single gene or the combined sequences among eleven leafhopper populations were 0.3–1.2%, which were all less than the species boundary of 2%. Moreover, there were at least two haplotypes shared by two distinct populations from different regions. The phylogenetic analysis based on single gene or combined sets also supported that tea green leafhoppers from Mainland China, Taiwan and Japan were closely related to each other, and there were at least two specimens from different regions clustered ahead of those from the same region. Therefore, we propose that the view of recognizing the dominant species of tea green leafhoppers in three adjacent tea production regions of East Asia as different species is unreliable or questionable and suggest that they are a single species. PMID:25506929

  16. Sequencing mitochondrial DNA polymorphisms by hybridization

    SciTech Connect

    Chee, M.S.; Lockhart, D.J.; Hubbell, E.

    1994-09-01

    We have investigated the use of DNA chips for genetic analysis, using human mitochondrial DNA (mtDNA) as a model. The DNA chips are made up of ordered arrays of DNA oligonucleotide probes, synthesized on a glass substrate using photolithographic techniques. The synthesis site for each different probe is specifically addressed by illumination of the substrate through a photolithographic mask, achieving selective deprotection Nucleoside phosphoramidites bearing photolabile protecting groups are coupled only to exposed sites. Repeated cycles of deprotection and coupling generate all the probes in parallel. The set of 4{sup N} N-mer probes can be synthesized in only 4N steps. Any subset can be synthesized in 4N steps. Any subset can be synthesized in 4N or fewer steps. Sequences amplified from the D-loop region of human mitochondrial DNA (mtDNA) were fluorescently labelled and hybridized to DNA chips containing probes specific for mtDNA. Each nucleotide of a 1.3 kb region spanning the D loop is represented by four probes on the chip. Each probe has a different base at the position of interest: together they comprise a set of A, C, G and T probes which are otherwise identical. In principle, only one probe-target hybrid will be a perfect match. The other three will be single base mismatches. Fluorescence imaging of the hybridized chip allows quantification of hybridization signals. Heterozygous mixtures of sequences can also be characterized. We have developed software to quantitate and interpret the hybridization signals, and to call the sequence automatically. Results of sequence analysis of human mtDNAs will be presented.

  17. Molecular phylogeny of western Atlantic Farfantepenaeus and Litopenaeus shrimp based on mitochondrial 16S partial sequences.

    PubMed

    Maggioni, R; Rogers, A D; Maclean, N; D'Incao, F

    2001-01-01

    Partial sequences for the 16S rRNA mitochondrial gene were obtained from 10 penaeid shrimp species: Farfantepenaeus paulensis, F. brasiliensis, F. subtilis, F. duorarum, F. aztecus, Litopenaeus schmitti, L. setiferus, and Xiphopenaeus kroyeri from the western Atlantic and L. vannamei and L. stylirostris from the eastern Pacific. Sequences were also obtained from an undescribed morphotype of pink shrimp (morphotype II) usually identified as F. subtilis. The phylogeny resulting from the 16S partial sequences showed that these species form two well-supported monophyletic clades consistent with the two genera proposed in a recent systematic review of the suborder Dendrobranchiata. This contrasted with conclusions drawn from recent molecular phylogenetic work on penaeid shrimps based on partial sequences of the mitochondrial COI region that failed to support recent revisions of the Dendrobranchiata based on morphological analysis. Consistent differences observed in the sequences for morphotype II, coupled with previous allozyme data, support the conclusion that this is a previously undescribed species of Farfantepenaeus. PMID:11161743

  18. Simple sequence repeats in bryophyte mitochondrial genomes.

    PubMed

    Zhao, Chao-Xian; Zhu, Rui-Liang; Liu, Yang

    2016-01-01

    Simple sequence repeats (SSRs) are thought to be common in plant mitochondrial (mt) genomes, but have yet to be fully described for bryophytes. We screened the mt genomes of two liverworts (Marchantia polymorpha and Pleurozia purpurea), two mosses (Physcomitrella patens and Anomodon rugelii) and two hornworts (Phaeoceros laevis and Nothoceros aenigmaticus), and detected 475 SSRs. Some SSRs are found conserved during the evolution, among which except one exists in both liverworts and mosses, all others are shared only by the two liverworts, mosses or hornworts. SSRs are known as DNA tracts having high mutation rates; however, according to our observations, they still can evolve slowly. The conservativeness of these SSRs suggests that they are under strong selection and could play critical roles in maintaining the gene functions. PMID:24491104

  19. Phylogenetic relationships among Octopodidae species in coastal waters of China inferred from two mitochondrial DNA gene sequences.

    PubMed

    Lü, Z M; Cui, W T; Liu, L Q; Li, H M; Wu, C W

    2013-01-01

    Octopus in the family Octopodidae (Mollusca: Cephalopoda) has been generally recognized as a "catch-all" genus. The monophyly of octopus species in China's coastal waters has not yet been studied. In this paper, we inferred the phylogeny of 11 octopus species (family Octopodidae) in China's coastal waters using nucleotide sequences of two mitochondrial DNA genes: cytochrome c oxidase subunit I (COI) and 16S rRNA. Sequence analysis of both genes revealed that the 11 species of Octopodidae fell into four distinct groups, which were genetically distant from one another and exhibited identical phylogenetic resolution. The phylogenies indicated strongly that the genus Octopus in China's coastal waters is also not monophyletic, and it is therefore clear that the Octopodidae systematics in this area requires major revision. It is demonstrated that partial sequence information of both the mitochondrial genes 16S rRNA and COI could be used as diagnostic molecular markers in the identification and resolution of the taxonomic ambiguity of Octopodidae species. PMID:24085437

  20. COI barcode versus morphological identification of Culex ( Culex ) (Diptera: Culicidae) species: a case study using samples from Argentina and Brazil

    PubMed Central

    Laurito, Magdalena; de Oliveira, Tatiane MP; Almirón, Walter Ricardo; Sallum, Maria Anice Mureb

    2013-01-01

    Sequences of the cytochrome c oxidase subunit I (COI) mitochondrial gene from adults of 22 Culex ( Culex ) species from Argentina and Brazil were employed to assess species identification and to test the usefulness of COI for barcoding using the best close match (BCM) algorithm. A pairwise Kimura two-parameter distance matrix including the mean intra and interspecific distances for 71 COI barcode sequences was constructed. Of the 12 COI lineages recovered in the Neighbour-joining topology, five confirmed recognised morphological species ( Cx. acharistus , Cx. chidesteri , Cx. dolosus , Cx. lygrus and Cx. saltanensis ) with intraspecific divergences lower than 1.75%. Cx. bilineatus is formally resurrected from the synonymy of Cx. dolosus . Cx. maxi , Cx. surinamensis and the Coronator group species included were clustered into an unresolved lineage. The intraspecific distance of Cx. pipiens (3%) was almost twice the interspecific between it and Cx. quinquefasciatus (1.6%). Regarding the BCM criteria, the COI barcode successfully identified 69% of all species. The rest of the sequences, approximately 10%, 18% and 3%, remained as ambiguously, mis and unidentified, respectively. The COI barcode does not contain enough information to distinguish Culex ( Cux. ) species. PMID:24473810

  1. COI barcode versus morphological identification of Culex (Culex) (Diptera: Culicidae) species: a case study using samples from Argentina and Brazil.

    PubMed

    Laurito, Magdalena; Oliveira, Tatiane M P de; Almirón, Walter Ricardo; Sallum, Maria Anice Mureb

    2013-01-01

    Sequences of the cytochrome c oxidase subunit I (COI) mitochondrial gene from adults of 22 Culex (Culex) species from Argentina and Brazil were employed to assess species identification and to test the usefulness of COI for barcoding using the best close match (BCM) algorithm. A pairwise Kimura two-parameter distance matrix including the mean intra and interspecific distances for 71 COI barcode sequences was constructed. Of the 12 COI lineages recovered in the Neighbour-joining topology, five confirmed recognised morphological species (Cx. acharistus, Cx. chidesteri, Cx. dolosus, Cx. lygrus and Cx. saltanensis) with intraspecific divergences lower than 1.75%. Cx. bilineatus is formally resurrected from the synonymy of Cx. dolosus. Cx. maxi , Cx. surinamensis and the Coronator group species included were clustered into an unresolved lineage. The intraspecific distance of Cx. pipiens (3%) was almost twice the interspecific between it and Cx. quinquefasciatus (1.6%). Regarding the BCM criteria, the COI barcode successfully identified 69% of all species. The rest of the sequences, approximately 10%, 18% and 3%, remained as ambiguously, mis and unidentified, respectively. The COI barcode does not contain enough information to distinguish Culex (Cux.) species. PMID:24473810

  2. The complete mitochondrial genome sequence of Plotosus japonicus (Siluriformes: Plotosidae) and phylogenetic studies of Siluriformes.

    PubMed

    Liu, Yan-Hua; Zhang, Ming-Hai

    2016-07-01

    In this study, we first determined and described the complete mitogenome sequence of Plotosus japonicus, which is a kind of marine fish widely distributed in Northwest Pacific. The complete mitogenome sequence is 16 472 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region (CR) and a light-strand replication origin (OL). The overall base composition is 31.9% A, 24.7% T, 27.7% C, 15.7% G, with a slight AT bias (56.6%), similar to other vertebrate mitochondrial genomes. All the protein-coding genes use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, while COII and ND4 use AGA, COIII and Cytb use an incomplete stop codon TA or T. Maximum Likelihood (ML) tree and Bayesian analyses based on concatenated nucleotide sequences of 12 mitochondrial protein-coding genes were constructed and both yielded identical topologies. These results are expected to provide useful molecular data for species identification and further phylogenetic studies of Siluriformes. PMID:26122342

  3. Sequencing and analysis of the complete mitochondrial genome in Anopheles culicifacies species B (Diptera: Culicidae).

    PubMed

    Hua, Ya-Qiong; Yan, Zhen-Tian; Fu, Wen-Bo; He, Qi-Yi; Zhou, Yong; Chen, Bin

    2016-07-01

    The complete mitochondrial genome sequence of Anopheles culicifacial species B was sequenced in this study. The length of the mitochondrial genome is 15 330 bp, which contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a non-coding control region. The gene order and the gene composition are consistent with those previously reported for other mosquito species. The initiation codon of the PCGs complies with the ATN rule except for COI using TCG and ND5 using GTG as a start codon, and the termination codon is TAA or imcomplete, an only T. The total base composition is 40.4% A, 38.1% T, 12.4% C, and 9.1% G. The phylogenetic tree based on the sequences of 13 protein-coding genes showed that these species were classified into two clades, corresponding to the subgenus Cellia and subgenus Nyssorhynchus. An. culicifacies species B of Myzomyia Series was clustered with An. gambiae of Pyretophorus Series with a high bootstrap value of 100%. The complete mitogenome data can provide a basis for molecular identification and phylogenetic studies of mosquito species. PMID:26114319

  4. Basal divergence of Eriophyoidea (Acariformes, Eupodina) inferred from combined partial COI and 28S gene sequences and CLSM genital anatomy.

    PubMed

    Chetverikov, P E; Cvrković, T; Makunin, A; Sukhareva, S; Vidović, B; Petanović, R

    2015-10-01

    Eriophyoids are an ancient group of highly miniaturized, morphologically simplified and diverse phytoparasitic mites. Their possible numerous host-switch events have been accompanied by considerable homoplastic evolution. Although several morphological cladistic and molecular phylogenetic studies attempted to reconstruct phylogeny of Eriophyoidea, the major lineages of eriophyoids, as well as the evolutionary relationships between them, are still poorly understood. New phylogenetically informative data have been provided by the recent discovery of the early derivative pentasetacine genus Loboquintus, and observations on the eriophyoid reproductive anatomy. Herein, we use COI and D1-2 rRNA data of 73 eriophyoid species (including early derivative pentasetacines) from Europe, the Americas and South Africa to reconstruct part of the phylogeny of the superfamily, and infer on the basal divergence of eriophyoid taxa. In addition, a comparative CLSM study of the female internal genitalia was undertaken in order to find putative apomorphies, which can be used to improve the taxonomy of Eriophyoidea. The following molecular clades, marked by differences in genital anatomy and prodorsal shield setation, were found in our analyses: Loboquintus(Pentasetacus((Eriophyidae + Diptilomiopidae)(Phytoptidae-1, Phytoptidae-2))). The results of this study suggest that the superfamily Eriophyoidea comprises basal paraphyletic pentasetacines (Loboquintus and Pentasetacus), and two large monophyletic groups: Eriophyidae s.l. [containing paraphyletic Eriophyidae sensu Amrine et al. 2003 (=Eriophyidae s.str.) and Diptilomiopidae sensu Amrine et al. 2003] and Phytoptidae s.l. [containing monophyletic Phytoptidae sensu Boczek et al. 1989 (=Phytoptidae s.str.) and Nalepellidae sensu Boczek et al. 1989]. Putative morphological apomorphies (including genital and gnathosomal characters) supporting the clades revealed in molecular analyses are briefly discussed. PMID:26126634

  5. The complete mitochondrial genome sequence of Hepatozoon catesbianae (Apicomplexa: Coccidia: Adeleorina), a blood parasite of the green frog, Lithobates (formerly Rana) clamitans.

    PubMed

    Leveille, Alexandre N; Ogedengbe, Mosun E; Hafeez, Mian A; Tu, Hsiang-Hsien Abby; Barta, John R

    2014-10-01

    A complete mitochondrial genome for the blood parasite Hepatozoon catesbianae (Alveolata; Apicomplexa; Coccidia; Adeleorina; Hepatozoidae) was obtained through PCR amplification and direct sequencing of resulting PCR products. The mitochondrial genome of H. catesbianae is 6,397 bp in length and contains 3 protein-coding genes (cytochrome c oxidase subunit I [COI]; cytochrome c oxidase subunit III [COIII]; and cytochrome B [CytB]). Sequence similarities to previously published mitochondrial genomes of other apicomplexan parasites permitted annotation of 23 putative rDNA fragments in the mitochondrial genome of H. catesbianae, 14 large subunit rDNA fragments, and 9 small subunit rDNA fragments. Sequences corresponding to rDNA fragments RNA5, RNA8, RNA11, and RNA19 of Plasmodium falciparum were not identified in the mitrochondrial genome sequence of H. catesbianae. Although the presence of 3 protein-coding regions and numerous putative rDNA fragments is a feature typical for apicomplexan mitochondrial genomes, the mitochondrial genome of H. catesbianae possesses a structure and gene organization that is distinct among the Apicomplexa. This is the first complete mitochondrial genome sequence obtained from any apicomplexan parasite in the suborder Adeleorina. PMID:24820055

  6. Molecular phylogeny and evolution of Scomber (Teleostei: Scombridae) based on mitochondrial and nuclear DNA sequences

    NASA Astrophysics Data System (ADS)

    Cheng, Jiao; Gao, Tianxiang; Miao, Zhenqing; Yanagimoto, Takashi

    2011-03-01

    A molecular phylogenetic analysis of the genus Scomber was conducted based on mitochondrial (COI, Cyt b and control region) and nuclear (5S rDNA) DNA sequence data in multigene perspective. A variety of phylogenetic analytic methods were used to clarify the current taxonomic Classification and to assess phylogenetic relationships and the evolutionary history of this genus. The present study produced a well-resolved phylogeny that strongly supported the monophyly of Scomber. We confirmed that S. japonicus and S. colias were genetically distinct. Although morphologically and ecologically similar to S. colias, the molecular data showed that S. japonicus has a greater molecular affinity with S. australasicus, which conflicts with the traditional taxonomy. This phylogenetic pattern was corroborated by the mtDNA data, but incompletely by the nuclear DNA data. Phylogenetic concordance between the mitochondrial and nuclear DNA regions for the basal nodes Supports an Atlantic origin for Scomber. The present-day geographic ranges of the species were compared with the resultant molecular phylogeny derived from partition Bayesian analyses of the combined data sets to evaluate possible dispersal routes of the genus. The present-day geographic distribution of Scomber species might be best ascribed to multiple dispersal events. In addition, our results suggest that phylogenies derived from multiple genes and long sequences exhibited improved phylogenetic resolution, from which we conclude that the phylogenetic reconstruction is a reliable representation of the evolutionary history of Scomber.

  7. Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome

    PubMed Central

    Dinwiddie, Darrell L.; Smith, Laurie D.; Miller, Neil A.; Atherton, Andrea M.; Farrow, Emily G.; Strenk, Meghan E.; Soden, Sarah E.; Saunders, Carol J.; Kingsmore, Stephen F.

    2015-01-01

    Mitochondrial diseases are notoriously difficult to diagnose due to extreme locus and allelic heterogeneity, with both nuclear and mitochondrial genomes potentially liable. Using exome sequencing we demonstrate the ability to rapidly and cost effectively evaluate both the nuclear and mitochondrial genomes to obtain a molecular diagnosis for four patients with three distinct mitochondrial disorders. One patient was found to have Leigh syndrome due to a mutation in MT-ATP6, two affected siblings were discovered to be compound heterozygous for mutations in the NDUFV1 gene, which causes mitochondrial complex I deficiency, and one patient was found to have coenzyme Q10 deficiency due to compound heterozygous mutations in COQ2. In all cases conventional diagnostic testing failed to identify a molecular diagnosis. We suggest that additional studies should be conducted to evaluate exome sequencing as a primary diagnostic test for mitochondrial diseases, including those due to mtDNA mutations. PMID:23631824

  8. Complete Mitochondrial Genome Sequence of the Pezizomycete Pyronema confluens

    PubMed Central

    2016-01-01

    The complete mitochondrial genome of the ascomycete Pyronema confluens has been sequenced. The circular genome has a size of 191 kb and contains 48 protein-coding genes, 26 tRNA genes, and two rRNA genes. Of the protein-coding genes, 14 encode conserved mitochondrial proteins, and 31 encode predicted homing endonuclease genes. PMID:27174271

  9. PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences

    PubMed Central

    Machida, Ryuji J.; Kweskin, Matthew; Knowlton, Nancy

    2012-01-01

    Background Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy. Methodology/Principal Findings A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI's Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans. Conclusions/Significance Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from many metazoans. PMID:22536450

  10. The complete mitochondrial genome sequence of Emperor Penguins (Aptenodytes forsteri).

    PubMed

    Xu, Qiwu; Xia, Yan; Dang, Xiao; Chen, Xiaoli

    2016-09-01

    The emperor penguin (Aptenodytes forsteri) is the largest living species of penguin. Herein, we first reported the complete mitochondrial genome of emperor penguin. The mitochondrial genome is a circular molecule of 17 301 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA, and one control region. To verify the accuracy and the utility of new determined mitogenome sequences, we constructed the species phylogenetic tree of emperor penguin together with 10 other closely species. This is the second complete mitochondrial genome of penguin, and this is going to be an important data to study mitochondrial evolution of birds. PMID:26403091

  11. Sequence analysis of the complete mitochondrial genome of Youxian sheldrake.

    PubMed

    He, Shao-Ping; Liu, Li-Li; Yu, Qi-Fang; Li, Si; He, Jian-Hua

    2016-01-01

    Youxian sheldrake is excellent native breeds in Hunan province in China. The complete mitochondrial (mt) genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. This is the first study to determine the complete mitochondrial genome sequence of Youxian sheldrake using PCR-based amplification and Sanger sequencing. The characteristic of the entire mitochondrial genome was analyzed in detail, the total length of the mitogenome is 16,605 bp, with the base composition of 29.21% A, 22.18% T, 32.84% C, 15.77% G in the Youxian sheldrake. It contained 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of Youxian sheldrake provided an important data for further study of the phylogenetics of poultry, and available data for the genetics and breeding. PMID:25090395

  12. Mitochondrial DNA sequence evolution in the Arctoidea.

    PubMed Central

    Zhang, Y P; Ryder, O A

    1993-01-01

    Some taxa in the superfamily Arctoidea, such as the giant panda and the lesser panda, have presented puzzles to taxonomists. In the present study, approximately 397 bases of the cytochrome b gene, 364 bases of the 12S rRNA gene, and 74 bases of the tRNA(Thr) and tRNA(Pro) genes from the giant panda, lesser panda, kinkajou, raccoon, coatimundi, and all species of the Ursidae were sequenced. The high transition/transversion ratios in cytochrome b and RNA genes prior to saturation suggest that the presumed transition bias may represent a trend for some mammalian lineages rather than strictly a primate phenomenon. Transversions in the 12S rRNA gene accumulate in arctoids at about half the rate reported for artiodactyls. Different arctoid lineages evolve at different rates: the kinkajou, a procyonid, evolves the fastest, 1.7-1.9 times faster than the slowest lineage that comprises the spectacled and polar bears. Generation-time effect can only partially explain the different rates of nucleotide substitution in arctoids. Our results based on parsimony analysis show that the giant panda is more closely related to bears than to the lesser panda; the lesser panda is neither closely related to bears nor to the New World procyonids. The kinkajou, raccoon, and coatimundi diverged from each other very early, even though they group together. The polar bear is closely related to the spectacled bear, and they began to diverge from a common mitochondrial ancestor approximately 2 million years ago. Relationships of the remaining five bear species are derived. PMID:8415740

  13. Mitochondrial DNA sequences in the nuclear genome of a locust.

    PubMed

    Gellissen, G; Bradfield, J Y; White, B N; Wyatt, G R

    The endosymbiotic theory of the origin of mitochondria is widely accepted, and implies that loss of genes from the mitochondria to the nucleus of eukaryotic cells has occurred over evolutionary time. However, evidence at the DNA sequence level for gene transfer between these organelles has so far been limited to a single example, the demonstration that a mitochondrial ATPase subunit gene of Neurospora crassa has an homologous partner in the nuclear genome. From a gene library of the insect, Locusta migratoria, we have now isolated two clones, representing separate fragments of nuclear DNA, which contain sequences homologous to the mitochondrial genes for ribosomal RNA, as well as regions of homology with highly repeated nuclear sequences. The results suggest the transfer of sequences between mitochondrial and nuclear genomes, followed by evolutionary divergence. PMID:6298629

  14. DNA Barcoding the Medusozoa using mtCOI

    NASA Astrophysics Data System (ADS)

    Ortman, Brian D.; Bucklin, Ann; Pagès, Francesc; Youngbluth, Marsh

    2010-12-01

    The Medusozoa are a clade within the Cnidaria comprising the classes Hydrozoa, Scyphozoa, and Cubozoa. Identification of medusozoan species is challenging, even for taxonomic experts, due to their fragile forms and complex, morphologically-distinct life history stages. In this study 231 sequences for a portion of the mitochondrial Cytochrome Oxidase I (mtCOI) gene were obtained from 95 species of Medusozoans including; 84 hydrozoans (61 siphonophores, eight anthomedusae, four leptomedusae, seven trachymedusae, and four narcomedusae), 10 scyphozoans (three coronatae, four semaeostomae, two rhizostomae, and one stauromedusae), and one cubozoan. This region of mtCOI has been used as a DNA barcode (i.e., a molecular character for species recognition and discrimination) for a diverse array of taxa, including some Cnidaria. Kimura 2-parameter (K2P) genetic distances between sequence variants within species ranged from 0 to 0.057 (mean 0.013). Within the 13 genera for which multiple species were available, K2P distance between congeneric species ranged from 0.056 to 0.381. A cluster diagram generated by Neighbor Joining (NJ) using K2P distances reliably clustered all barcodes of the same species with ≥99% bootstrap support, ensuring accurate identification of species. Intra- and inter-specific variation of the mtCOI gene for the Medusozoa are appropriate for this gene to be used as a DNA barcode for species-level identification, but not for phylogenetic analysis or taxonomic classification of unknown sequences at higher taxonomic levels. This study provides a set of molecular tools that can be used to address questions of speciation, biodiversity, life-history, and population boundaries in the Medusozoa.

  15. A novel mutation MT-COIII m.9267G>C and MT-COI m.5913G>A mutation in mitochondrial genes in a Tunisian family with maternally inherited diabetes and deafness (MIDD) associated with sever nephropathy

    SciTech Connect

    Tabebi, Mouna; Mkaouar-Rebai, Emna; Mnif, Mouna; Kallabi, Fakhri; Ben Mahmoud, Afif; Ben Saad, Wafa; Charfi, Nadia; Keskes-Ammar, Leila; Kamoun, Hassen; Abid, Mohamed; Fakhfakh, Faiza

    2015-04-10

    Mitochondrial diabetes (MD) is a heterogeneous disorder characterized by a chronic hyperglycemia, maternal transmission and its association with a bilateral hearing impairment. Several studies reported mutations in mitochondrial genes as potentially pathogenic for diabetes, since mitochondrial oxidative phosphorylation plays an important role in glucose-stimulated insulin secretion from beta cells. In the present report, we studied a Tunisian family with mitochondrial diabetes (MD) and deafness associated with nephropathy. The mutational analysis screening revealed the presence of a novel heteroplasmic mutation m.9276G>C in the mitochondrial COIII gene, detected in mtDNA extracted from leukocytes of a mother and her two daughters indicating that this mutation is maternally transmitted and suggest its implication in the observed phenotype. Bioinformatic tools showed that m.9267G>C mutation (p.A21P) is « deleterious » and it can modify the function and the stability of the MT-COIII protein by affecting the assembly of mitochondrial COX subunits and the translocation of protons then reducing the activity of the respective OXPHOS complexes of ATP synthesis. The nonsynonymous mutation (p.A21P) has not been reported before, it is the first mutation described in the COXIII gene which is related to insulin dependent mitochondrial diabetes and deafness and could be specific to the Tunisian population. The m.9267G>C mutation was present with a nonsynonymous inherited mitochondrial homoplasmic variation MT-COI m.5913 G>A (D4N) responsible of high blood pressure, a clinical feature detected in all explored patients. - Highlights: • MT-COX3 m.9267G>C (p.A21P), heteroplasmic substitution, is not reported in any database. • m.9267G>C can be responsible of the MIDD associated with nephropaty. • This substitution can modify the function and the stability of the MT-CO3 protein. • This substitution can modify MT-CO3 structure (2D and 3D). • MT-COX3 m.9267G>C is associated

  16. Phylogenetic Relationships of Japanese Auritibicen Species (Hemiptera: Cicadidae: Cryptotympanini) Inferred from Mitochondrial and Nuclear Gene Sequences.

    PubMed

    Sota, Teiji; Kojima, Takanori; Lee, Young June; Lin, Chung-Ping

    2016-08-01

    We investigated the phylogenetic relationships and divergence times within the genus Auritibicen(Cicadidae: Cicadinae: Cryptotympanini), analyzing five Japanese species (A. japonicus, A. bihamatus,A. kyushyuensis, A. esakii and A. flammatus) and three species from East Asian mainland and Taiwan (A. atrofasciatus, A. intermedius and A. chujoi) using mitochondrial cytochrome oxidase subunit I (COI) and nuclear elongation factor 1-alpha (EF-1a) gene sequences. Although the EF-1a gene tree did not resolve the relationships among these Auritibicen species, the trees based on COI gene and the combined data set showed that Japanese taxa comprised three distinct lineages: the individual species A. flammatus and A. bihamatus, and the A. japonicus group, comprising A. japonicus, A. esakii and A. kyushyuensis from Japan and A. intermedius from Korea. In A. kyushyuensis, which comprises three populations in Kyushu, western Honshu and Shikoku, the specimens from western Honshu and Shikoku were closely related to each other, but not to the specimen from Kyushu; instead, they were sister to the Korean A. intermedius. The incongruence between the gene tree and species tree necessitates further population genetic and morphological studies to confirm the classification and species status of the western Honshu and Shikoku populations of A. kyushyuensis, which were originally described as two independent species. Divergence time estimation suggested that the most recent common ancestor of Auritibicen species studied dated back to the late Pliocene and that the species of the A. japonicus group diverged during the mid Pleistocene. Thus, the Pleistocene climatic fluctuation may have promoted the divergence of the Auritibicen species. PMID:27498799

  17. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

    PubMed Central

    Miller, Webb; Drautz, Daniela I.; Janecka, Jan E.; Lesk, Arthur M.; Ratan, Aakrosh; Tomsho, Lynn P.; Packard, Mike; Zhang, Yeting; McClellan, Lindsay R.; Qi, Ji; Zhao, Fangqing; Gilbert, M. Thomas P.; Dalén, Love; Arsuaga, Juan Luis; Ericson, Per G.P.; Huson, Daniel H.; Helgen, Kristofer M.; Murphy, William J.; Götherström, Anders; Schuster, Stephan C.

    2009-01-01

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%–15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples’ heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes. PMID:19139089

  18. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).

    PubMed

    Miller, Webb; Drautz, Daniela I; Janecka, Jan E; Lesk, Arthur M; Ratan, Aakrosh; Tomsho, Lynn P; Packard, Mike; Zhang, Yeting; McClellan, Lindsay R; Qi, Ji; Zhao, Fangqing; Gilbert, M Thomas P; Dalén, Love; Arsuaga, Juan Luis; Ericson, Per G P; Huson, Daniel H; Helgen, Kristofer M; Murphy, William J; Götherström, Anders; Schuster, Stephan C

    2009-02-01

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes. PMID:19139089

  19. Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons

    PubMed Central

    Chan, Yi-Chiao; Roos, Christian; Inoue-Murayama, Miho; Inoue, Eiji; Shih, Chih-Chin; Pei, Kurtis Jai-Chyi; Vigilant, Linda

    2010-01-01

    Background Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. Methodology/Principal Findings We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. Conclusions/Significance Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species. PMID:21203450

  20. The complete mitochondrial genome sequence of an Isospora sp. (Eimeriidae, Eucoccidiorida, Coccidiasina, Apicomplexa) causing systemic coccidiosis in domestic Canaries (Serinus canaria Linn.).

    PubMed

    Ogedengbe, Mosun E; Brash, Marina; Barta, John R

    2016-09-01

    We report a complete mitochondrial genome sequence for an Isospora sp. causing systemic coccidiosis in canaries, Serinus canaria. The A + T rich (65.2%) genome was 6216 bp in length and possessed 3 protein-coding genes, (COI; COIII and CytB), 19 LSU and 14 SSU rDNA fragments, including 1 newly identified putative LSU fragment. Arrangement of coding regions was identical to that of available Eimeria sp. mt genomes and start codon usage for protein-coding genes was conventional. The similar mitochondrial genome sequences and structures of Isospora and Eimeria species confirm the close relationship between these eimeriid genera of apicomplexan parasites. PMID:25714148

  1. COI Structural Analysis Presentation

    NASA Technical Reports Server (NTRS)

    Cline, Todd; Stahl, H. Philip (Technical Monitor)

    2001-01-01

    This report discusses the structural analysis of the Next Generation Space Telescope Mirror System Demonstrator (NMSD) developed by Composite Optics Incorporated (COI) in support of the Next Generation Space Telescope (NGST) project. The mirror was submitted to Marshall Space Flight Center (MSFC) for cryogenic testing and evaluation. Once at MSFC, the mirror was lowered to approximately 40 K and the optical surface distortions were measured. Alongside this experiment, an analytical model was developed and used to compare to the test results. A NASTRAN finite element model was provided by COI and a thermal model was developed from it. Using the thermal model, steady state nodal temperatures were calculated based on the predicted environment of the large cryogenic test chamber at MSFC. This temperature distribution was applied in the structural analysis to solve for the deflections of the optical surface. Finally, these deflections were submitted for optical analysis and comparison to the interferometer test data.

  2. The complete mitochondrial genome sequence of Diaphorina citri (Hemiptera: Psyllidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The first complete mitochondrial genome (mitogenome) sequence of Asian citrus psyllid, Diaphorina citri (Hemiptera: Psyllidae), from Guangzhou, China is presented. The circular mitogenome is 14,996 bp in length with an A+T content of 74.5%, and contains 13 protein-coding genes (PCGs), 22 tRNA genes ...

  3. Mitochondrial control region sequences from an Egyptian population sample.

    PubMed

    Saunier, Jessica L; Irwin, Jodi A; Strouss, Katharine M; Ragab, Hisham; Sturk, Kimberly A; Parsons, Thomas J

    2009-06-01

    Entire mitochondrial control region data was generated for 277 unrelated Egyptian individuals. High-throughput robotics, a redundant sequencing approach, and several quality control checks were implemented to generate a high-quality database. The data presented here will augment the limited Egyptian mtDNA reference data currently available for forensic comparisons. PMID:19414160

  4. The complete mitochondrial genome sequence of the budgerigar, Melopsittacus undulatus.

    PubMed

    Guan, Xiaojing; Xu, Jun; Smith, Edward J

    2016-01-01

    Here, we describe the budgie's mitochondrial genome sequence, a resource that can facilitate this parrot's use as a model organism as well as for determining its phylogenetic relatedness to other parrots/Psittaciformes. The estimated total length of the sequence was 18,193 bp. In addition to the to the 13 protein and tRNA and rRNA coding regions, the sequence also includes a duplicated hypervariable region, a feature unique to only a few birds. The two hypervariable regions shared a sequence identity of about 86%. PMID:24660934

  5. Complete mitochondrial genome sequence of Romanogobio tenuicorpus (Amur whitefin gudgeon).

    PubMed

    Dong, Fang; Tong, Guang-Xiang; Kuang, You-Yi; Sun, Xiao-Wen

    2015-01-01

    Amur whitefin gudgeon (Romanogobio tenuicorpus) belongs to the family Cyprinidae, it is freshwater aquaculture species in China. In the report, we determined the complete mitochondrial genome sequence of Romanogobio tenuicorpus, which is 16,600 bp long circular molecule with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, the conserved sequence blocks, CSB1, CSB2 and CSB3 were also detected. PMID:24409923

  6. Complete mitochondrial genome sequence of Grundulus bogotensis (Humboldt, 1821).

    PubMed

    Isaza, Juan P; Alzate, Juan F; Maldonado-Ocampo, Javier A

    2016-05-01

    The Grundulus bogotensis is an Endangered fish in Colombia. In this study, we report the complete mitochondrial DNA sequences of G. bogotensis. The entire genome comprised 17.123 bases and a GC content of 39.84%. The mitogenome sequence of G. bogotensis would contribute to better understand population genetics, and evolution of this lineage. Molecule was deposited at the GenBank database under the accession number KM677190. PMID:25405907

  7. Molecular phylogeny of Diabrotica beetles (Coleoptera: Chrysomelidae) inferred from analysis of combined mitochondrial and nuclear DNA sequences.

    PubMed

    Clark, T L; Meinke, L J; Foster, J E

    2001-08-01

    The phylogenetic relationships of thirteen Diabrotica (representing virgifera and fucata species groups) and two outgroup Acalymma beetle species (Coleoptera: Chrysomelidae) were inferred from the phylogenetic analysis of a combined data set of 1323 bp of mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) and the entire second internal transcribed spacer region (ITS-2) of nuclear ribosomal DNA of 362 characters. Species investigated were D. adelpha, D. balteata, D. barberi, D. cristata, D. lemniscata, D. longicornis, D. porracea, D. speciosa, D. undecimpunctata howardi, D. u. undecimpunctata, D. virgifera virgifera, D. v. zeae, D. viridula, and outgroup A. blandulum and A. vittatum. Maximum parsimony (MP), minimum evolution (ME), and maximum likelihood (ML) analyses of combined COI and ITS-2 sequences clearly place species into their traditional morphological species groups with MP and ME analyses resulting in identical topologies. Results generally confer with a prior work based on allozyme data, but within the virgifera species group, D. barberi and D. longicornis strongly resolve as sister taxa as well as monophyletic with the neotropical species, D. viridula, D. cristata and D. lemniscata also resolve as sister taxa. Both relationships are not in congruence with the prior allozyme-based hypothesis. Within the fucata species group, D. speciosa and D. balteata resolve as sister taxa. Results also strongly supported the D. virgifera and D. undecimpunctata subspecies complexes. Our proposed phylogeny provides some insight into current hypotheses regarding distribution status and evolution of various life history traits for Diabrotica. PMID:11520353

  8. Comparison of the northern snakehead (Channa argus) and blotched snakehead (Channa maculata) and their reciprocal hybrids (C. maculata ♀ × C. argus ♂ and C. argus ♀ × C. maculata ♂) based on complete mitochondrial DNA sequences.

    PubMed

    Xincheng, Zhang; Xinping, Zhu; Kunci, Chen; Jian, Zhao; Qing, Luo; Xiaoyou, Hong

    2015-01-01

    The complete mitochondrial DNA of Channa argus, Channa maculata, C. maculate ♀ × C. argus ♂ and C. argus ♀ × C. maculata ♂ were sequenced to characterize and compare their mitochondrial genomes. The lengths were 16,558, 16,559, 16,558 and 16,559 bp respectively. Start codon of 13 protein-coding genes was ATG, except that COI was GTG. The control region of the mitogenome were 907, 908, 907 and 908 bp in C. argus, C. maculata and their reciprocal hybrids (C. argus ♀ × C. maculata ♂ and C. maculate ♀ × C. argus ♂), respectively. PMID:24409853

  9. THE PHYLOGENETIC RELATIONSHIPS OF WHALE-FALL VESICOMYID CLAMS BASED ON MITOCHONDRIAL COI DNA SEQUENCES. (U915626)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  10. Population dynamics of the Bemisia tabaci B and Q biotypes as determined by microsatellite marker and mitochondrial COI sequence comparisons

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The current understanding of Bemisia tabaci phylogenetics suggests that this organism exists as a cryptic species complex. This complex is composed of what are most commonly called biotypes, at least some of which appear to have pre and/or post zygotic barriers to hybridization. Numerous studies hav...

  11. Relationships and origin of endemic Lake Baikal gastropods (Caenogastropoda: Rissooidea) based on mitochondrial DNA sequences.

    PubMed

    Hausdorf, Bernhard; Röpstorf, Peter; Riedel, Frank

    2003-03-01

    The phylogenetic relationships and the origin of two groups of rissooid freshwater snails endemic to Lake Baikal were investigated using partial mitochondrial COI, 12S rDNA, and 16S rDNA sequences. The Baikalian Benedictiinae proved to be closely related to the Lithoglyphinae. According to a molecular clock estimate the two groups diverged in the Paleogene. The Benedictiinae might have evolved autochthonously in precursors of Lake Baikal. The Baikalian Baicaliidae are probably most closely related to the Amnicolidae and the Bithyniidae. These groups diverged at the latest during the Cretaceous. Thus the origin of the Baicaliidae predates the origin of the Baikal rift zone. The Baicaliidae evolved probably in other Central Asian freshwater reservoirs. However, the radiation of the extant Baicaliidae only started in the Neogene and might have occurred autochthonously in Lake Baikal. The conchological similarity of the Baicaliidae and the Pyrgulidae is due to convergence. The Pyrgulidae diverged from the common stem lineage of the other hydrobiid families at the latest in the Jurassic. The Bithyniidae is derived from hydrobiids and is related to the Amnicolidae. PMID:12644402

  12. Divergent RNA editing frequencies in hornwort mitochondrial nad5 sequences.

    PubMed

    Duff, R Joel

    2006-02-01

    Hornwort mitochondrial genomes have some of the highest rates of RNA editing among plants. Comparison of eleven partial mitochondrial nad5 genomic and cDNA sequences from diverse taxa of hornworts reveal 125 edited sites in only 1107 nt. No single sample exhibits more than half of these sites. Ten of the 11 hornwort taxa have between 35 and 54 edited sties each; whereas, the eleventh taxon, Leiosporoceros, which represents a potential sister taxa to all other hornworts, has only eight sites. Comparison of multiple cDNA sequences from several individuals reveals the presence of many immature transcripts showing the heterogonous nature of the progression of editing. Phylogenetic analyses of hornwort genomic and cDNAs sequences reveal that 65 of the 94 phylogenetically informative sites within the hornwort clade are edited positions. PMID:16376027

  13. The complete mitochondrial genome sequence of Mustela eversmannii (Carnivora: Mustelidae).

    PubMed

    Liu, Guangshuai; Yang, Xiufeng; Zhang, Honghai; Sun, Guolei; Zhao, Chao; Dou, Huashan

    2016-09-01

    In this study, the complete mitochondrial genome of Steppe polecat, Mustela eversmannii, was sequenced for the first time using muscle tissue. The mitochondrial genome is a circular molecule of 16 463 bp in length and overall base composition is A (32.7%), T (27.3%), C (26.1%), and G (13.9%), which indicates a strong A-T bias. A phylogenetic analysis on the basis of 13 protein-coding genes and two rRNA genes of 10 Mustela species' mitochondrial genomes using maximum likelihood (ML) and Bayesian inference (BI) demonstrated that these Mustela species were clustered into two clades and M. eversmannii was close to M. putorius. PMID:26367202

  14. The complete mitochondrial genome sequence of Aspergillus flavus.

    PubMed

    Yan, Zhengsong; Chen, Dan; Shen, Yiping; Ye, Baodong

    2016-07-01

    Aspergillus flavus is a haploid filamentous fungus that is common in the environment and has been implicated in human infections. The complete mitochondrial genome of A. flavus has been determined by high-throughput sequencing technology in this work. Our study revealed that the mitochondrial genome of A. flavus is 31,602 bp long, with an A + T content of 74.83%, which consists of a usual set of mitochondrial proteins and RNA genes, including large and small ribosomal RNAs, 15 proteins, and 20 tRNA genes and contains two introns. Notably, it also contains two hypothetical proteins without obvious homology to any known proteins. All structural genes are located on one strand and are apparently transcribed in one direction. Codon usage analysis indicated that all protein coding genes employ the standard fungal mitochondrial start and stop codons; and the nucleotide bias toward AT was also reflected in the codon usage. The complete mitochondrial genomes of A. flavus would be useful for future investigation of the genetic, evolution, and clinical identification of Aspergillus species. PMID:25922962

  15. Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data.

    PubMed

    Law, Chris J; Dorgan, Kelly M; Rouse, Greg W

    2013-01-01

    Thoracophelia (Annelida, Opheliidae) are burrowing deposit feeders generally found in the mid- to upper intertidal areas of sandy beaches. Thoracophelia mucronata (Treadwell, 1914) is found along the west coast of North America, including at Dillon Beach, CA. Two additional species, Thoracophelia dillonensis (Hartman, 1938) and T. williamsi (Hartman, 1938) were also described from this beach. These three sympatric species have been primarily distinguished by branchial morphology, and efforts to determine the validity of the species have been based on morphological, reproductive and ecological studies. Here we demonstrate using mitochondrial and nuclear DNA sequence data that these three species are valid. Mitochondrial Cytochrome c subunit 1 (COI) sequences show uncorrected interspecific distances of ~9-13%. We found no inter-specific differences in body color or in hemoglobin concentration, but found that reproductive males were pinkish-red in color and had lower hemoglobin concentrations than purplish-red reproductive females. PMID:24614448

  16. Complete mitochondrial genome sequence of Heliocidaris crassispina (Camarodonta, Echinometridae).

    PubMed

    Jung, Gila; Kim, Choong-Gon; Lee, Youn-Ho

    2016-07-01

    The whole mitochondrial genome sequence of sea urchin Heliocidaris crassispina of the family Echinometridae is determined for the first time in this study. The circular mitogenome (15,702 bp) consists of typical Camarodonta gene order and its components including 2 rRNA, 22 tRNA, 13 protein-coding genes and a control region. Phylogenetic analysis based on the 13 concatenated protein-coding gene sequences shows that H. crassispina is closer to the species of Strongylocentrotidae than Parechinidae, but the separation between H. crassispina and the Strongylocentrotid species occurred early in their evolution. The complete mitochondrial genome presented in this study is useful for inferring the phylogenetic relationship among the families of Echinidea sea urchins. PMID:26006289

  17. The complete mitochondrial genome sequence of Schizothorax lissolabiatus (Cypriniformes: Cyprinidae).

    PubMed

    Yue, Xingjian; Shi, Jinrong; Zou, Yuanchao; Wang, Bin

    2016-07-01

    Schizothorax lissolabiatus is a widely distributed fish species in Lancang River, Yuanjiang River, Pearl River, Nujiang River in China. The complete mitochondrial genome sequence of S. lissolabiatus from Yuanjiang River (the upper Red River) has been sequenced, which is 16,583 bp in length and contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 2 main non-coding regions: origin of light-strand replication and control region. Except for eight tRNA and ND6 genes, most of the genes are encoded on the heavy strand. The length of mitochondrial genome, the order, composition and anticodons of all genes are exactly similar to that of S. dolichonema. The phylogenetic tree suggested S. prenanti, S. dolichonema and S. lissolabiatus may have closer affinities than other fish of the genus Schizothorax. PMID:25976234

  18. Complete mitochondrial genome sequence of Aoluguya reindeer (Rangifer tarandus).

    PubMed

    Ju, Yan; Liu, Huamiao; Rong, Min; Yang, Yifeng; Wei, Haijun; Shao, Yuanchen; Chen, Xiumin; Xing, Xiumei

    2016-05-01

    The complete mitochondria genome of the reindeer, Rangifer tarandus, was determined by accurate polymerase chain reaction. The entire genome is 16,357 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a D-loop region, all of which are arranged in a typical vertebrate manner. The overall base composition of the reindeer's mitochondrial genome is 33.7% of A, 23.1% of C, 30.1% of T and 13.2%of G. A termination associated sequence and several conserved central sequence block domains were discovered within the control region. PMID:25469816

  19. Genetic variability of Taenia saginata inferred from mitochondrial DNA sequences.

    PubMed

    Rostami, Sima; Salavati, Reza; Beech, Robin N; Babaei, Zahra; Sharbatkhori, Mitra; Harandi, Majid Fasihi

    2015-04-01

    Taenia saginata is an important tapeworm, infecting humans in many parts of the world. The present study was undertaken to identify inter- and intraspecific variation of T. saginata isolated from cattle in different parts of Iran using two mitochondrial CO1 and 12S rRNA genes. Up to 105 bovine specimens of T. saginata were collected from 20 slaughterhouses in three provinces of Iran. DNA were extracted from the metacestode Cysticercus bovis. After PCR amplification, sequencing of CO1 and 12S rRNA genes were carried out and two phylogenetic analyses of the sequence data were generated by Bayesian inference on CO1 and 12S rRNA sequences. Sequence analyses of CO1 and 12S rRNA genes showed 11 and 29 representative profiles respectively. The level of pairwise nucleotide variation between individual haplotypes of CO1 gene was 0.3-2.4% while the overall nucleotide variation among all 11 haplotypes was 4.6%. For 12S rRNA sequence data, level of pairwise nucleotide variation was 0.2-2.5% and the overall nucleotide variation was determined as 5.8% among 29 haplotypes of 12S rRNA gene. Considerable genetic diversity was found in both mitochondrial genes particularly in 12S rRNA gene. PMID:25687521

  20. Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida

    PubMed Central

    Young, Monica R; Hebert, Paul D. N.

    2015-01-01

    Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI) from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders and 43% of its families (267/625). It examines divergences at three taxonomic levels—among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10–0.39), while the mean of the Family Distances for the ten orders ranges fivefold (0.07–0.35). BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration. Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is ‘locked down’ in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in ‘locked down’ taxa. PMID:26308206

  1. Exome Sequencing Identifies Mitochondrial Alanyl-tRNA Synthetase Mutations in Infantile Mitochondrial Cardiomyopathy

    PubMed Central

    Götz, Alexandra; Tyynismaa, Henna; Euro, Liliya; Ellonen, Pekka; Hyötyläinen, Tuulia; Ojala, Tiina; Hämäläinen, Riikka H.; Tommiska, Johanna; Raivio, Taneli; Oresic, Matej; Karikoski, Riitta; Tammela, Outi; Simola, Kalle O.J.; Paetau, Anders; Tyni, Tiina; Suomalainen, Anu

    2011-01-01

    Infantile cardiomyopathies are devastating fatal disorders of the neonatal period or the first year of life. Mitochondrial dysfunction is a common cause of this group of diseases, but the underlying gene defects have been characterized in only a minority of cases, because tissue specificity of the manifestation hampers functional cloning and the heterogeneity of causative factors hinders collection of informative family materials. We sequenced the exome of a patient who died at the age of 10 months of hypertrophic mitochondrial cardiomyopathy with combined cardiac respiratory chain complex I and IV deficiency. Rigorous data analysis allowed us to identify a homozygous missense mutation in AARS2, which we showed to encode the mitochondrial alanyl-tRNA synthetase (mtAlaRS). Two siblings from another family, both of whom died perinatally of hypertrophic cardiomyopathy, had the same mutation, compound heterozygous with another missense mutation. Protein structure modeling of mtAlaRS suggested that one of the mutations affected a unique tRNA recognition site in the editing domain, leading to incorrect tRNA aminoacylation, whereas the second mutation severely disturbed the catalytic function, preventing tRNA aminoacylation. We show here that mutations in AARS2 cause perinatal or infantile cardiomyopathy with near-total combined mitochondrial respiratory chain deficiency in the heart. Our results indicate that exome sequencing is a powerful tool for identifying mutations in single patients and allows recognition of the genetic background in single-gene disorders of variable clinical manifestation and tissue-specific disease. Furthermore, we show that mitochondrial disorders extend to prenatal life and are an important cause of early infantile cardiac failure. PMID:21549344

  2. Mitochondrial DNA sequences from a 7000-year old brain.

    PubMed Central

    Pääbo, S; Gifford, J A; Wilson, A C

    1988-01-01

    Pieces of mitochondrial DNA from a 7000-year-old human brain were amplified by the polymerase chain reaction and sequenced. Albumin and high concentrations of polymerase were required to overcome a factor in the brain extract that inhibits amplification. For this and other sources of ancient DNA, we find an extreme inverse dependence of the amplification efficiency on the length of the sequence to be amplified. This property of ancient DNA distinguishes it from modern DNA and thus provides a new criterion of authenticity for use in research on ancient DNA. The brain is from an individual recently excavated from Little Salt Spring in southwestern Florida and the anthropologically informative sequences it yielded are the first obtained from archaeologically retrieved remains. The sequences show that this ancient individual belonged to a mitochondrial lineage that is rare in the Old World and not previously known to exist among Native Americans. Our finding brings to three the number of maternal lineages known to have been involved in the prehistoric colonization of the New World. Images PMID:3186445

  3. Comparison of mitochondrial genome sequences of pangolins (Mammalia, Pholidota).

    PubMed

    Hassanin, Alexandre; Hugot, Jean-Pierre; van Vuuren, Bettine Jansen

    2015-04-01

    The complete mitochondrial genome was sequenced for three species of pangolins, Manis javanica, Phataginus tricuspis, and Smutsia temminckii, and comparisons were made with two other species, Manis pentadactyla and Phataginus tetradactyla. The genome of Manidae contains the 37 genes found in a typical mammalian genome, and the structure of the control region is highly conserved among species. In Manis, the overall base composition differs from that found in African genera. Phylogenetic analyses support the monophyly of the genera Manis, Phataginus, and Smutsia, as well as the basal division between Maninae and Smutsiinae. Comparisons with GenBank sequences reveal that the reference genomes of M. pentadactyla and P. tetradactyla (accession numbers NC_016008 and NC_004027) were sequenced from misidentified taxa, and that a new species of tree pangolin should be described in Gabon. PMID:25746396

  4. The complete mitochondrial genome sequence of Schizopygopsis anteroventris (Cypriniformes: Cyprinidae).

    PubMed

    Liang, Yangyang; Chen, Yifeng; Li, Chunhua; He, Dekui

    2016-09-01

    Schizopygopsis anteroventris (Cyprinidae: Schizothoracinae) is an ecologically and economically important cyprinid endemic to Qinghai-Tibet Plateau, China. In this study, we sequenced the complete mitochondrial genome of S. anteroventris by DNA sequencing based on PCR fragments. The mitogenome of S. anteroventris is 16,620 in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions: the control region (D-loop) and the origin of light-strand replication (OL). The gene order in the mitogenome is identical with common vertebrate form. The complete mitogenome sequence is useful for further genetic studies, phylogenetic analysis and resource protection of S. anteroventris. PMID:25791361

  5. Mitochondrial restriction fragment length polymorphism (RFLP) and sequence variation among closely related avian species and the genetic characterization of hybrid Dendroica warblers.

    PubMed

    Lovette, I J; Bermingham, E; Rohwer, S; Wood, C

    1999-09-01

    To address several interconnected goals, we used mitochondrial DNA (mtDNA) sequences to explore evolutionary relationships among four potentially hybridizing taxa in a North American avian superspecies (Dendroica occidentalis, D. townsendi, D. virens, and D. nigrescens). We first compared the results of a previous restriction fragment length polymorphism (RFLP)-based study with 1453 nucleotides from the mitochondrial cytochrome oxidase subunit I (COI), ATP-synthase 6 (ATPase 6), and ATP-synthase 8 (ATPase 8) genes. Separate phylogenetic analyses of the RFLP and sequence data provided identical and well-supported hierarchical species-level reconstructions that grouped occidentalis and townsendi as sister taxa. We then explored several general features of mitochondrial evolution via a comparison of the RFLP and sequence data sets. Qualitative rate differences that seemed evident in highly autocorrelated comparisons of RFLP vs. sequence pairwise distances were not supported when autocorrelation was removed. We also noted a high variance in corresponding RFLP and sequence distances after the removal of autocorrelation effects. This variance suggests that caution should be used when combining RFLP and sequence-based data in studies that require the large-scale synthesis of divergence estimates drawn from sources employing different molecular techniques. Finally, we used our parallel RFLP and sequence data to design and validate a rapid and inexpensive polymerase chain reaction-RFLP (PCR-RFLP) protocol for determining species-specific mitochondrial haplotypes. This PCR-RFLP technique will be applied in ongoing studies of the occidentalis/townsendi hybrid zone, where the historic and geographical complexity of the interbreeding populations necessitates the genotyping of thousands of individual warblers. PMID:10564448

  6. The Complete Mitochondrial Genome Sequence of the Planthopper, Sivaloka damnosus

    PubMed Central

    Song, Nan; Liang, Ai-Ping; Ma, Chuan

    2010-01-01

    The complete mitochondrial genome (mitogenome) sequence was determined from the plant hopper, Sivaloka damnosus Chow and Lu (Hemiptera: Issidae), a representative of the insect family Issidae. The genome is a circular molecule of 15,287 bp with a total A+T content of 76.5%. The gene content, order, and structure are identical to that in Drosophila melanogaster, which is considered ancestral for insects. All 13 protein-coding genes of the S. damnosus mitogenome have a putative inframe ATR methionine or ATT isoleucine codons as start signals. The usual termination codons (TAA and TAG) were found in 11 protein-coding genes. However, atp6, and nad4 have incomplete termination codons. All tRNAs show stable canonical clover-leaf structures similar to other insect mitochondrial tRNAs, except for tRNASer(AGN), which has a reduced DHU arm. The A+T-rich region or putative control region includes two extensive repeat regions. The first repeat region is composed of two sets of complicated repeat units, and these repetitive sequences are arranged alternately; the second contains ten 20 bp tandemly repetitive sequences. In the phylogenetic analyses based on protein-coding genes, Cicadomorpha is a sister to Fulgoromorpha+Sternorrhyncha, and Heteroptera is a sister to all other Hemiptera. PMID:20673194

  7. The complete mitochondrial genome sequence of Shrew Gymnure, Neotetracus sinensis.

    PubMed

    Lu, Lu; Tu, Feiyun; Yan, Chaochao; Zhang, Xiuyue; Yue, Bisong; Zeng, Tao

    2013-06-01

    The Shrew Gymnure Neotetracus sinensis belongs to family Erinaceidae, and distributes in China, Myanmar, and northern Vietnam. In this study, the whole mitochondrial genome of N. sinensis was first sequenced and characterized. The genome is 16,982 bases in length. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes on the heavy strand. Phylogenetic analyses further confirm the subfamily Galericinae diverged prior to the subfamily Erinaceinae, support the species N. sinensis was in distinct genus Neotetracus rather than Hylomys, and N. sinensis diverged later than Echinosorex gymnura. PMID:23206249

  8. Nuclear and mitochondrial DNA sequences from two Denisovan individuals.

    PubMed

    Sawyer, Susanna; Renaud, Gabriel; Viola, Bence; Hublin, Jean-Jacques; Gansauge, Marie-Theres; Shunkov, Michael V; Derevianko, Anatoly P; Prüfer, Kay; Kelso, Janet; Pääbo, Svante

    2015-12-22

    Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans. PMID:26630009

  9. Nuclear and mitochondrial DNA sequences from two Denisovan individuals

    PubMed Central

    Sawyer, Susanna; Renaud, Gabriel; Viola, Bence; Hublin, Jean-Jacques; Gansauge, Marie-Theres; Shunkov, Michael V.; Derevianko, Anatoly P.; Prüfer, Kay; Pääbo, Svante

    2015-01-01

    Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans. PMID:26630009

  10. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing

    PubMed Central

    Green, Richard E.; Malaspinas, Anna-Sapfo; Krause, Johannes; Briggs, Adrian W.; Johnson, Philip L. F.; Uhler, Caroline; Meyer, Matthias; Good, Jeffrey M.; Maricic, Tomislav; Stenzel, Udo; Prüfer, Kay; Siebauer, Michael; Burbano, Hernán A.; Ronan, Michael; Rothberg, Jonathan M.; Egholm, Michael; Rudan, Pavao; Brajković, Dejana; Kućan, Željko; Gušić, Ivan; Wikström, Mårten; Laakkonen, Liisa; Kelso, Janet; Slatkin, Montgomery; Pääbo, Svante

    2008-01-01

    Summary A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000-year-old Neandertal individual using 8,341 mtDNA sequences identified among 4.8 Gb of DNA generated from ~0.3 grams of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs and allows an estimate of the divergence date between the two mtDNA lineages of 660,000±140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared to other primate lineages suggesting that the effective population size of Neandertals was small. PMID:18692465

  11. The complete mitochondrial genome sequence of Brachirus orientalis (Pleuronectiformes: Soleidae).

    PubMed

    Shi, Wei; Gong, Li; Wang, Shu-Ying; Kong, Xiao-Yu

    2016-01-01

    The oriental sole Brachirus orientalis (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and orbicular-ovate body. In this paper, the complete mitochondrial genome sequence of this sole was first determined. The total length is 16,602 bp, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region and a putative L-strand replication origin (OL). Gene contents, locations, and arrangements are identical to those of typical bony fishes. Overall base composition of the mitogenome is 30.4%, 28.6%, 15.3%, and 25.7% for A, C, G, and T, with a high A + T content (56.1%). The determination of B. orientalis complete mitogenome sequence could contribute to phylogenetic study on Soleidae and Pleuronectiformes. PMID:24845451

  12. The complete mitochondrial genome sequence of Heteromycteris japonicus (Pleuronectiformes: Soleidae).

    PubMed

    Shi, Wei; Jiang, Jin-Xia; Miao, Xian-Guang; Kong, Xiao-Yu

    2014-08-01

    The bamboo sole Heteromycteris japonicus (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and a rostral hook. In this article, the complete mitochondrial genome sequence of this sole was first determined. The total length is 17,111 bp, including 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes (12 S and 16 S), as well as a putative control region and a putative L-strand replication origin (OL). Gene contents, locations and arrangements are identical to those of typical bony fishes. Overall base composition of the mitogenome is 29.2%, 27.5%, 16.3% and 27.1% for A, C, G and T, with a high A + T content (56.3%). The determination of H. japonicus mitogenome sequence could contribute to understanding the systematic evolution of the genus Heteromycteris and further phylogenetic study on Soleidae and Pleuronectiformes. PMID:23808925

  13. The complete mitochondrial genome sequence of Malus hupehensis var. pinyiensis.

    PubMed

    Duan, Naibin; Sun, Honghe; Wang, Nan; Fei, Zhangjun; Chen, Xuesen

    2016-07-01

    The complete mitochondrial genome sequence of Malus hupehensis var. pinyiensis, a widely used apple rootstock, was determined using the Illumina high-throughput sequencing approach. The genome is 422,555 bp in length and has a GC content of 45.21%. It is separated by a pair of inverted repeats of 32,504 bp, to form a large single copy region of 213,055 bp and a small single copy region of 144,492 bp. The genome contains 38 protein-coding genes, four pseudogenes, 25 tRNA genes, and three rRNA genes. The genome is 25,608 bp longer than that of M. domestica, and several structural variations between these two mitogenomes were detected. PMID:26539696

  14. The complete mitochondrial genome sequence of Chuanchia labiosa (Cypriniformes: Cyprinidae).

    PubMed

    He, Dekui; Li, Chunhua; Tao, Juan; Chen, Yifeng

    2016-05-01

    Chuanchia labiosa Herzenstein, 1891 (Cyprinidae: Schizothoracinae) is the sole species of genus Chuanchia and is endemic to China. This species plays an important role in the upper reaches of the Yellow River and has been listed in both the China Red Data Book of Endangered Animal and the China Species Red List. In this study, the complete mitochondrial DNA genome sequence of C. labiosa was determined. The mitogenome is 16,705 bp in length, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Overall basic composition of mitochondrial genome of C. labiosa is 28.39% for A, 27.16% for T, 26.09% for C, and 18.36% for G with a slightly high A + T content (55.55%). The complete mitogenome sequence of C. labiosa would be useful for stock evaluation and further conservation genetic studies for this endangered species. PMID:25208160

  15. The complete mitochondrial genome of Hydra vulgaris (Hydroida: Hydridae).

    PubMed

    Pan, Hong-Chun; Fang, Hong-Yan; Li, Shi-Wei; Liu, Jun-Hong; Wang, Ying; Wang, An-Tai

    2014-12-01

    The complete mitochondrial genome of Hydra vulgaris (Hydroida: Hydridae) is composed of two linear DNA molecules. The mitochondrial DNA (mtDNA) molecule 1 is 8010 bp long and contains six protein-coding genes, large subunit rRNA, methionine and tryptophan tRNAs, two pseudogenes consisting respectively of a partial copy of COI, and terminal sequences at two ends of the linear mtDNA, while the mtDNA molecule 2 is 7576 bp long and contains seven protein-coding genes, small subunit rRNA, methionine tRNA, a pseudogene consisting of a partial copy of COI and terminal sequences at two ends of the linear mtDNA. COI gene begins with GTG as start codon, whereas other 12 protein-coding genes start with a typical ATG initiation codon. In addition, all protein-coding genes are terminated with TAA as stop codon. PMID:23841615

  16. Cloning, expression and characterization of COI1 gene (AsCOI1) from Aquilaria sinensis (Lour.) Gilg.

    PubMed

    Liao, Yongcui; Wei, Jianhe; Xu, Yanhong; Zhang, Zheng

    2015-09-01

    Aquilaria sinensis, a kind of typically wounding-induced medicinal plant with a great economical value, is widely used in the production of traditional Chinese medicine, perfume and incense. Coronatine-insensitive protein 1 (COI1) acts as a receptor in jasmonate (JA) signaling pathway, and regulates the expression of JA-responsive genes in plant defense. However, little is known about the COI1 gene in A. sinensis. Here, based on the transcriptome data, a full-length cDNA sequence of COI1 (termed as AsCOI1) was firstly cloned by RT-PCR and rapid-amplification of cDNA ends (RACE) strategies. AsCOI1 is 2330 bp in length (GenBank accession No. KM189194), and contains a complete open frame (ORF) of 1839 bp. The deduced protein was composed of 612 amino acids, with a predicted molecular weight of 68.93 kDa and an isoelectric point of 6.56, and was predicted to possess F-box and LRRs domains. Combining bioinformatics prediction with subcellular localization experiment analysis, AsCOI1 was appeared to locate in nucleus. AsCOI1 gene was highly expressed in roots and stems, the major organs of agarwood formation. Methyl jasmonate (MeJA), mechanical wounding and heat stress could significantly induce the expression level of AsCOI1 gene. AsCOI1 is an early wound-responsive gene, and it likely plays some role in agarwood formation. PMID:26579478

  17. Cloning, expression and characterization of COI1 gene (AsCOI1) from Aquilaria sinensis (Lour.) Gilg

    PubMed Central

    Liao, Yongcui; Wei, Jianhe; Xu, Yanhong; Zhang, Zheng

    2015-01-01

    Aquilaria sinensis, a kind of typically wounding-induced medicinal plant with a great economical value, is widely used in the production of traditional Chinese medicine, perfume and incense. Coronatine-insensitive protein 1 (COI1) acts as a receptor in jasmonate (JA) signaling pathway, and regulates the expression of JA-responsive genes in plant defense. However, little is known about the COI1 gene in A. sinensis. Here, based on the transcriptome data, a full-length cDNA sequence of COI1 (termed as AsCOI1) was firstly cloned by RT–PCR and rapid-amplification of cDNA ends (RACE) strategies. AsCOI1 is 2330 bp in length (GenBank accession No. KM189194), and contains a complete open frame (ORF) of 1839 bp. The deduced protein was composed of 612 amino acids, with a predicted molecular weight of 68.93 kDa and an isoelectric point of 6.56, and was predicted to possess F-box and LRRs domains. Combining bioinformatics prediction with subcellular localization experiment analysis, AsCOI1 was appeared to locate in nucleus. AsCOI1 gene was highly expressed in roots and stems, the major organs of agarwood formation. Methyl jasmonate (MeJA), mechanical wounding and heat stress could significantly induce the expression level of AsCOI1 gene. AsCOI1 is an early wound-responsive gene, and it likely plays some role in agarwood formation. PMID:26579478

  18. The Effectiveness of Three Regions in Mitochondrial Genome for Aphid DNA Barcoding: A Case in Lachininae

    PubMed Central

    Chen, Rui; Jiang, Li-Yun; Qiao, Ge-Xia

    2012-01-01

    Background The mitochondrial gene COI has been widely used by taxonomists as a standard DNA barcode sequence for the identification of many animal species. However, the COI region is of limited use for identifying certain species and is not efficiently amplified by PCR in all animal taxa. To evaluate the utility of COI as a DNA barcode and to identify other barcode genes, we chose the aphid subfamily Lachninae (Hemiptera: Aphididae) as the focus of our study. We compared the results obtained using COI with two other mitochondrial genes, COII and Cytb. In addition, we propose a new method to improve the efficiency of species identification using DNA barcoding. Methodology/Principal Findings Three mitochondrial genes (COI, COII and Cytb) were sequenced and were used in the identification of over 80 species of Lachninae. The COI and COII genes demonstrated a greater PCR amplification efficiency than Cytb. Species identification using COII sequences had a higher frequency of success (96.9% in “best match” and 90.8% in “best close match”) and yielded lower intra- and higher interspecific genetic divergence values than the other two markers. The use of “tag barcodes” is a new approach that involves attaching a species-specific tag to the standard DNA barcode. With this method, the “barcoding overlap” can be nearly eliminated. As a result, we were able to increase the identification success rate from 83.9% to 95.2% by using COI and the “best close match” technique. Conclusions/Significance A COII-based identification system should be more effective in identifying lachnine species than COI or Cytb. However, the Cytb gene is an effective marker for the study of aphid population genetics due to its high sequence diversity. Furthermore, the use of “tag barcodes” can improve the accuracy of DNA barcoding identification by reducing or removing the overlap between intra- and inter-specific genetic divergence values. PMID:23056258

  19. Complete mitochondrial genome sequence of Heteropneustes fossilis obtained by paired end next generation sequencing.

    PubMed

    Sahoo, Lakshman; Kumar, Santosh; Das, Sofia P; Patnaik, Siddhi; Bit, Amrita; Sundaray, Jitendra Kumar; Jayasankar, P; Das, Paramananda

    2016-07-01

    In the present study, the complete mitochondrial genome sequence of Heteropneustes fossilis is reported using massive parallel sequence technology. The complete mitogenome of H. fossilis is obtained by de novo assembly of paired end Illumina sequences using CLC Genomics Workbench version 7.0.4, which is 16,489 bp in length. It comprised of 13 protein- coding genes, 22 tRNAs, 2 rRNA genes and a putative control region along with the gene order and organization, being similar to most of vertebrates. The mitogenome in the present study has 99% similarity to the complete mitogneome sequence of H. Fossilis, as reported earlier. Phylogenetic analysis of Siluriformes depicted that Heteropneustids were closer to Clariids. The mitogenome sequence of H. fossilis contributes better understanding of population genetics, phylogenetics and evolution of Indian catfish species. PMID:26016883

  20. A revised molecular phylogeny of the globally distributed hawkmoth genus Hyles (Lepidoptera: Sphingidae), based on mitochondrial and nuclear DNA sequences.

    PubMed

    Hundsdoerfer, Anna K; Rubinoff, Daniel; Attié, Marc; Wink, Michael; Kitching, Ian J

    2009-09-01

    The hawkmoth genus Hyles comprises some 29 species with a global distribution. In this study, we augment the previous taxon sampling with more species and add sequences from a nuclear gene to produce a refined phylogenetic hypothesis. A total evidence reconstruction based on Bayesian analysis of the combined mitochondrial (COI, t-RNA-Leu, COII; 2284 bp) and nuclear (EF1alpha; 773 bp) sequences is discussed and compared with the results from separate analyses of the two genes. The total evidence phylogeny corroborates many of the phylogenetic relationships previously postulated within the genus. In addition, the hitherto unsampled enigmatic species Hyles biguttata from Madagascar appears as sister group to Hyles livornicoides from Australia, although support for the relationship is relatively weak. The high level of differentiation of Hyles perkinsi from H. calida (both Hawaii), and the status of these two as sister species, is corroborated by both sources of sequence data. However, their phylogenetic position when mt DNA sequences alone are considered differs markedly from that under total evidence. The previously postulated relationships within the Hyles euphorbiae complex (HEC) s.s. are largely corroborated, but H. dahlii is now more closely related and the HEC s.l. is redefined to include H. zygophylli and H. stroehlei (two species that had not been studied previously using molecular data) and to exclude H. siehei and H. hippophaes. The nuclear sequences alone are insufficiently variable to fully resolve all lineages and the phylogeny suggests that nuclear gene swapping and incomplete lineage sorting have occurred implying recent divergence. The results from the total evidence analysis provide a phylogenetic hypothesis that both corroborates and complements the previous biogeographic scenario, and provides new insights into the origins of several of the included taxa. PMID:19482093

  1. The complete mitochondrial genome sequence of Herzensteinia microcephalus (Cypriniformes: Cyprinidae).

    PubMed

    Li, Chunhua; Chen, Yifeng; Liu, Chunlong; Juan, Tao; He, Dekui

    2016-05-01

    Herzensteinia microcephalus (Herzenstein, 1891) is the highest naturally occurring cyprinid in the world, and inhabits rivers in the Tibetan Plateau at elevations of 4500-5200 m. Few studies on this species have been contributed. In this study, we got the mitochondrial genome sequences of H. microcephalus. The mitogenome of H. microcephalus is16,726 in length, which includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The overall nucleotide base composition is 28.41% for A, 27.16% for T, 26.04% for C and 18.38% for G. This study can provide important molecular theory basis for carrying out the study on the genetics, phylogeny and adaptive evolution of Herzensteinia. PMID:25431822

  2. [Nucleotide sequence determination of yeast mitochondrial phenylalanine-tRNA].

    PubMed

    Martin, R; Sibler, A P; Schneller, J M; Keith, G; Stahl, A J; Dirheimer, G

    1978-10-01

    The primary structure of mitochondrial tRNAPhe from Saccharomyces cerevisiae, purified by two-dimensional polyacrylamide gel electrophoresis, was determined using, standard procedures on in vivo 32P-labeled tRNA, as well as the new 5'-end postlabeling techniques. We propose a cloverleaf model which allows for tertiary interaction between cytosine in position 46 and guanine in position 15 and maximizes base pairing in the psi C stem, thus excluding the uracile in position 50 from base pairing in the psi C stem. Comparison of the primary structure of this tRNA with all other known procaryotic, chloroplastic or cytoplasmic tRNAsPhe sequences does not lead to any conclusion about the endosymbiotic theory of mitochondria evolution. PMID:103657

  3. Identification of Sequences Encoding Symbiodinium minutum Mitochondrial Proteins.

    PubMed

    Butterfield, Erin R; Howe, Christopher J; Nisbet, R Ellen R

    2016-02-01

    The dinoflagellates are an extremely diverse group of algae closely related to the Apicomplexa and the ciliates. Much work has previously been undertaken to determine the presence of various biochemical pathways within dinoflagellate mitochondria. However, these studies were unable to identify several key transcripts including those encoding proteins involved in the pyruvate dehydrogenase complex, iron-sulfur cluster biosynthesis, and protein import. Here, we analyze the draft nuclear genome of the dinoflagellate Symbiodinium minutum, as well as RNAseq data to identify nuclear genes encoding mitochondrial proteins. The results confirm the presence of a complete tricarboxylic acid cycle in the dinoflagellates. Results also demonstrate the difficulties in using the genome sequence for the identification of genes due to the large number of introns, but show that it is highly useful for the determination of gene duplication events. PMID:26798115

  4. Identification of Sequences Encoding Symbiodinium minutum Mitochondrial Proteins

    PubMed Central

    Butterfield, Erin R.; Howe, Christopher J.; Nisbet, R. Ellen R.

    2016-01-01

    The dinoflagellates are an extremely diverse group of algae closely related to the Apicomplexa and the ciliates. Much work has previously been undertaken to determine the presence of various biochemical pathways within dinoflagellate mitochondria. However, these studies were unable to identify several key transcripts including those encoding proteins involved in the pyruvate dehydrogenase complex, iron–sulfur cluster biosynthesis, and protein import. Here, we analyze the draft nuclear genome of the dinoflagellate Symbiodinium minutum, as well as RNAseq data to identify nuclear genes encoding mitochondrial proteins. The results confirm the presence of a complete tricarboxylic acid cycle in the dinoflagellates. Results also demonstrate the difficulties in using the genome sequence for the identification of genes due to the large number of introns, but show that it is highly useful for the determination of gene duplication events. PMID:26798115

  5. The complete mitochondrial genome sequence of Eimeria magna (Apicomplexa: Coccidia).

    PubMed

    Tian, Si-Qin; Cui, Ping; Fang, Su-Fang; Liu, Guo-Hua; Wang, Chun-Ren; Zhu, Xing-Quan

    2015-01-01

    In the present study, we determined the complete mitochondrial DNA (mtDNA) sequence of Eimeria magna from rabbits for the first time, and compared its gene contents and genome organizations with that of seven Eimeria spp. from domestic chickens. The size of the complete mt genome sequence of E. magna is 6249 bp, which consists of 3 protein-coding genes (cytb, cox1 and cox3), 12 gene fragments for the large subunit (LSU) rRNA, and 7 gene fragments for the small subunit (SSU) rRNA, without transfer RNA genes, in accordance with that of Eimeria spp. from chickens. The putative direction of translation for three genes (cytb, cox1 and cox3) was the same as those of Eimeria species from domestic chickens. The content of A + T is 65.16% for E. magna mt genome (29.73% A, 35.43% T, 17.09 G and 17.75% C). The E. magna mt genome sequence provides novel mtDNA markers for studying the molecular epidemiology and population genetics of Eimeria spp. and has implications for the molecular diagnosis and control of rabbit coccidiosis. PMID:24328820

  6. Mitochondrial DNA Sequence Analysis - Validation and Use for Forensic Casework.

    PubMed

    Holland, M M; Parsons, T J

    1999-06-01

    With the discovery of the polymerase chain reaction (PCR) in the mid-1980's, the last in a series of critical molecular biology techniques (to include the isolation of DNA from human and non-human biological material, and primary sequence analysis of DNA) had been developed to rapidly analyze minute quantities of mitochondrial DNA (mtDNA). This was especially true for mtDNA isolated from challenged sources, such as ancient or aged skeletal material and hair shafts. One of the beneficiaries of this work has been the forensic community. Over the last decade, a significant amount of research has been conducted to develop PCR-based sequencing assays for the mtDNA control region (CR), which have subsequently been used to further characterize the CR. As a result, the reliability of these assays has been investigated, the limitations of the procedures have been determined, and critical aspects of the analysis process have been identified, so that careful control and monitoring will provide the basis for reliable testing. With the application of these assays to forensic identification casework, mtDNA sequence analysis has been properly validated, and is a reliable procedure for the examination of biological evidence encountered in forensic criminalistic cases. PMID:26255820

  7. A 454 sequencing approach to dipteran mitochondrial genome research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The availability of complete mitochondrial genome data for Diptera, one of the largest Metazoan orders, in public databases is limited. Herein, we generated the complete or nearly complete mitochondrial genomes for Cochliomyia hominivorax, Haematobia irritans, Phormia regina and Sarcophaga crassipa...

  8. COI barcodes and phylogeny of doves (Columbidae family).

    PubMed

    Khan, Haseeb Ahmad; Arif, Ibrahim Abdulwahid

    2013-12-01

    Cytochrome oxidase subunit I (COI) gene has been recognized as an authentic tool for species identification. Besides its potential barcoding capacity, COI sequences have also been used for inferring the phylogeny. Phylogenetic relationships among genera of Columbidae (pigeons and doves family) have not been fully resolved because of scarce sampling of taxa and limited availability of sequence data. In this study, we have evaluated the efficiency of COI barcodes for species identification and phylogenetic analysis of various doves. We sequenced the 693 bp region of COI gene of three species of doves including Oena capensis, Streptopelia decaocto, and Streptopelia senegalensis. After retrieving the relevant sequences from the GenBank, the entire data-set of 85 sequences represented 25 dove species from 11 different genera of the family Columbidae. The COI sequences of four species including Chalcophaps indica (two specimens), Columbina inca (five specimens), Geopelia striata (three specimens), and Macropygia phasianella (three specimens) were identical. The mean intraspecific base differences ranged from 0 to 37 while the P-distances ranged between 0 and 0.058. For most of the species, the P-distances were ≤ 0.008. Phylogenetic analysis differentiated the taxa into three major clusters. One of the clusters grouped five genera including Claravis, Columbina, Gallicolumba, Geopelia, and Geotrygon. The remaining two clusters grouped three genera each including Chalcophaps, Oena, and Turtur in one cluster and Macropygia, Streptopelia, and Zenaida in another cluster. Further sub-clustering clearly separated all the genera into individual clusters except two discrepancies for the genera Streptopelia and Turtur. Species-level cladistics clearly separated all the species into distinctive clades. In conclusion, COI barcoding is a powerful tool for species identification with added information on phylogenetic inference. The finding of this study will help to understand the

  9. Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita.

    PubMed

    Das, Sofia P; Bit, Amrita; Patnaik, Siddhi; Sahoo, L; Meher, P K; Jayasankar, P; Saha, T M; Patel, A B; Patel, Namrata; Koringa, P; Joshi, C G; Agarwal, Suyash; Pandey, Manmohan; Srivastava, Shreya; Kushwaha, B; Kumar, Ravindra; Nagpure, N S; Iquebal, M A; Jaiswal, Sarika; Kumar, Dinesh; Jena, J K; Das, P

    2016-09-01

    Labeo rohita, popularly known as rohu, is a widely cultured species in whole Indian subcontinent. In the present study, we used in-silico approach to resolve complete mitochondrial genome of rohu. Low-depth shotgun sequencing using Roche 454 GS FLX (Branford, Connecticut, USA) followed by de novo assembly in CLC Genomics Workbench version 7.0.4 (Aarhus, Denmark) revealed the complete mitogenome of L. rohita to be 16 606 bp long (accession No. KR185963). It comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 putative control region. The gene order and organization are similar to most vertebrates. The mitogenome in the present investigation has 99% similarity with that of previously reported mitogenomes of rohu and this is also evident from the phylogenetic study using maximum-likelihood (ML) tree method. This study was done to determine the feasibility, accuracy and reliability of low-depth sequence data obtained from NGS platform as compared to the Sanger sequencing. Thus, NGS technology has proven to be competent and a rapid in-silico alternative to resolve the complete mitochondrial genome sequence, thereby reducing labors and time. PMID:26260184

  10. Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 5′ End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic

    PubMed Central

    Matsuda, Tomoko; Morishita, Maiko; Hinomoto, Norihide; Gotoh, Tetsuo

    2014-01-01

    The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered. PMID:25289639

  11. Mitochondrial sequence variation in the Guahibo Amerindian population from Venezuela.

    PubMed

    Vona, Giuseppe; Falchi, Alessandra; Moral, Pedro; Calò, Carla M; Varesi, Laurent

    2005-07-01

    New data were obtained on mitochondrial DNA (mtDNA) from Guahibo from Venezuela, a group so far not studied using molecular data. A population sample (n = 59) was analyzed for mtDNA variation in two control-region hypervariable segments (HV1 and HV2) by sequencing. The presence or absence of a 9-bp polymorphism in the COII/tRNA(Lys) region was studied by direct amplification and electrophoretic identification. Thirty-eight variable sites were detected in regions HV1 and HV2, defining 26 mtDNA lineages; 23.7% of these were present in a single individual. The 9-bp deletion was found in 3.39% of individuals. Nucleotide and haplotype diversities were relatively high compared with other New World populations. The identified sequence haplotypes were classified into four major haplogroups (A-D) according to previous studies, with high frequencies for A (47.46%) and C (49.15%), low frequency for B (3.39%), and an absence of D. PMID:15558610

  12. Mitochondrial sequences show diverse evolutionary histories of African hominoids.

    PubMed

    Gagneux, P; Wills, C; Gerloff, U; Tautz, D; Morin, P A; Boesch, C; Fruth, B; Hohmann, G; Ryder, O A; Woodruff, D S

    1999-04-27

    Phylogenetic trees for the four extant species of African hominoids are presented, based on mtDNA control region-1 sequences from 1,158 unique haplotypes. We include 83 new haplotypes of western chimpanzees and bonobos. Phylogenetic analysis of this enlarged database, which takes intraspecific geographic variability into account, reveals different patterns of evolution among species and great heterogeneity in species-level variation. Several chimpanzee and bonobo clades (and even single social groups) have retained substantially more mitochondrial variation than is seen in the entire human species. Among the 811 human haplotypes, those that branch off early are predominantly but not exclusively African. Neighbor joining trees provide strong evidence that eastern chimpanzee and human clades have experienced reduced effective population sizes, the latter apparently since the Homo sapiens-neanderthalensis split. Application of topiary pruning resolves ambiguities in the phylogenetic tree that are attributable to homoplasies in the data set. The diverse patterns of mtDNA sequence variation seen in today's hominoid taxa probably reflect historical differences in ecological plasticity, female-biased dispersal, range fragmentation over differing periods of time, and competition among social groups. These results are relevant to the origin of zoonotic diseases, including HIV-1, and call into question some aspects of the current taxonomic treatment and conservation management of gorillas and chimpanzees. PMID:10220421

  13. A Molecular Phylogeny of Hemiptera Inferred from Mitochondrial Genome Sequences

    PubMed Central

    Song, Nan; Liang, Ai-Ping; Bu, Cui-Ping

    2012-01-01

    Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses. PMID:23144967

  14. Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

    PubMed Central

    Timmermans, M. J. T. N.; Dodsworth, S.; Culverwell, C. L.; Bocak, L.; Ahrens, D.; Littlewood, D. T. J.; Pons, J.; Vogler, A. P.

    2010-01-01

    Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags (‘barcodes’). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three ‘bait’ sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species ‘barcodes’ that currently use the cox1 gene only. PMID:20876691

  15. Aminoglycoside-induced and non-syndromic hearing loss is associated with the G7444A mutation in the mitochondrial COI/tRNA{sup Ser(UCN)} genes in two Chinese families

    SciTech Connect

    Zhu Yi; Liao Zhisu; Li Zhiyuan; Chen Jianfu; Qian Yaping; Tang Xiaowen; Wang Jindan; Yang Li; Li Ronghua; Ji Jinzhang; Choo, Daniel I. |; Lu Jianxin . E-mail: jx@mail.wz.zj.cn; Guan Minxin |||. E-mail: min-xin.guan@chmcc.org

    2006-04-14

    We report here the clinical, genetic, and molecular characterization of two Chinese families with aminoglycoside induced and non-syndromic hearing impairment. Clinical and genetic evaluations revealed the variable severity and age-of-onset in hearing impairment in these families. Strikingly, there were extremely low penetrances of hearing impairment in these Chinese families. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the distinct sets of mtDNA polymorphism, in addition to the identical G7444A mutation associated with hearing loss. Indeed, the G7444A mutation in the CO1 gene and the precursor of tRNA{sup Ser(UCN)} gene is present in homoplasmy only in the maternal lineage of those pedigrees but not other members of these families and 164 Chinese controls. Their mitochondrial genomes belong to the Eastern Asian haplogroups C5a and D4a, respectively. In fact, the occurrence of the G7444A mutation in these several genetically unrelated subjects affected by hearing impairment strongly indicates that this mutation is involved in the pathogenesis of hearing impairment. However, there was the absence of other functionally significant mtDNA mutations in two Chinese pedigrees carrying the G7444A mutation. Therefore, nuclear modifier gene(s) or aminoglycoside(s) may play a role in the phenotypic expression of the deafness-associated G7444A mutation in these Chinese pedigrees.

  16. Evidence of a Native Northwest Atlantic COI Haplotype Clade in the Cryptogenic Colonial Ascidian Botryllus schlosseri.

    PubMed

    Yund, Philip O; Collins, Catherine; Johnson, Sheri L

    2015-06-01

    The colonial ascidian Botryllus schlosseri should be considered cryptogenic (i.e., not definitively classified as either native or introduced) in the Northwest Atlantic. Although all the evidence is quite circumstantial, over the last 15 years most research groups have accepted the scenario of human-mediated dispersal and classified B. schlosseri as introduced; others have continued to consider it native or cryptogenic. We address the invasion status of this species by adding 174 sequences to the growing worldwide database for the mitochondrial gene cytochrome c oxidase subunit I (COI) and analyzing 1077 sequences to compare genetic diversity of one clade of haplotypes in the Northwest Atlantic with two hypothesized source regions (the Northeast Atlantic and Mediterranean). Our results lead us to reject the prevailing view of the directionality of transport across the Atlantic. We argue that the genetic diversity patterns at COI are far more consistent with the existence of at least one haplotype clade in the Northwest Atlantic (and possibly a second) that substantially pre-dates human colonization from Europe, with this native North American clade subsequently introduced to three sites in Northeast Atlantic and Mediterranean waters. However, we agree with past researchers that some sites in the Northwest Atlantic have more recently been invaded by alien haplotypes, so that some populations are currently composed of a mixture of native and invader haplotypes. PMID:26124447

  17. The complete mitochondrial genome sequence of Sua-type cytoplasmic male sterility of tobacco (Nicotiana tabacum).

    PubMed

    Li, Fengxia; Yang, Aiguo; Lv, Jing; Gong, Daping; Sun, Yuhe

    2016-07-01

    To uncover the cytoplasmic male sterility (CMS)-associated mitochondrial genes of tobacco (Nicotiana tabacum), we determined the complete nucleotide sequence of Sua-CMS mitochondrial genome. The Sua-CMS mtDNA sequence is 522,731 bp in length and contains 34 protein-coding genes, 25 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. The nucleotide sequence data of 34 protein-coding genes of 14 mitochondrial genomes were used for constructing the phylogenetic tree. The results showed that Nicotiana tabacum Sua-CMS exhibits most close relationship with other solanaceae species. PMID:27158790

  18. Novel genetic diversity within Anopheles punctimacula s.l.: phylogenetic discrepancy between the Barcode cytochrome c oxidase I (COI) gene and the rDNA second internal transcribed spacer (ITS2).

    PubMed

    Loaiza, Jose R; Scott, Marilyn E; Bermingham, Eldredge; Sanjur, Oris I; Rovira, Jose R; Dutari, Larissa C; Linton, Yvonne-Marie; Bickersmith, Sara; Conn, Jan E

    2013-10-01

    Anopheles punctimacula s.l. is a regional malaria vector in parts of Central America, but its role in transmission is controversial due to its unresolved taxonomic status. Two cryptic species, An. malefactor and An. calderoni, have been previously confused with this taxon, and evidence for further genetic differentiation has been proposed. In the present study we collected and morphologically identified adult female mosquitoes of An. punctimacula s.l. from 10 localities across Panama and one in Costa Rica. DNA sequences from three molecular regions, the three prime end of the mitochondrial cytochrome c oxidase I gene (3' COI), the Barcode region in the five prime end of the COI (5' COI), and the rDNA second internal transcribed spacer (ITS2) were used to test the hypothesis of new molecular lineages within An. punctimacula s.l. Phylogenetic analyses using the 3' COI depicted six highly supported molecular lineages (A-F), none of which was An. malefactor. In contrast, phylogenetic inference with the 5' COI demonstrated paraphyly. Tree topologies based on the combined COI regions and ITS2 sequence data supported the same six lineages as the 3' COI alone. As a whole this evidence suggests that An. punctimacula s.l. comprises two geographically isolated lineages, but it is not clear whether these are true species. The phylogenetic structure of the An. punctimacula cluster as well as that of other unknown lineages (C type I vs C type II; D vs E) appears to be driven by geographic partition, because members of these assemblages did not overlap spatially. We report An. malefactor for the first time in Costa Rica, but our data do not support the presence of An. calderoni in Panama. PMID:23806568

  19. Novel genetic diversity within Anopheles punctimacula s.l.: Phylogenetic discrepancy between the Barcode cytochrome c oxidase I (COI) gene and the rDNA second internal transcribed spacer (ITS2)

    PubMed Central

    Loaiza, Jose R.; Scott, Marilyn E.; Bermingham, Eldredge; Sanjur, Oris I.; Rovira, Jose R.; Dutari, Larissa C.; Linton, Yvonne-Marie; Bickersmith, Sara; Conn, Jan E.

    2013-01-01

    Anopheles punctimacula s.l. is a regional malaria vector in parts of Central America, but its role in transmission is controversial due to its unresolved taxonomic status. Two cryptic species, An. malefactor and An. calderoni, have been previously confused with this taxon, and evidence for further genetic differentiation has been proposed. In the present study we collected and morphologically identified adult female mosquitoes of An. punctimacula s.l. from 10 localities across Panama and one in Costa Rica. DNA sequences from three molecular regions, the three prime end of the mitochondrial cytochrome c oxidase I gene (3´ COI), the Barcode region in the five prime end of the COI (5´ COI), and the rDNA second internal transcribed spacer (ITS2) were used to test the hypothesis of new molecular lineages within An. punctimacula s.l. Phylogenetic analyses using the 3´ COI depicted six highly supported molecular lineages (A–F), none of which was An. malefactor. In contrast, phylogenetic inference with the 5´ COI demonstrated paraphyly. Tree topologies based on the combined COI regions and ITS2 sequence data supported the same six lineages as the 3´ COI alone. As a whole this evidence suggests that An. punctimacula s.l. comprises two geographically isolated lineages, but it is not clear whether these are true species. The phylogenetic structure of the An. punctimacula cluster as well as that of other unknown lineages (C type I vs C type II; D vs E) appears to be driven by geographic partition, because members of these assemblages did not overlap spatially. We report An. malefactor for the first time in Costa Rica, but our data do not support the presence of An. calderoni in Panama. PMID:23806568

  20. The complete mitochondrial genome sequence of Hemibagrus sp. (Siluriformes: Bagridae).

    PubMed

    Hao, Rong-Chao; Wang, Guo-Hua

    2016-05-01

    At present, the phylogenetic and taxonomic positions of Bagridae and Siluriformes have long been unclear. In this paper, we sequenced and annotated the complete mitogenome of Hemibagrus sp. The total length was 16,529 bp, and was typically consist of 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNA, a light-strand replication origin (OL) and a single large control region (CR). Except for eight tRNA and ND6 genes, all other mitochondrial genes were encoded on the heavy strand (H-strand). The gene content, organization and arrangement were identical to that of a typical bony fish. The overall base composition was 26.5%, 26.8%, 31.7% and 15.0% for T, C, A and G, respectively, with a slight bias on AT content (58.2%). This information could not only contribute to provide useful molecular data for the species identification, but also to further taxonomic and phylogenetic studies of Hemibagrus and Bagridae. PMID:25319292

  1. The complete mitochondrial genome sequence of Platypharodon extremus (Cypriniformes: Cyprinidae).

    PubMed

    Li, Chunhua; Xiong, Wen; Chen, Yifeng; He, Dekui

    2016-05-01

    Platypharodon extremus Herzenstein, 1891 (Cyprinidae: Schizothoracinae), is a monotypic genus species only found in the Qinghai-Tibet plateau of China. Due to human disturbance and related environmental change since the 1950s, the population of P. extremus declined rapidly. As a result, it was listed in the China Red Data Book of Endangered Animal and the China's Protected Species Priority List. There exist very limited researches done on P. extremus. The poor understanding of this species limits the effective protection on this species. Here, we determined the complete mitochondrial DNA sequence of P. extremus. The results show that the mitogenome is 16,651 bp in length, which includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions: control region (D-loop) and origin of light-strand replication (OL). These baseline mitogenomic data provided by this study will facilitate the studies on P. extremus in genetics, developmental biology and conservation biology in the future. PMID:25231713

  2. Mitochondrial control-region sequence variation in aboriginal Australians.

    PubMed

    van Holst Pellekaan, S; Frommer, M; Sved, J; Boettcher, B

    1998-02-01

    The mitochondrial D-loop hypervariable segment 1 (mt HVS1) between nucleotides 15997 and 16377 has been examined in aboriginal Australian people from the Darling River region of New South Wales (riverine) and from Yuendumu in central Australia (desert). Forty-seven unique HVS1 types were identified, varying at 49 nucleotide positions. Pairwise analysis by calculation of BEPPI (between population proportion index) reveals statistically significant structure in the populations, although some identical HVS1 types are seen in the two contrasting regions. mt HVS1 types may reflect more-ancient distributions than do linguistic diversity and other culturally distinguishing attributes. Comparison with sequences from five published global studies reveals that these Australians demonstrate greatest divergence from some Africans, least from Papua New Guinea highlanders, and only slightly more from some Pacific groups (Indonesian, Asian, Samoan, and coastal Papua New Guinea), although the HVS1 types vary at different nucleotide sites. Construction of a median network, displaying three main groups, suggests that several hypervariable nucleotide sites within the HVS1 are likely to have undergone mutation independently, making phylogenetic comparison with global samples by conventional methods difficult. Specific nucleotide-site variants are major separators in median networks constructed from Australian HVS1 types alone and for one global selection. The distribution of these, requiring extended study, suggests that they may be signatures of different groups of prehistoric colonizers into Australia, for which the time of colonization remains elusive. PMID:9463317

  3. The complete mitochondrial genome sequence of Tylototriton taliangensis (Amphibia: Caudata).

    PubMed

    Jiang, Ye; Li, Ziyuan; Liu, Jiabin; Li, Yan; Ni, Qingyong; Yao, Yongfang; Xu, Huailiang; Li, Ying; Zhang, Mingwang

    2016-07-01

    Tylototriton taliangensis was listed as a Near Threatened amphibian in IUCN red list. In this study, we sequenced the complete mitochondrial (mt) genome of this species (GenBank: KP979646) and found it contains 16,265 base pairs, which encode 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA) and 1 control region (CR). We also found that almost all PCGs and tRNA genes are located on the H-strand, except for ND6 subunit gene and eight tRNA genes, which were distributed on the L-strand. The PCGs used "ATG" and "GTG" as the start codon, while used four types of stop codons. Almost all tRNA genes were folded into typical cloverleaf secondary structures. The L-strand replication origin (OL) and a non-coding region were also found. The new mitogenomic phylogenetic tree confirms the reciprocally monophyly of the genus Tylototriton, Echinotriton and Pleurodeles with high bootstrap value. The present study will provide information for future studies on the conservation genetics and phylogeny of this species and its relatives. PMID:26024138

  4. Sequence analysis of mitochondrial DNA hypervariable regions using infrared fluorescence detection.

    PubMed

    Steffens, D L; Roy, R

    1998-06-01

    The non-coding region of the mitochondrial genome provides an attractive target for human forensic identification studies. Two hypervariable (HV) regions, each approximately 250-350 bp in length, contain the majority of mitochondrial DNA (mtDNA) sequence variability among different individuals. Various approaches to determine mtDNA sequence were evaluated utilizing highly sensitive infrared (IR) fluorescence detection. HV regions were amplified either together or separately and cycle-sequenced using a Thermo Sequenase protocol. An M13 universal primer sequence tail covalently attached to the 5' terminus of an amplification primer facilitated electrophoretic analysis and direct sequencing of the amplification products using IR detection. PMID:9631201

  5. The History of Slavs Inferred from Complete Mitochondrial Genome Sequences

    PubMed Central

    Mielnik-Sikorska, Marta; Daca, Patrycja; Malyarchuk, Boris; Derenko, Miroslava; Skonieczna, Katarzyna; Perkova, Maria; Dobosz, Tadeusz; Grzybowski, Tomasz

    2013-01-01

    To shed more light on the processes leading to crystallization of a Slavic identity, we investigated variability of complete mitochondrial genomes belonging to haplogroups H5 and H6 (63 mtDNA genomes) from the populations of Eastern and Western Slavs, including new samples of Poles, Ukrainians and Czechs presented here. Molecular dating implies formation of H5 approximately 11.5–16 thousand years ago (kya) in the areas of southern Europe. Within ancient haplogroup H6, dated at around 15–28 kya, there is a subhaplogroup H6c, which probably survived the last glaciation in Europe and has undergone expansion only 3–4 kya, together with the ancestors of some European groups, including the Slavs, because H6c has been detected in Czechs, Poles and Slovaks. Detailed analysis of complete mtDNAs allowed us to identify a number of lineages that seem specific for Central and Eastern Europe (H5a1f, H5a2, H5a1r, H5a1s, H5b4, H5e1a, H5u1, some subbranches of H5a1a and H6a1a9). Some of them could possibly be traced back to at least ∼4 kya, which indicates that some of the ancestors of today's Slavs (Poles, Czechs, Slovaks, Ukrainians and Russians) inhabited areas of Central and Eastern Europe much earlier than it was estimated on the basis of archaeological and historical data. We also sequenced entire mitochondrial genomes of several non-European lineages (A, C, D, G, L) found in contemporary populations of Poland and Ukraine. The analysis of these haplogroups confirms the presence of Siberian (C5c1, A8a1) and Ashkenazi-specific (L2a1l2a) mtDNA lineages in Slavic populations. Moreover, we were able to pinpoint some lineages which could possibly reflect the relatively recent contacts of Slavs with nomadic Altaic peoples (C4a1a, G2a, D5a2a1a1). PMID:23342138

  6. Repetitive sequences in the crocodilian mitochondrial control region: poly-A sequences and heteroplasmic tandem repeats.

    PubMed

    Ray, David A; Densmore, Llewellyn D

    2003-06-01

    Heteroplasmic tandem repeats in the mitochondrial control region have been documented in a wide variety of vertebrate species. We have examined the control region from 11 species in the family Crocodylidae and identified two different types of heteroplasmic repetitive sequences in the conserved sequence block (CSB) domain-an extensive poly-A tract that appears to be involved in the formation of secondary structure and a series of tandem repeats located downstream ranging from approximately 50 to approximately 80 bp in length. We describe this portion of the crocodylian control region in detail and focus on members of the family Crocodylidae. We then address the origins of the tandemly repeated sequences in this family and suggest hypotheses to explain possible mechanisms of expansion/contraction of the sequences. We have also examined control region sequences from Alligator and Caiman and offer hypotheses for the origin of tandem repeats found in those taxa. Finally, we present a brief analysis of intraindividual and interindividual haplotype variation by examining representatives of Morelet's crocodile (Crocodylus moreletii). PMID:12716979

  7. Next-generation sequencing reveals deletions in mitochondrial mutants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cucumber mitochondria have three unique characteristics: paternal transmission, huge genome size, and mitochondrially encoded mosaic phenotypes. The cucumber mitochondrial DNA at 1.6 Mb is one of largest among angiosperms, and is divided into three chromosomes of 1.5 Mb, 84 Kb and 45 Kb. Paternally...

  8. Complete mitochondrial genome sequence of the Asian golden cat, Catopuma temminckii.

    PubMed

    Huang, Kui-Hua; Deng, Jia-Bo; Yu, Jian-Qiu; Cai, Zhi-Gang; Liu, Yu-Liang; Peng, Rui

    2016-09-01

    In this study, the mitochondrial genome of Asian golden cat (Catopuma temminckii) is sequenced. The mitochondrial genome was 16,985 bp long, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 1 control region and 1 origin of light-strand replication. The overall base composition of the mitochondrial genome was 32.76% A, 27.49 % T, 25.75 % C, and 13.99 % G. The complete mitochondrial genome of Catopuma temminckii could contribute to understanding taxonomic status and phylogenetic relationship of genus Catopuma. PMID:25630725

  9. The complete sequence of the mitochondrial genome of Sandu black pig (Sus Scrofa).

    PubMed

    Wang, Ling-Yu; Xu, Dong; Ma, Hai-Ming

    2016-05-01

    Sandu black pig is one of the native breed in Guizhou province in China. The total length of mitochondrial genome of Sandu black pig is 16,741 bp. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. This is the first report of the complete mitochondrial genome sequence about Sandu black pig. The mitochondrial genome data of Sandu black pig presented is useful novel markers for further studying the population genetics of sus scrofa. PMID:25259459

  10. The mitochondrial targeting sequence tilts the balance between mitochondrial and cytosolic dual localization.

    PubMed

    Regev-Rudzki, Neta; Yogev, Ohad; Pines, Ophry

    2008-07-15

    Dual localization of proteins in the cell has appeared in recent years to be a more abundant phenomenon than previously reported. One of the mechanisms by which a single translation product is distributed between two compartments, involves retrograde movement of a subset of processed molecules back through the organelle-membrane. Here, we investigated the specific contribution of the mitochondrial targeting sequence (MTS), as a cis element, in the distribution of two proteins, aconitase and fumarase. Whereas the cytosolic presence of fumarase is obvious, the cytosolic amount of aconitase is minute. Therefore, we created (1) MTS-exchange mutants, exchanging the MTS of aconitase and fumarase with each other as well as with those of other proteins and, (2) a set of single mutations, limited to the MTS of these proteins. Distribution of both proteins is affected by mutations, a fact particularly evident for aconitase, which displays extraordinary amounts of processed protein in the cytosol. Thus, we show for the first time, that the MTS has an additional role beyond targeting: it determines the level of retrograde movement of proteins back into the cytosol. Our results suggest that the translocation rate and folding of proteins during import into mitochondria determines the extent to which molecules are withdrawn back into the cytosol. PMID:18577574

  11. A database of mitochondrial DNA hypervariable regions I and II sequences of individuals from Slovakia.

    PubMed

    Lehocký, Ivan; Baldovic, Marian; Kádasi, Ludevít; Metspalu, Ene

    2008-09-01

    In order to identify polymorphic positions and to determine their frequencies and the frequency of haplotypes in the human mitochondrial control region, two hypervariable regions (HV1 and HV2) of the mitochondrial DNA (mtDNA) of 374 unrelated individuals from Slovakia were amplified and sequenced. Sequence comparison led to the identification of 284 mitochondrial lineages as defined by 163 variable sites. Genetic diversity (GD) was estimated at 0.997 and the probability of two randomly selected individuals from population having identical mtDNA types (random match probability, RMP) for the both regions is 0.60%. PMID:19083829

  12. A protocol for isolating insect mitochondrial genomes: a case study of NUMT in Melipona flavolineata (Hymenoptera: Apidae).

    PubMed

    Françoso, Elaine; Gomes, Fernando; Arias, Maria Cristina

    2016-07-01

    Nuclear mitochondrial DNA insertions (NUMTs) are mitochondrial DNA sequences that have been transferred into the nucleus and are recognized by the presence of indels and stop codons. Although NUMTs have been identified in a diverse range of species, their discovery was frequently accidental. Here, our initial goal was to develop and standardize a simple method for isolating NUMTs from the nuclear genome of a single bee. Subsequently, we tested our new protocol by determining whether the indels and stop codons of the cytochrome c oxidase subunit I (COI) sequence of Melipona flavolineata are of nuclear origin. The new protocol successfully demonstrated the presence of a COI NUMT. In addition to NUMT investigations, the protocol described here will also be very useful for studying mitochondrial mutations related to diseases and for sequencing complete mitochondrial genomes with high read coverage by Next-Generation technology. PMID:26061343

  13. Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.

    PubMed

    Warren, Jessica M; Simmons, Mark P; Wu, Zhiqiang; Sloan, Daniel B

    2016-02-01

    The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses. PMID:26759362

  14. Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes

    PubMed Central

    Warren, Jessica M.; Simmons, Mark P.; Wu, Zhiqiang; Sloan, Daniel B.

    2016-01-01

    The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses. PMID:26759362

  15. Single-Molecule LATE-PCR Analysis of Human Mitochondrial Genomic Sequence Variations

    PubMed Central

    Osborne, Adam; Reis, Arthur H.; Bach, Loren; Wangh, Lawrence J.

    2009-01-01

    It is thought that changes in mitochondrial DNA are associated with many degenerative diseases, including Alzheimer's and diabetes. Much of the evidence, however, depends on correlating disease states with changing levels of heteroplasmy within populations of mitochondrial genomes, rather than individual mitochondrial genomes. Thus these measurements are likely to either overestimate the extent of heteroplasmy due to technical artifacts, or underestimate the actual level of heteroplasmy because only the most abundant changes are observable. In contrast, Single Molecule (SM) LATE-PCR analysis achieves efficient amplification of single-stranded amplicons from single target molecules. The product molecules, in turn, can be accurately sequenced using a convenient Dilute-‘N’-Go protocol, as shown here. Using these novel technologies we have rigorously analyzed levels of mitochondrial genome heteroplasmy found in single hair shafts of healthy adult individuals. Two of the single molecule sequences (7% of the samples) were found to contain mutations. Most of the mtDNA sequence changes, however, were due to the presence of laboratory contaminants. Amplification and sequencing errors did not result in mis-identification of mutations. We conclude that SM-LATE-PCR in combination with Dilute-‘N’-Go Sequencing are convenient technologies for detecting infrequent mutations in mitochondrial genomes, provided great care is taken to control and document contamination. We plan to use these technologies in the future to look for age, drug, and disease related mitochondrial genome changes in model systems and clinical samples. PMID:19461959

  16. The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans

    PubMed Central

    Shoguchi, Eiichi; Shinzato, Chuya; Hisata, Kanako; Satoh, Nori; Mungpakdee, Sutada

    2015-01-01

    Even though mitochondrial genomes, which characterize eukaryotic cells, were first discovered more than 50 years ago, mitochondrial genomics remains an important topic in molecular biology and genome sciences. The Phylum Alveolata comprises three major groups (ciliates, apicomplexans, and dinoflagellates), the mitochondrial genomes of which have diverged widely. Even though the gene content of dinoflagellate mitochondrial genomes is reportedly comparable to that of apicomplexans, the highly fragmented and rearranged genome structures of dinoflagellates have frustrated whole genomic analysis. Consequently, noncoding sequences and gene arrangements of dinoflagellate mitochondrial genomes have not been well characterized. Here we report that the continuous assembled genome (∼326 kb) of the dinoflagellate, Symbiodinium minutum, is AT-rich (∼64.3%) and that it contains three protein-coding genes. Based upon in silico analysis, the remaining 99% of the genome comprises transcriptomic noncoding sequences. RNA edited sites and unique, possible start and stop codons clarify conserved regions among dinoflagellates. Our massive transcriptome analysis shows that almost all regions of the genome are transcribed, including 27 possible fragmented ribosomal RNA genes and 12 uncharacterized small RNAs that are similar to mitochondrial RNA genes of the malarial parasite, Plasmodium falciparum. Gene map comparisons show that gene order is only slightly conserved between S. minutum and P. falciparum. However, small RNAs and intergenic sequences share sequence similarities with P. falciparum, suggesting that the function of noncoding sequences has been preserved despite development of very different genome structures. PMID:26199191

  17. The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans.

    PubMed

    Shoguchi, Eiichi; Shinzato, Chuya; Hisata, Kanako; Satoh, Nori; Mungpakdee, Sutada

    2015-08-01

    Even though mitochondrial genomes, which characterize eukaryotic cells, were first discovered more than 50 years ago, mitochondrial genomics remains an important topic in molecular biology and genome sciences. The Phylum Alveolata comprises three major groups (ciliates, apicomplexans, and dinoflagellates), the mitochondrial genomes of which have diverged widely. Even though the gene content of dinoflagellate mitochondrial genomes is reportedly comparable to that of apicomplexans, the highly fragmented and rearranged genome structures of dinoflagellates have frustrated whole genomic analysis. Consequently, noncoding sequences and gene arrangements of dinoflagellate mitochondrial genomes have not been well characterized. Here we report that the continuous assembled genome (∼326 kb) of the dinoflagellate, Symbiodinium minutum, is AT-rich (∼64.3%) and that it contains three protein-coding genes. Based upon in silico analysis, the remaining 99% of the genome comprises transcriptomic noncoding sequences. RNA edited sites and unique, possible start and stop codons clarify conserved regions among dinoflagellates. Our massive transcriptome analysis shows that almost all regions of the genome are transcribed, including 27 possible fragmented ribosomal RNA genes and 12 uncharacterized small RNAs that are similar to mitochondrial RNA genes of the malarial parasite, Plasmodium falciparum. Gene map comparisons show that gene order is only slightly conserved between S. minutum and P. falciparum. However, small RNAs and intergenic sequences share sequence similarities with P. falciparum, suggesting that the function of noncoding sequences has been preserved despite development of very different genome structures. PMID:26199191

  18. Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia.

    PubMed

    Meganathan, P R; Dubey, Bhawna; Batzer, Mark A; Ray, David A; Haque, Ikramul

    2011-06-01

    Crocodylus is the largest genus within the Order Crocodylia consisting of eleven species. This paper reports the complete mitochondrial genome sequences of three Crocodylus species, Crocodylus moreletii, Crocodylus johnstoni and Crocodylus palustris, and compares the newly obtained mitochondrial DNA sequences with other crocodilians, available in the public databases. The mitochondrial genomes of C. moreletii, C. johnstoni and C. palustris are 16,827 bp, 16,851 bp and 16,852 bp in length, respectively. These mitochondrial genomes consist of 13 protein coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The mitochondrial genomes of all the Crocodylus species, studied herein show identical characteristics in terms of nucleotide composition and codon usage, suggestive of the existence of analogous evolutionary patterns within the genus, Crocodylus. The synonymous and non-synonymous substitution rates for all the protein coding genes of Crocodylus were observed in between 0.001 and 0.275 which reveal the prevalence of purifying selection in these genes. The phylogenetic analyses based on complete mitochondrial DNA data substantiate the previously established crocodilian phylogeny. This study provides a better understanding of the crocodilian mitochondrial genome and the data described herein will prove useful for future studies concerning crocodilian mitochondrial genome evolution. PMID:21310220

  19. Median network analysis of defectively sequenced entire mitochondrial genomes from early and contemporary disease studies.

    PubMed

    Bandelt, Hans-Jürgen; Yao, Yong-Gang; Bravi, Claudio M; Salas, Antonio; Kivisild, Toomas

    2009-03-01

    Sequence analysis of the mitochondrial genome has become a routine method in the study of mitochondrial diseases. Quite often, the sequencing efforts in the search of pathogenic or disease-associated mutations are affected by technical and interpretive problems, caused by sample mix-up, contamination, biochemical problems, incomplete sequencing, misdocumentation and insufficient reference to previously published data. To assess data quality in case studies of mitochondrial diseases, it is recommended to compare any mtDNA sequence under consideration to their phylogenetically closest lineages available in the Web. The median network method has proven useful for visualizing potential problems with the data. We contrast some early reports of complete mtDNA sequences to more recent total mtDNA sequencing efforts in studies of various mitochondrial diseases. We conclude that the quality of complete mtDNA sequences generated in the medical field in the past few years is somewhat unsatisfactory and may even fall behind that of pioneer manual sequencing in the early nineties. Our study provides a paradigm for an a posteriori evaluation of sequence quality and for detection of potential problems with inferring a pathogenic status of a particular mutation. PMID:19322152

  20. Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

    PubMed Central

    Margam, Venu M.; Coates, Brad S.; Hellmich, Richard L.; Agunbiade, Tolulope; Seufferheld, Manfredo J.; Sun, Weilin; Ba, Malick N.; Sanon, Antoine; Binso-Dabire, Clementine L.; Baoua, Ibrahim; Ishiyaku, Mohammad F.; Covas, Fernando G.; Srinivasan, Ramasamy; Armstrong, Joel; Murdock, Larry L.; Pittendrigh, Barry R.

    2011-01-01

    We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes. PMID:21311752

  1. The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

    PubMed

    Smith, David Roy

    2016-01-01

    The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank-an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission. PMID:26117139

  2. The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

    PubMed Central

    2016-01-01

    The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank—an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission. PMID:26117139

  3. Tripartite mitochondrial genome of spinach: physical structure, mitochondrial gene mapping, and locations of transposed chloroplast DNA sequences.

    PubMed Central

    Stern, D B; Palmer, J D

    1986-01-01

    A complete physical map of the spinach mitochondrial genome has been established. The entire sequence content of 327 kilobase pairs (kb) is postulated to occur as a single circular molecule. Two directly repeated elements of approximately 6 kb, located on this "master chromosome", are proposed to participate in an intragenomic recombination event that reversibly generates two "subgenomic" circles of 93 kb and 234 kb. The positions of protein and ribosomal RNA-encoding genes, determined by heterologous filter hybridizations, are scattered throughout the genome, with duplicate 26S rRNA genes located partially or entirely within the 6 kb repeat elements. Filter hybridizations between spinach mitochondrial DNA and cloned segments of spinach chloroplast DNA reveal at least twelve dispersed regions of inter-organellar sequence homology. Images PMID:3016660

  4. Complete genome sequence of mitochondrial DNA (mtDNA) of Chlorella sorokiniana.

    PubMed

    Orsini, Massimiliano; Costelli, Cristina; Malavasi, Veronica; Cusano, Roberto; Concas, Alessandro; Angius, Andrea; Cao, Giacomo

    2016-01-01

    The complete sequence of mitochondrial genome of the Chlorella sorokiniana strain (SAG 111-8 k) is presented in this work. Within the Chlorella genus, it represents the second species with a complete sequenced and annotated mitochondrial genome (GenBank accession no. KM241869). The genome consists of circular chromosomes of 52,528 bp and encodes a total of 31 protein coding genes, 3 rRNAs and 26 tRNAs. The overall AT contents of the C. sorokiniana mtDNA is 70.89%, while the coding sequence is of 97.4%. PMID:25186028

  5. A Cost-Effective Approach to Sequence Hundreds of Complete Mitochondrial Genomes.

    PubMed

    Nunez, Joaquin C B; Oleksiak, Marjorie F

    2016-01-01

    We present a cost-effective approach to sequence whole mitochondrial genomes for hundreds of individuals. Our approach uses small reaction volumes and unmodified (non-phosphorylated) barcoded adaptors to minimize reagent costs. We demonstrate our approach by sequencing 383 Fundulus sp. mitochondrial genomes (192 F. heteroclitus and 191 F. majalis). Prior to sequencing, we amplified the mitochondrial genomes using 4-5 custom-made, overlapping primer pairs, and sequencing was performed on an Illumina HiSeq 2500 platform. After removing low quality and short sequences, 2.9 million and 2.8 million reads were generated for F. heteroclitus and F. majalis respectively. Individual genomes were assembled for each species by mapping barcoded reads to a reference genome. For F. majalis, the reference genome was built de novo. On average, individual consensus sequences had high coverage: 61-fold for F. heteroclitus and 57-fold for F. majalis. The approach discussed in this paper is optimized for sequencing mitochondrial genomes on an Illumina platform. However, with the proper modifications, this approach could be easily applied to other small genomes and sequencing platforms. PMID:27505419

  6. Complete mitochondrial genome sequence of the heart failure model of cardiomyopathic Syrian hamster (Mesocricetus auratus).

    PubMed

    Hu, Bo; Liu, Dong-Xing; Zhang, Yu-Qing; Song, Jian-Tao; Ji, Xian-Fei; Hou, Zhi-Qiang; Zhang, Zhen-Hai

    2016-05-01

    In this study we sequenced the complete mitochondrial genome sequencing of a heart failure model of cardiomyopathic Syrian hamster (Mesocricetus auratus) for the first time. The total length of the mitogenome was 16,267 bp. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region. PMID:25469817

  7. The mitochondrial genome sequence of a diabetes disease Rattus norvegicus Wistar strain.

    PubMed

    Tang, Yu-Xiao; Dong, Yao-Zhong; Wang, Ji-Chang; Meng, Xiao-Mei

    2016-05-01

    We sequenced a diabetic Rattus norvegicus Wistar strain mitochondrial genome for the first time (GenBank Accession No. KM114608). Its mitogenome was 16,311 bp and coding 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes. This mitogenome sequence will provide definite genetic information for diabetes disease. PMID:25317643

  8. Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete sequences of the mitochondrial genomes of the oomycetes Phytophthora ramorum and P. sojae were determined during the course of their complete nuclear genome sequencing (Tyler et al. 2006). Both are circular, with sizes of 39,314 bp for P. ramorum and 42,977 bp for P. sojae. Each contain...

  9. A Cost-Effective Approach to Sequence Hundreds of Complete Mitochondrial Genomes

    PubMed Central

    Oleksiak, Marjorie F.

    2016-01-01

    We present a cost-effective approach to sequence whole mitochondrial genomes for hundreds of individuals. Our approach uses small reaction volumes and unmodified (non-phosphorylated) barcoded adaptors to minimize reagent costs. We demonstrate our approach by sequencing 383 Fundulus sp. mitochondrial genomes (192 F. heteroclitus and 191 F. majalis). Prior to sequencing, we amplified the mitochondrial genomes using 4–5 custom-made, overlapping primer pairs, and sequencing was performed on an Illumina HiSeq 2500 platform. After removing low quality and short sequences, 2.9 million and 2.8 million reads were generated for F. heteroclitus and F. majalis respectively. Individual genomes were assembled for each species by mapping barcoded reads to a reference genome. For F. majalis, the reference genome was built de novo. On average, individual consensus sequences had high coverage: 61-fold for F. heteroclitus and 57-fold for F. majalis. The approach discussed in this paper is optimized for sequencing mitochondrial genomes on an Illumina platform. However, with the proper modifications, this approach could be easily applied to other small genomes and sequencing platforms. PMID:27505419

  10. A molecular approach to the genus Alburnoides using COI sequences data set and the description of a new species, A. damghani, from the Damghan River system (the Dasht-e Kavir Basin, Iran) (Actinopterygii, Cyprinidae)

    PubMed Central

    Roudbar, Arash Jouladeh; Eagderi, Soheil; Esmaeili, Hamid Reza; Coad, Brian W.; Bogutskaya, Nina

    2016-01-01

    Abstract The molecular status of nine species of the genus Alburnoides from different river drainages in Iran and additionally by seven species from Europe was assessed. mtDNA COI gene sequences from freshly collected specimens and available NCBI data revealed four major phylogenetic lineages. Based on the results, a distinct taxon from the Cheshmeh Ali (Ali Spring), a Damghan River tributary in the endorheic Dasht-e Kavir basin, northern Iran, which is the closest sister to Alburnoides namaki (Namak Lake basin) + Alburnoides coadi (Nam River in the endorheic Dasht-e Kavir basin) is considered as a new species, Alburnoides damghani sp. n. It is distinguished from other Alburnoides species in Iran by a combination of character states including: a weakly-developed, variably-scaled, ventral keel from completely scaleless to completely scaled, a short snout with the tip of the mouth cleft on a level with the lower margin of the pupil or slightly lower, a small eye (eye horizontal diameter slightly to markedly less than interorbital width), commonly 8½ branched dorsal-fin rays, commonly 11−12½ branched anal-fin rays, 40−46(47) total lateral-line scales, 2.5–4.2 or 2.5–4.1 pharyngeal teeth, gill rakers short and widely spaced, 6−8 in total, 39−41 (commonly 40), total vertebrae, (19)20(21) abdominal vertebrae, 19−21 (most commonly 20) caudal vertebrae, abdominal vertebral region most commonly equal to or longer than caudal region, and most common vertebral formulae 20+20 and 21+19. PMID:27110204

  11. Molecular diversification of Trichuris spp. from Sigmodontinae (Cricetidae) rodents from Argentina based on mitochondrial DNA sequences.

    PubMed

    Callejón, Rocío; Robles, María Del Rosario; Panei, Carlos Javier; Cutillas, Cristina

    2016-08-01

    A molecular phylogenetic hypothesis is presented for the genus Trichuris based on sequence data from mitochondrial cytochrome c oxidase 1 (cox1) and cytochrome b (cob). The taxa consisted of nine populations of whipworm from five species of Sigmodontinae rodents from Argentina. Bayesian Inference, Maximum Parsimony, and Maximum Likelihood methods were used to infer phylogenies for each gene separately but also for the combined mitochondrial data and the combined mitochondrial and nuclear dataset. Phylogenetic results based on cox1 and cob mitochondrial DNA (mtDNA) revealed three clades strongly resolved corresponding to three different species (Trichuris navonae, Trichuris bainae, and Trichuris pardinasi) showing phylogeographic variation, but relationships among Trichuris species were poorly resolved. Phylogenetic reconstruction based on concatenated sequences had greater phylogenetic resolution for delimiting species and populations intra-specific of Trichuris than those based on partitioned genes. Thus, populations of T. bainae and T. pardinasi could be affected by geographical factors and co-divergence parasite-host. PMID:27083190

  12. DmTTF, a novel mitochondrial transcription termination factor that recognises two sequences of Drosophila melanogaster mitochondrial DNA

    PubMed Central

    Roberti, Marina; Polosa, Paola Loguercio; Bruni, Francesco; Musicco, Clara; Gadaleta, Maria Nicola; Cantatore, Palmiro

    2003-01-01

    Using a combination of bioinformatic and molecular biology approaches a Drosophila melanogaster protein, DmTTF, has been identified, which exhibits sequence and structural similarity with two mitochondrial transcription termination factors, mTERF (human) and mtDBP (sea urchin). Import/processing assays indicate that DmTTF is synthesised as a precursor of 410 amino acids and is imported into mitochondria, giving rise to a mature product of 366 residues. Band-shift and DNase I protection experiments show that DmTTF binds two homologous, short, non-coding sequences of Drosophila mitochondrial DNA, located at the 3′ end of blocks of genes transcribed on opposite strands. The location of the target sequences coincides with that of two of the putative transcription termination sites previously hypothesised. These results indicate that DmTTF is the termination factor of mitochondrial transcription in Drosophila. The existence of two DmTTF binding sites might serve not only to stop transcription but also to control the overlapping of a large number of transcripts generated by the peculiar transcription mechanism operating in this organism. PMID:12626700

  13. Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation

    PubMed Central

    2013-01-01

    Background Rapid and reliable identification of quarantine pests is essential for plant inspection services to prevent introduction of invasive species. For insects, this may be a serious problem when dealing with morphologically similar cryptic species complexes and early developmental stages that lack distinctive characters useful for taxonomic identification. DNA based barcoding could solve many of these problems. The standard barcode fragment, an approx. 650 base pairs long sequence of the 5′end of the mitochondrial cytochrome oxidase I (COI), enables differentiation of a very wide range of arthropods. However, problems remain in some taxa, such as Tephritidae, where recent genetic differentiation among some of the described species hinders accurate molecular discrimination. Results In order to explore the full species discrimination potential of COI, we sequenced the barcoding region of the COI gene of a range of economically important Tephritid species and complemented these data with all GenBank and BOLD entries for the systematic group available as of January 2012. We explored the limits of species delimitation of this barcode fragment among 193 putative Tephritid species and established operational taxonomic units (OTUs), between which discrimination is reliably possible. Furthermore, to enable future development of rapid diagnostic assays based on this sequence information, we characterized all single nucleotide polymorphisms (SNPs) and established “near-minimal” sets of SNPs that differentiate among all included OTUs with at least three and four SNPs, respectively. Conclusions We found that although several species cannot be differentiated based on the genetic diversity observed in COI and hence form composite OTUs, 85% of all OTUs correspond to described species. Because our SNP panels are developed based on all currently available sequence information and rely on a minimal pairwise difference of three SNPs, they are highly reliable and hence

  14. Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae.

    PubMed

    Frank, Krisztián; Barta, Endre; Bana, Nóra Á; Nagy, János; Horn, Péter; Orosz, László; Stéger, Viktor

    2016-06-01

    Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is mitochondrial DNA analysis, which can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We determined the complete mitochondrial genome of a Central European red deer, Cervus elaphus hippelaphus, from Hungary by a next generation sequencing technology. The mitochondrial genome is 16 354 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region, all of which are arranged similar as in other vertebrates. We made phylogenetic analyses with the new sequence and 76 available mitochondrial sequences of Cervidae, using Bos taurus mitochondrial sequence as outgroup. We used 'neighbor joining' and 'maximum likelihood' methods on whole mitochondrial genome sequences; the consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Cervinae and Capreolinae, and five tribes, Cervini, Muntiacini, Alceini, Odocoileini, and Capreolini. The evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; which method could be used broadly in phylogenetic evolutionary analysis of animal taxa. PMID:27165525

  15. Mitochondrial Genome Sequences of Nematocera (Lower Diptera): Evidence of Rearrangement following a Complete Genome Duplication in a Winter Crane Fly

    PubMed Central

    Beckenbach, Andrew T.

    2012-01-01

    The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented. PMID:22155689

  16. Gene organization and complete sequence of the mitochondrial genome of Linwu mallard.

    PubMed

    Tian, Ke-Xiong; Liu, Li-Li; Yu, Qi-Fang; He, Shao-Ping; He, Jian-Hua

    2016-01-01

    Linwu mallard is an excellent native breeds from Hunan province in China. This is the first study to determine the complete mitochondrial genome sequence of L. mallard using PCR-based amplification and Sanger sequencing. The characteristic of the entire mitochondrial genome was analyzed in detail, with the base composition of 29.19% A, 22.19% T, 32.83% C, 15.79% G in the L. mallard (16,605 bp in length). It contained 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of L. mallard will be useful for the phylogenetics of poultry, and be available as basic data for the genetics and breeding. PMID:24938102

  17. Determination and analysis of the complete mitochondrial genome sequence of Taoyuan chicken.

    PubMed

    Liu, Li-Li; Xie, Hong-Bing; Yu, Qi-Fang; He, Shao-Ping; He, Jian-Hua

    2016-01-01

    Taoyuan chicken is excellent native breeds in China. This study firstly determined the complete mitochondrial genome sequence of Taoyuan chicken using PCR-based amplification and Sanger sequencing. The characteristic of the entire mitochondrial genome was analyzed in detail, with the base composition of 30.26% A, 23.79% T, 32.44% C, 13.50% G in the Taoyuan chicken (16,784 bp in length). It contained 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of Taoyuan chicken will be useful for the phylogenetics of poultry, and be available as basic data for the genetics and breeding. PMID:24617480

  18. Sequencing and analysis of complete mitochondrial genome of Niviventer fulvescens (Muridae).

    PubMed

    Yong, Bin; Wei, Haixue; Jia, Qiang; Chen, Shunde

    2016-09-01

    The complete mitochondrial genome was sequenced and annotated newly from an individual of Niviventer fulvescens (Muridae) from Sichuan province. The total length of the N. fulvescens mitogenome is 16 296 bp and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region, with a base composition of 34.3%A, 29.1%T, 24.2%C and 12.4%G. The nucleotide sequence data of 12 heavy-strand protein-coding genes of N. fulvescens and other 18 rodents were used for mitochondrial genome phylogenetic analyses. Bayesian phylogenetic tree demonstrated the genus Niviventer was embedded within the genus Leopoldamys, although three Niviventer species constituted a monophyletic group. More complete mitochondrial genome sequences are required to illuminate the molecular phylogenetic relationship between Niviventer and Leopoldamys. PMID:26329164

  19. The complete mitochondrial genome sequence of Margaritiana dahurica Middendorff.

    PubMed

    Yang, Shoubao; Mi, Zhongxiang; Tao, Gang; Liu, Xiaofeng; Wei, Min; Wang, Heng

    2015-01-01

    In this study, the total mitochondrial genome of a freshwater pearl mussel Margaritiana dahurica Middendorff (Eulamellibranchia: Margaritanidae) was first determined. The genome is 16,112 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 HORF. The overall nucleotide composition of the H-strand of M. dahurica Middendorff mitochondrial genome is A: 37.85%, G: 13.22%, T: 23.74% and C: 25.19%, respectively, with an A + T rich feature (61.59%). These results provide useful information to further study of the molecular systematics, species identification and conservation genetics of M. dahurica Middendorff. PMID:24617476

  20. Use of yeast nuclear DNA sequences to define the mitochondrial RNA polymerase promoter in vitro.

    PubMed Central

    Marczynski, G T; Schultz, P W; Jaehning, J A

    1989-01-01

    We have extended an earlier observation that the TATA box for the nuclear GAL10 gene serves as a promoter for the mitochondrial RNA polymerase in in vitro transcription reactions (C. S. Winkley, M. J. Keller, and J. A. Jaehning, J. Biol. Chem. 260:14214-14223, 1985). In this work, we demonstrate that other nuclear genes also have upstream sequences that function in vitro as mitochondrial RNA polymerase promoters. These genes include the GAL7 and MEL1 genes, which are regulated in concert with the GAL10 gene, the sigma repetitive element, and the 2 microns plasmid origin of replication. We used in vitro transcription reactions to test a large number of nuclear DNA sequences that contain critical mitochondrial promoter sequences as defined by Biswas et al. (T. K. Biswas, J. C. Edwards, M. Rabinowitz, and G. S. Getz, J. Biol. Chem. 262:13690-13696, 1987). The results of these experiments allowed us to extend the definition of essential promoter elements. This extended sequence, -ACTATAAACGatcATAG-, was frequently found in the upstream regulatory regions of nuclear genes. On the basis of these observations, we hypothesized that either (i) a catalytic RNA polymerase related to the mitochondrial enzyme functions in the nucleus of the yeast cell or (ii) a DNA sequence recognition factor is shared by the two genetic compartments. By using cells deficient in the catalytic core of the mitochondrial RNA polymerase (rpo41-) and sensitive assays for transcripts initiating from the nuclear promoter sequences, we have conclusively ruled out a role for the catalytic RNA polymerase in synthesizing transcripts from all of the nuclear sequences analyzed. The possibility that a DNA sequence recognition factor functions in both the nucleus and the mitochondria remains to be tested. Images PMID:2677667

  1. Insect mitochondrial genomics: the complete mitochondrial genome sequence of the meadow spittlebug Philaenus spumarius (Hemiptera: Auchenorrhyncha: Cercopoidae).

    PubMed

    Stewart, James Bruce; Beckenbach, Andrew T

    2005-02-01

    We present the complete mitochondrial genome sequence of the meadow spittlebug Philaenus spumarius (Auchenorrhyncha: Cercopoidae). This contribution represents the second mitochondrial genome from the Hemiptera and the second of the three hemipteran suborders sampled. The genome is a circular molecule of 16 324 bp with a total A+T content of 77.0% and 76.7% for coding regions only. The gene content, order, and structure are consistent with the Drosophila yakuba genome structure (Clary and Wolstenholme 1985) and the hypothesized ancestral arthropod genome arrangement (Crease 1999). Nucleotide composition and codon usage are near the means observed in other insect mitochondria sequenced to date but have a higher A+T richness compared with the other hemipteran example, the kissing bug Triatoma dimidiata (Dotson and Beard. 2001. Insect Mol. Biol. 10: 205-215). The major noncoding region (the A+T rich region or putative control region) between the small ribosomal subunit and the tRNAIle gene includes two extensive repeat regions. The first repeat region includes 19 tandem repeats of a 46-bp sequence, whereas the second contains a longer sequence (146 bp) tandemly repeated four times. PMID:15729396

  2. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-F.

    PubMed

    Fan, Xiao; Wang, Shuai; Xu, Dong; Zhang, Xiaowen; Xu, Le; Miao, Yu; Ye, Naihao

    2016-09-01

    The complete sequence (37 657 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-F was determined using Illumina sequencing data (Illumina Inc., San Diego, CA). The genome contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA), and 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. A phylogenetic analysis based on the mitochondrial genomes of brown algae indicated that Saccharina sp. ye-F and Saccharina longissima, Saccharina japonica are the most closely related species, which strongly supports their close phylogenetic affinity. PMID:26358639

  3. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-W.

    PubMed

    Wang, Shuai; Fan, Xiao; Xu, Dong; Zhang, Xiaowen; Miao, Yu; Xu, Le; Ye, Naihao

    2016-07-01

    The complete sequence (37 657 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-W was determined using Illumina sequencing data. The genome contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA), 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. Phylogenetic analysis based on the mitochondrial genomes of brown algae indicated that Saccharina sp. ye-W and Saccharina longissima, Saccharina japonica are the most closely related species, which strongly supports their close phylogenetic affinity. PMID:26153752

  4. The First Complete Mitochondrial Genome Sequences for Stomatopod Crustaceans: Implications for Phylogeny

    SciTech Connect

    Swinstrom, Kirsten; Caldwell, Roy; Fourcade, H. Matthew; Boore, Jeffrey L.

    2005-09-07

    We report the first complete mitochondrial genome sequences of stomatopods and compare their features to each other and to those of other crustaceans. Phylogenetic analyses of the concatenated mitochondrial protein-coding sequences were used to explore relationships within the Stomatopoda, within the malacostracan crustaceans, and among crustaceans and insects. Although these analyses support the monophyly of both Malacostraca and, within it, Stomatopoda, it also confirms the view of a paraphyletic Crustacea, with Malacostraca being more closely related to insects than to the branchiopod crustaceans.

  5. Complete mitochondrial genome sequence of northeastern sika deer (Cervus nippon hortulorum).

    PubMed

    Shao, Yuanchen; Zha, Daiming; Xing, Xiumei; Su, Weilin; Liu, Huamiao; Zhang, Ranran

    2016-01-01

    The complete mitochondrial genome of the northeastern sika deer, Cervus nippon hortulorum, was determined by accurate polymerase chain reaction. The entire genome is 16,434 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region, all of which are arranged in a typical vertebrate manner. The overall base composition of the northeastern sika deer's mitochondrial genome is 33.3% of A, 24.5% of C, 28.7% of T and 13.5% of G. A termination associated sequence and several conserved central sequence block domains were discovered within the control region. PMID:24660928

  6. Complete mitochondrial genome sequence of tarim red deer (Cervus elaphus yarkandensis).

    PubMed

    Shao, Yuanchen; Xing, Xiumei; Zha, Daiming; Yang, Fuhe

    2016-01-01

    The complete mitochondrial genome of the tarim red deer, Cervus elaphus yarkandensis, was determined by accurate polymerase chain reaction. The entire genome was 16,351 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region, all of which were arranged in a typical vertebrate manner. The overall base composition of the northeast sika deer's mitochondrial genome was 33.3% of A, 24.4% of C, 28.9% of T and 13.4% of G. A termination-associated sequence and several conserved central sequence block domains were discovered within the control region. PMID:24438284

  7. The complete mitochondrial genome sequence of the Tibetan red fox (Vulpes vulpes montana).

    PubMed

    Zhang, Jin; Zhang, Honghai; Zhao, Chao; Chen, Lei; Sha, Weilai; Liu, Guangshuai

    2015-01-01

    In this study, the complete mitochondrial genome of the Tibetan red fox (Vulpes Vulpes montana) was sequenced for the first time using blood samples obtained from a wild female red fox captured from Lhasa in Tibet, China. Qinghai--Tibet Plateau is the highest plateau in the world with an average elevation above 3500 m. Sequence analysis showed it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region (CR). The variable tandem repeats in CR is the main reason of the length variability of mitochondrial genome among canide animals. PMID:24456141

  8. Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics.

    PubMed

    Hancock-Hanser, Brittany L; Frey, Amy; Leslie, Matthew S; Dutton, Peter H; Archer, Frederick I; Morin, Phillip A

    2013-03-01

    Next-generation sequencing (NGS) is emerging as an efficient and cost-effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi-genomic DNA from multiplexed samples. Here, we detail our synthesis of protocols for targeted resequencing of mitochondrial and nuclear loci by generating indexed genomic libraries for multiplexing up to 100 individuals in a single sequencing pool, and then enriching the pooled library using custom DNA capture arrays. Our use of DNA sequence from one species to capture and enrich the sequencing libraries of another species (i.e. cross-species DNA capture) indicates that efficient enrichment occurs when sequences are up to about 12% divergent, allowing us to take advantage of genomic information in one species to sequence orthologous regions in related species. In addition to a complete mitochondrial genome on each array, we have included between 43 and 118 nuclear loci for low-coverage sequencing of between 18 kb and 87 kb of DNA sequence per individual for single nucleotide polymorphisms discovery from 50 to 100 individuals in a single sequencing lane. Using this method, we have generated a total of over 500 whole mitochondrial genomes from seven cetacean species and green sea turtles. The greater variation detected in mitogenomes relative to short mtDNA sequences is helping to resolve genetic structure ranging from geographic to species-level differences. These NGS and analysis techniques have allowed for simultaneous population genomic studies of mtDNA and nDNA with greater genomic coverage and phylogeographic resolution than has previously been possible in marine mammals and turtles. PMID:23351075

  9. Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae).

    PubMed

    Failla, A J; Vasquez, A A; Hudson, P; Fujimoto, M; Ram, J L

    2016-02-01

    Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or 'species group' level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor

  10. Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae)

    USGS Publications Warehouse

    Failla, Andrew Joseph; Vasquez, Adrian Amelio; Hudson, Patrick L.; Fujimoto, Masanori; Ram, Jeffrey L.

    2016-01-01

    Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or ‘species group’ level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor

  11. Improved DNA barcoding method for Bemisia tabaci and related Aleyrodidae: Development of universal and Bemisia tabaci biotype-specific mitochondrial cytochrome c oxidase I polymerase chain reaction primers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whitefly is the common name of heteropteran insects that comprise the Aleyrodidae family composed of over 160 genera and 1500 different species. The mitochondrial cytochome c oxidase I (mtCOI) sequence has been used extensively in whitefly phylogenetic comparisons and in biotype identification of th...

  12. Overview of worldwide diversity of Diaphorina citri Kuwayama mitochondrial cytochrome oxidase 1 haplotypes: two Old World lineages and a New World invasion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We utilized a Bayesian phylogenetic technique to resolve global relationships of Diaphorina citri populations. This is the first global phylogenetic study of D. citri. New mitochondrial primers were designed from an EST library and an 821 base pair region of the COI was amplified and sequenced. The ...

  13. The complete sequence of the mitochondrial genome of Dahuabai pig (SusScrofa).

    PubMed

    Mao-Liang, Ran; He, Jun; Yang, An-Qi; Li, Zhi; Dong, Lian-Hua; Chen, Bin

    2016-05-01

    Dahuabai pig is one of the most important indigenous breed of the Guangzhou province of China. It is the first time that the complete mitochondrial genome sequence of Dahuabai pig is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,709 bp, which contains a control region (D-loop region), 2 ribosomal RNA genes, 13 protein-coding genes and 22 tRNA genes. The total base composition of Dahuabai pig mitochondrial genome is 34.68% for A, 26.20% for C, 25.81% for T and 13.32% for G, in the order A > C > T > G. The complete mitochondrial genome of Dahuabai pig provides an important data in studying mitochondrial DNA's role in the process of metabolism and programmed cell death. PMID:25423516

  14. Pairwise Comparisons of Mitochondrial DNA Sequences in Subdivided Populations and Implications for Early Human Evolution

    PubMed Central

    Marjoram, P.; Donnelly, P.

    1994-01-01

    We consider the effect on the distribution of pairwise differences between mitochondrial DNA sequences of the incorporation into the underlying population genetics model of two particular effects that seem realistic for human populations. The first is that the population size was roughly constant before growing to its current level. The second is that the population is geographically subdivided rather than panmictic. In each case these features tend to encourage multimodal distributions of pairwise differences, in contrast to existing, unimodal datasets. We argue that population genetics models currently used to analyze such data may thus fail to reflect important features of human mitochondrial DNA evolution. These may include selection on the mitochondrial genome, more realistic mutation mechanisms, or special population or migration dynamics. Particularly in view of the variability inherent in the single available human mitochondrial genealogy, it is argued that until these effects are better understood, inferences from such data should be rather cautious. PMID:8150290

  15. The complete mitochondrial genome of Cheilinus undulates based on high-throughput sequencing technique.

    PubMed

    Han, Yulong; Chen, Guohua; Luo, Jian; Wen, Xin; Li, Wenshen; Wang, Jun

    2016-05-01

    Cheilinus undulatus is a Critically Endangered ocean fish, which is also a higher level predator in coral reef. The complete mitochondrial genome of Cheilinus undulatus has been sequenced by high-throughput sequencing technology. According to the results, the mitochondrial genome of Cheilinus undulatus is 17,184 bp long and consists of 38 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The nucleotides compositions of the light strand are 27.62% of A, 24.82% of T, 16.66% of G and 30.90% of C. With the exception of ND6 and 8 tRNA genes, all other mitochondrial genes are encoded on the heavy strand. C. undulates mitochondrial genome contains a 568 bp sequences that is a non-coding DNA domain. No homology sequence had been found through BLAST in GenBank. The sequences are probably characteristic species marker of C. undulates. PMID:25329275

  16. Interspecific Comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    SciTech Connect

    Millenbaugh, Bonnie A; Pangilinan, Jasmyn L.; Torriani, Stefano F.F.; Goodwin, Stephen B.; Kema, Gert H.J.; McDonald, Bruce A.

    2007-12-07

    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has shown discordant patterns of nuclear and mitochondrial diversity. The mitochondrial genome of M. graminicola is a circular molecule of approximately 43,960 bp containing the typical genes coding for 14 proteins related to oxidative phosphorylation, one RNA polymerase, two rRNA genes and a set of 27 tRNAs. The mitochondrial DNA of M. graminicola lacks the gene encoding the putative ribosomal protein (rps5-like), commonly found in fungal mitochondrial genomes. Most of the tRNA genes were clustered with a gene order conserved with many other ascomycetes. A sample of thirty-five additional strains representing the known global mt diversity was partially sequenced to measure overall mitochondrial variability within the species. Little variation was found, confirming previous RFLP-based findings of low mitochondrial diversity. The mitochondrial sequence of M. graminicola is the first reported from the family Mycosphaerellaceae or the order Capnodiales. The sequence also provides a tool to better understand the development of fungicide resistance and the conflicting pattern of high nuclear and low mitochondrial diversity in global populations of this fungus.

  17. Mitochondrial DNA and nuclear DNA from normal rat liver have a common sequence.

    PubMed Central

    Hadler, H I; Dimitrijevic, B; Mahalingam, R

    1983-01-01

    Although Pst I does not cut the circular mitochondrial genome of the rat, BamHI generates from this genome two unequal fragments of DNA. Each of these fragments was cloned in pBR322. Nuclear DNA was digested from rat liver singly or doubly with Pst I and BamHI, and it was demonstrated that nuclear DNA shared a common sequence with the larger mitochondrial DNA BamHI fragment. The cloned larger mitochondrial DNA fragment was further subdivided with HindIII into four pieces that were labeled and then used to probe the double-digested nuclear DNA. The hybridization data showed that the common sequence is less than 3 kilobase pairs long and lies within the part of the mitochondrial genome containing the D-loop and a portion of the rRNA genes. It therefore appears that, as in lower eukaryotes, there are shared sequences between the nuclear and mitochondrial genomes in mammals. Images PMID:6579536

  18. Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani.

    PubMed

    Zardoya, Rafael; Malaga-Trillo, Edward; Veith, Michael; Meyer, Axel

    2003-10-23

    The complete nucleotide sequence (16,650 bp) of the mitochondrial genome of the salamander Mertensiella luschani (Caudata, Amphibia) was determined. This molecule conforms to the consensus vertebrate mitochondrial gene order. However, it is characterized by a long non-coding intervening sequence with two 124-bp repeats between the tRNA(Thr) and tRNA(Pro) genes. The new sequence data were used to reconstruct a phylogeny of jawed vertebrates. Phylogenetic analyses of all mitochondrial protein-coding genes at the amino acid level recovered a robust vertebrate tree in which lungfishes are the closest living relatives of tetrapods, salamanders and frogs are grouped together to the exclusion of caecilians (the Batrachia hypothesis) in a monophyletic amphibian clade, turtles show diapsid affinities and are placed as sister group of crocodiles+birds, and the marsupials are grouped together with monotremes and basal to placental mammals. The deduced phylogeny was used to characterize the molecular evolution of vertebrate mitochondrial proteins. Amino acid frequencies were analyzed across the main lineages of jawed vertebrates, and leucine and cysteine were found to be the most and least abundant amino acids in mitochondrial proteins, respectively. Patterns of amino acid replacements were conserved among vertebrates. Overall, cartilaginous fishes showed the least variation in amino acid frequencies and replacements. Constancy of rates of evolution among the main lineages of jawed vertebrates was rejected. PMID:14604788

  19. Comparison of whole mitochondrial genome sequences from two clades of the invasive ascidian, Didemnum vexillum.

    PubMed

    Smith, Kirsty F; Abbott, Cathryn L; Saito, Yasunori; Fidler, Andrew E

    2015-02-01

    The mitochondria are the main source of cellular energy production and have an important role in development, fertility, and thermal limitations. Adaptive mitochondrial DNA mutations have the potential to be of great importance in determining aspects of the life history of an organism. Phylogenetic analyses of the globally invasive marine ascidian Didemnum vexillum using the mitochondrial cytochrome c oxidase 1 (COX1) coding region, revealed two distinct clades. Representatives of one clade (denoted by 'B') are geographically restricted to D. vexillum's native region (north-west Pacific Ocean, including Japan), whereas members of the other clade (denoted by 'A') have been introduced and become invasive in temperate coastal areas around the world. Persistence of clade B's restricted distribution may reflect it being inherently less invasive than clade A. To investigate this we sought to determine if the two clades differ significantly in other mitochondrial genes of functional significance, specifically, alterations in amino acids encoded in mitochondrial enzyme subunits. Differences in functional mitochondrial genes could indicate an increased ability for clade A colonies to tolerate a wider range of environmental temperature. Full mitochondrial genomic sequences from D. vexillum clades A and B were obtained and they predict significant sequence differences in genes encoding for enzymes involved in oxidative phosphorylation. Diversity levels were relatively high and showed divergence across almost all genes, with p-distance values between the two clades indicating recent divergence. Both clades showed an excess of rare variants, which is consistent with balancing selection or a recent population expansion. Results presented here will inform future research focusing on examining the functional properties of the corresponding mitochondrial respiration enzymes, of A and B clade enzymes. By comparing closely related taxa that have differing distributions it is possible

  20. Molecular Phylogeny of a tick, Ixodes granulatus (Acari: Ixodidae) based on cytochrome oxidase subunit I (COI) marker

    NASA Astrophysics Data System (ADS)

    Lah, Ernieenor Faraliana Che; Yaakop, Salmah; Ahamad, Mariana; George, Ernna; Nor, Shukor Md

    2014-09-01

    Identification of a local species of tick, Ixodes granulatus from the family Ixodidae is essential because it has potential to be vector for spotted fever group (SFG) rickettsia and tick thypus. The aim of this study is to portray the relationships among several populations of I. granulatus collected from different species of animal hosts and localities in Peninsular Malaysia. Polymerase Chain Reaction was conducted by amplifying mitochondrial DNA marker, namely cytochrome oxidase subunit I (COI) sequences from 15 individual ticks that attached to five different hosts caught from three different localities. Confirmation of the species identity was accomplished using BLAST program. Neighbor-joining (NJ) and Maximum Parsimony (MP) tree based on COI sequences were constructed by using PAUP 4.0b10 to identify the relationship among species. The result of this study showed a high genetic heterogeneity between I. granulatus and other species of the same genus (7.2-23.7%). Furthermore, a low intraspecific variation was observed among the species of I. granulatus collected from different localities (0-3.7%). This study produced the first establishment of molecular marker for clarifying genetic species variation and diversity of local I. granulatus tick which contribute to the control of tick-borne infections.

  1. Increased Inter-Colony Fusion Rates Are Associated with Reduced COI Haplotype Diversity in an Invasive Colonial Ascidian Didemnum vexillum

    PubMed Central

    Smith, Kirsty F.; Stefaniak, Lauren; Saito, Yasunori; Gemmill, Chrissen E. C.; Cary, S. Craig; Fidler, Andrew E.

    2012-01-01

    Considerable progress in our understanding of the population genetic changes associated with biological invasions has been made over the past decade. Using selectively neutral loci, it has been established that reductions in genetic diversity, reflecting founder effects, have occurred during the establishment of some invasive populations. However, some colonial organisms may actually gain an ecological advantage from reduced genetic diversity because of the associated reduction in inter-colony conflict. Here we report population genetic analyses, along with colony fusion experiments, for a highly invasive colonial ascidian, Didemnum vexillum. Analyses based on mitochondrial cytochrome oxidase I (COI) partial coding sequences revealed two distinct D. vexillum clades. One COI clade appears to be restricted to the probable native region (i.e., north-west Pacific Ocean), while the other clade is present in widely dispersed temperate coastal waters around the world. This clade structure was supported by 18S ribosomal DNA (rDNA) sequence data, which revealed a one base-pair difference between the two clades. Recently established populations of D. vexillum in New Zealand displayed greatly reduced COI genetic diversity when compared with D. vexillum in Japan. In association with this reduction in genetic diversity was a significantly higher inter-colony fusion rate between randomly paired New Zealand D. vexillum colonies (80%, standard deviation ±18%) when compared with colonies found in Japan (27%, standard deviation ±15%). The results of this study add to growing evidence that for colonial organisms reductions in population level genetic diversity may alter colony interaction dynamics and enhance the invasive potential of newly colonizing species. PMID:22303442

  2. Intraspecific comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has show...

  3. Filling the gap - COI barcode resolution in eastern Palearctic birds

    PubMed Central

    2009-01-01

    Background The Palearctic region supports relatively few avian species, yet recent molecular studies have revealed that cryptic lineages likely still persist unrecognized. A broad survey of cytochrome c oxidase I (COI) sequences, or DNA barcodes, can aid on this front by providing molecular diagnostics for species assignment. Barcodes have already been extensively surveyed in the Nearctic, which provides an interesting comparison to this region; faunal interchange between these regions has been very dynamic. We explored COI sequence divergence within and between species of Palearctic birds, including samples from Russia, Kazakhstan, and Mongolia. As of yet, there is no consensus on the best method to analyze barcode data. We used this opportunity to compare and contrast three different methods routinely employed in barcoding studies: clustering-based, distance-based, and character-based methods. Results We produced COI sequences from 1,674 specimens representing 398 Palearctic species. These were merged with published COI sequences from North American congeners, creating a final dataset of 2,523 sequences for 599 species. Ninety-six percent of the species analyzed could be accurately identified using one or a combination of the methods employed. Most species could be rapidly assigned using the cluster-based or distance-based approach alone. For a few select groups of species, the character-based method offered an additional level of resolution. Of the five groups of indistinguishable species, most were pairs, save for a larger group comprising the herring gull complex. Up to 44 species exhibited deep intraspecific divergences, many of which corresponded to previously described phylogeographic patterns and endemism hotspots. Conclusion COI sequence divergence within eastern Palearctic birds is largely consistent with that observed in birds from other temperate regions. Sequence variation is primarily congruent with taxonomic boundaries; deviations from this trend

  4. The complete mitochondrial genome sequence of Symphysodon discus Heckel (1840).

    PubMed

    Yu, Yongliang; Chen, Zaizhong; Li, Zhongpu; Wang, Lei; Luo, Xiaoxi; Gao, Jianzhong

    2016-07-01

    The complete mitochondrial genome of Symphysodon discus Heckel was 16 544 bp in length, consisting of 22 tRNA genes, 13 protein-coding genes, 2 ribosomal rRNA genes, and a control region or displacement loop (D-loop). With the exception of 8 tRNAs and ND6 genes, the others were encoded on H-strand. The base composition on H-strand was 30.04% C, 28.39% A, 26.49% T and 15.07% G, exhibiting an A + T rich pattern. The codon usage was consistent with the other vertebrate mitochondrial pattern, i.e. start codon is ATG or GTG and stop codons are TAA, TAG or T- -. Stop codon TAG was only found in the ND6. There were 8 regions of gene overlapped with the length of 26 bp in total and 12 intergenic spacer regions (99 bp in total). PMID:26288117

  5. The complete sequence of mitochondrial genome of Wuzhishan pig (Sus Scrofa).

    PubMed

    Chai, Yu-Lan; Xu, Dong; Ma, Hai-Ming

    2016-01-01

    In the present study, we sequenced the complete mitochondrial genome of Wuzhishan pig, which was 16,741 bp in size and had a nucleotide composition in A and T (60.46%). The genome consisted of a major non-coding control region (D-loop region) and 37 genes, including 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), and 22 transfer RNA (tRNA) genes. The genes in the mitochondrial genomes of Wuzhishan pig used three kinds of initiation codons (ATA, ATG, and GTG) and four kinds of termination codons (TAA, AGA, TAG, and an incomplete termination codons T-). The complete mitochondrial genome sequence of Wuzhishan pig provides an important data set for further study on genetic mechanism. PMID:26490573

  6. Inferring patterns in mitochondrial DNA sequences through hypercube independent spanning trees.

    PubMed

    da Silva, Eduardo Sant' Ana; Pedrini, Helio

    2016-03-01

    Given a graph G, a set of spanning trees rooted at a vertex r of G is said vertex/edge independent if, for each vertex v of G, v≠r, the paths of r to v in any pair of trees are vertex/edge disjoint. Independent spanning trees (ISTs) provide a number of advantages in data broadcasting due to their fault tolerant properties. For this reason, some studies have addressed the issue by providing mechanisms for constructing independent spanning trees efficiently. In this work, we investigate how to construct independent spanning trees on hypercubes, which are generated based upon spanning binomial trees, and how to use them to predict mitochondrial DNA sequence parts through paths on the hypercube. The prediction works both for inferring mitochondrial DNA sequences comprised of six bases as well as infer anomalies that probably should not belong to the mitochondrial DNA standard. PMID:26802544

  7. Sequencing and analysis of the whole mitochondrial genome of a variegated racerunner from Taklamakan Desert.

    PubMed

    Zhou, Tianhe; Wan, Xiaoqin; Guo, Xianguang

    2016-07-01

    The whole mitochondrial genome of a variegated racerunner (Eremias vermiculata) from the Taklamakan Desert was determined using polymerase chain reaction and directly sequenced with a primer walking method. The mitogenome sequence was 19 796 bp in size, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop), which is similar to the typical mtDNA of vertebrates. Mitochondrial genomes analyses using maximum parsimony and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the seven Eremias species. Monophyly of the genus Eremias and E. vermiculata was recovered. The mitogenome presented here will contribute to the examination of genetic differentiation for E. vermiculata and understanding of the mitochondrial DNA evolution in Eremias. PMID:26153740

  8. The mitochondrial genome of Anopheles quadrimaculatus species A: complete nucleotide sequence and gene organization.

    PubMed

    Mitchell, S E; Cockburn, A F; Seawright, J A

    1993-12-01

    The complete sequence (15,455 bp) of the mitochondrial DNA of the mosquito Anopheles quadrimaculatus species A is reported. This genome is compact and very A+T rich (77.4% A+T). It contains genes for 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and 13 subunits of the mitochondrial inner membrane respiratory complexes. The gene arrangement is the same as in Drosophila yakuba, except that the positions of two contiguous tRNAs are reversed and a third tRNA is transcribed from the complementary strand. Protein-coding genes, rRNAs, and most tRNAs were similar to D. yakuba. Two tRNAs had nonstandard secondary structures comparable with those of nematode mitochondrial tRNAs. The very small putative control region (625 bp) contains no sequence motifs similar to those used in vertebrates and other insects for initiation of transcription and replication. PMID:8112570

  9. Complete genome sequence of the mitochondrial DNA of the sparkling enope squid, Watasenia scintillans.

    PubMed

    Hayashi, Keiko; Kawai, Yuri L; Yura, Kei; Yoshida, Masa-Aki; Ogura, Atsushi; Hata, Kenichiro; Nakabayashi, Kazuhiko; Okamura, Kohji

    2016-05-01

    The sparkling enope squid, Watasenia scintillans, is a deep-sea mollusk inhabiting the western part of the Pacific Ocean. It has the peculiar ability to illuminate its body without the involvement of other organisms. In this study, we extracted the brain DNA from a single squid female caught in the Japan Sea and determined the complete genome sequence of its mitochondrial DNA using the Illumina sequencing platform. The circular sequence is 20,089 bp in length. Using the next-generation sequencing data, we also estimated the mean copy number of mitochondria per cell in the brain to be 108 by comparing the depths of the read data in the nuclear and mitochondrial genomes. The haploid genome size was calculated to be 4.78 Gb. Six heteroplasmy sites were also identified, together with their allele frequencies, in this individual. Our methodology is shown to be useful in mitochondrion-related studies. PMID:25329271

  10. Mitochondrial genome sequence and expression profiling for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report on the assembly of the 14,146 base pairs (bp) near complete mitochondrial sequencing of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which was used to estimate divergence and relationships within the lepidopteran lineage. Arrangement and orientation of 13 protein c...

  11. Complete mitochondrial genome sequence of a phytophagous ladybird beetle, Henosepilachna pusillanima (Mulsant) (Coleoptera: Coccinellidae).

    PubMed

    Behere, G T; Firake, D M; Tay, W T; Azad Thakur, N S; Ngachan, S V

    2016-01-01

    Ladybird beetles are generally considered as agriculturally beneficial insects, but the ladybird beetles in the coleopteran subfamily Epilachninae are phytophagous and major plant feeding pest species which causes severe economic losses to cucurbitaceous and solanaceous crops. Henosepilachna pusillanima (Mulsant) is one of the important pest species of ladybird beetle. In this report, we sequenced and characterized the complete mitochondrial genome of H. pusillanima. For sequencing of the complete mitochondrial genome, we used the Ion Torrent sequencing platform. The complete circular mitochondrial genome of the H. pusillanima was determined to be 16,216 bp long. There were totally 13 protein coding genes, 22 transfer RNA, 2 ribosomal RNA and a control (A + T-rich) region estimated to be 1690 bp. The gene arrangement and orientations of assembled mitogenome were identical to the reported predatory ladybird beetle Coccinella septempunctata L. This is the first completely sequenced coleopteran mitochondrial genome from the beetle subfamily Epilachninae from India. Data generated in this study will benefit future comparative genomics studies for understanding the evolutionary relationships between predatory and phytophagous coccinellid beetles. PMID:24617459

  12. Mitochondrial Genome Sequence of the Galápagos Endemic Land Snail Naesiotus nux

    PubMed Central

    Hunter, Samuel S.; Settles, Matthew L.; New, Daniel D.; Parent, Christine E.

    2016-01-01

    We report herein the draft mitochondrial genome sequence of Naesiotus nux, a Galápagos endemic land snail species of the genus Naesiotus. The circular genome is 15 kb and encodes 13 protein-coding genes, 2 rRNA genes, and 21 tRNA genes. PMID:26798085

  13. Draft Plastid and Mitochondrial Genome Sequences from Antarctic Alga Prasiola crispa.

    PubMed

    Carvalho, Evelise Leis; Wallau, Gabriel da Luz; Rangel, Darlene Lopes; Machado, Laís Ceschini; da Silva, Alexandre Freitas; da Silva, Luiz Fernando Duarte; Macedo, Pablo Echeverria; Pereira, Antonio Batista; Victoria, Filipe de Carvalho; Boldo, Juliano Tomazzoni; Dal Belo, Cháriston André; Pinto, Paulo Marcos

    2015-01-01

    The organelle genomes of the Antarctic alga Prasiola crispa (Lightfoot) Kützing have been sequenced. The plastid and mitochondrial genomes have a total length of 196,502 bp and 89,819 bp, respectively. These genomes have 19 putative photosynthesis-related genes and 17 oxidative metabolism-related genes, respectively. PMID:26450727

  14. Draft Plastid and Mitochondrial Genome Sequences from Antarctic Alga Prasiola crispa

    PubMed Central

    Carvalho, Evelise Leis; Wallau, Gabriel da Luz; Rangel, Darlene Lopes; Machado, Laís Ceschini; da Silva, Alexandre Freitas; da Silva, Luiz Fernando Duarte; Macedo, Pablo Echeverria; Pereira, Antonio Batista; Victoria, Filipe de Carvalho; Boldo, Juliano Tomazzoni; Dal Belo, Cháriston André

    2015-01-01

    The organelle genomes of the Antarctic alga Prasiola crispa (Lightfoot) Kützing have been sequenced. The plastid and mitochondrial genomes have a total length of 196,502 bp and 89,819 bp, respectively. These genomes have 19 putative photosynthesis-related genes and 17 oxidative metabolism-related genes, respectively. PMID:26450727

  15. Solving a sequencing problem in the vertebrate mitochondrial control region using phylogenetic comparisons.

    PubMed

    Feinstein, Julie; Cracraft, Joel

    2004-01-01

    The mitochondrial control region (mtCR) of the bird-of-paradise, Phonygammus keraudrenii, the Trumpet Manucode, contains a unique arrangement of homopolymers and short tandem repeats. Homopolymers occur within a few hundred bases of each other, trapping sequence information between unsequenceable barriers. A comparative strategy, involving other manucode species, allowed the prediction of primer sites in the inaccessible region. The method is suggested for similar sequencing problems. PMID:15621664

  16. Complete mitochondrial genome sequence of Piaractus mesopotamicus (Holmberg, 1887).

    PubMed

    Pimentel, Juliana da Silva Martins; Carmo, Anderson Oliveira do; Maciel, Danielle de Cássia Lima; Siqueira, Flávia de Faria; Kalapothakis, Evanguedes

    2016-05-01

    The migratory species Piaractus Mesopotamicus, popularly known as the pacu, was determined to have a complete mitochondrial genome of 16,722 bp with 45% GC content. The genome contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a 1048 bp Control Region (D-loop). Almost all the PCGs used the standard ATG start codon, except for Cox1 that used a GTG start codon. Five of the 13 PCGs had a TAA stop codon, two had the incomplete stop codon TA- (Atp6 and Cox3), and five had the incomplete stop codon T-- (Nd2, Cox2, Nd3, Nd4, and Cytb). AGG was the stop codon of Cox1. PMID:25319283

  17. Complete mitochondrial genome sequence of Brycon orbignyanus (Characiformes, Bryconidae).

    PubMed

    Siqueira, Flávia de Faria; Carmo, Anderson Oliveira do; Pimentel, Juliana da Silva Martins; Kalapothakis, Evanguedes

    2016-05-01

    We report the whole mitochondrial genome of the Brycon orbignyanus, commonly known as the piracanjuba. The mitogenome was determined to be a circular, 16,800 bp DNA molecule, containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and one 1160 bp noncoding control region. Twelve of the PCGs were located on the heavy strand, and one PCG (Nd6) was located on the light strand. The most common start codon was ATG; however, the Cox1 gene displayed the GTG start codon. Seven PCGs had incomplete stop codons: specifically, Cox2, Cox3, Nd3, Nd4, and Cytb contained the T- - codon, and Nd2 and Atp6 contained the TA- codon. The Cox1 gene contained the AGG stop codon. PMID:25329263

  18. A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius)

    PubMed Central

    McGettigan, Paul A.; Lohan, Amanda J.; Murphy, Alison; Finlay, Emma K.; Shapiro, Beth; Chamberlain, Andrew T.; Richards, Martin B.; Bradley, Daniel G.; Loftus, Brendan J.; MacHugh, David E.

    2010-01-01

    Background The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. Methodology DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738±68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. Conclusions For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen

  19. Pronounced population genetic differentiation in the rock bream Oplegnathus fasciatus inferred from mitochondrial DNA sequences.

    PubMed

    Xiao, Yongshuang; Li, Jun; Ren, Guijing; Ma, Daoyuan; Wang, Yanfeng; Xiao, ZhiZhong; Xu, Shihong

    2016-05-01

    The population genetic structure of the rock bream (Oplegnathus fasciatus) along the coastal waters of China was estimated based on three mtDNA fragments (D-loop, COI, and Cytb). A total of 112 polymorphic sites were checked, which defined 63 haplotypes. A pattern with high levels of haplotype diversity (hCOI = 0.886 ± 0.034, hCytb = 0.874 ± 0.023) and low levels of nucleotide diversity (лCOI = 0.009 ± 0.005, лCytb = 0.006 ± 0.003) was detected based on the COI and Cytb fragments, and high levels of genetic diversity (hD-loop = 0.995 ± 0.007, лD-loop = 0.021 ± 0.011) were detected from the mtDNA D-loop. The population genetic diversity of O. fasciatus in south China was significantly higher than those of north China. Three genealogical clades were checked in the O. fasciatus populations based on the NJ and MST analyses of mtDNA COI gene sequence, and the genetic distances among the clades ranged from 0.018 to 0.025. Significant population genetic differentiation was also checked based on the Fst (0.331, p = 0.000) and exact p (0.000) test analyses. No significant population differentiations were checked based on mtDNA D-loop and Cytb fragments. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidences, we inferred that the genetic make-up of extant populations of O. fasciatus was shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (neutrality tests, mismatch distribution analysis, and Bayesian skyline analyses) showed that the species along coastline of China has experienced population expansions originated in its most recent history at about 169-175 kya before present. PMID:25427804

  20. Next Generation Sequencing to Characterize Mitochondrial Genomic DNA Heteroplasmy

    PubMed Central

    Huang, Taosheng

    2015-01-01

    This protocol is to describe the methodology to characterize mitochondria DNA (mtDNA) heteroplasmy with parallel sequencing. Mitochondria play a very important role in important cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondria genomes. The mutant mtDNA and the wild type may co-exist as heteroplasmy, and cause human disease. The purpose of this methodology is to simultaneously determine mtDNA sequence and to quantify the heteroplasmy level. The protocol includes two-fragment mitochondria genome DNA PCR amplification. The PCR product is then mixed at an equimolar ratio. The samples will be barcoded and sequenced with high-throughput next-generation sequencing technology. We found that this technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the degree of heteroplasmic level. PMID:21975941

  1. High-Throughput Sequencing of Complete Mitochondrial Genomes.

    PubMed

    Briscoe, Andrew George; Hopkins, Kevin Peter; Waeschenbach, Andrea

    2016-01-01

    Next-generation sequencing has revolutionized mitogenomics, turning a cottage industry into a high throughput process. This chapter outlines methodologies used to sequence, assemble, and annotate mitogenomes of non-model organisms using Illumina sequencing technology, utilizing either long-range PCR amplicons or gDNA as starting template. Instructions are given on how to extract DNA, conduct long-range PCR amplifications, generate short Sanger barcode tag sequences, prepare equimolar sample pools, construct and assess quality library preparations, assemble Illumina reads using either seeded reference mapping or de novo assembly, and annotate mitogenomes in the absence of an automated pipeline. Notes and recommendations, derived from our own experience, are given throughout this chapter. PMID:27460369

  2. Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris).

    PubMed

    Zhang, Wenping; Zhang, Zhihe; Shen, Fujun; Hou, Rong; Lv, Xiaoping; Yue, Bisong

    2006-08-01

    Using oligonucleotide primers designed to match hypervariable segments I (HVS-1) of Panthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses indicated that the sequence of 287 bp was a D-loop-like nuclear mitochondrial sequence (Numts), indicating a nuclear transfer that occurred approximately 4.8-17 million years ago in the tiger and 4.6-16 million years ago in the leopard. Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard. Thus, such sequences represent molecular 'fossils' that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis. This is also proved by comparing the phylogenetic trees reconstructed using the D-loop sequence of snow leopard and the 287-bp Numts as outgroup. PMID:17072079

  3. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.

    PubMed

    Lassiter, Erica S; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda C; Olarte, Rodrigo A; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L; Ristaino, Jean B

    2015-11-01

    Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there. PMID:25754775

  4. Complete mitochondrial genome sequence of the polychaete annelidPlatynereis dumerilii

    SciTech Connect

    Boore, Jeffrey L.

    2004-08-15

    Complete mitochondrial genome sequences are now available for 126 metazoans (see Boore 1999; Mitochondrial Genomics link at http://www.jgi.doe.gov), but the taxonomic representation is highly biased. For example, 80 are from a single phylum, Chordata, and show little variation for many molecular features. Arthropoda is represented by 16 taxa, Mollusca by eight, and Echinodermata by five, with only 17 others from the remaining {approx}30 metazoan phyla. With few exceptions (see Wolstenholme 1992 and Boore 1999) these are circular DNA molecules, about 16 kb in size, and encode the same set of 37 genes. A variety of non-standard names are sometimes used for animal mitochondrial genes; see Boore (1999) for gene nomenclature and a table of synonyms. Mitochondrial genome comparisons serve as a model of genome evolution. In this system, much smaller and simpler than that of the nucleus, are all of the same factors of genome evolution, where one may find tractable the changes in tRNA structure, base composition, genetic code, gene arrangement, etc. Further, patterns of mitochondrial gene rearrangements are an exceptionally reliable indicator of phylogenetic relationships (Smith et al.1993; Boore et al. 1995; Boore, Lavrov, and Brown 1998; Boore and Brown 1998, 2000; Dowton 1999; Stechmann and Schlegel 1999; Kurabayashi and Ueshima 2000). To these ends, we are sampling further the variation among major animal groups in features of their mitochondrial genomes.

  5. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora Ic clade species

    PubMed Central

    Lassiter, Erica S.; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda; Olarte, Rodrigo; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L.; Ristaino, Jean B.

    2015-01-01

    Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species including P. phaseoli, P. ipomoeae, P. mirabilis, and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans in order to resolve the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests further sampling in the Americasis warranted to understand the distribution of this species hybrid in nature. PMID:25754775

  6. Mitochondrial Genome Sequences of Spirometra erinaceieuropaei and S. decipiens (Cestoidea: Diphyllobothriidae)

    PubMed Central

    Eom, Keeseon S.; Park, Hansol; Lee, Dongmin; Choe, Seongjun; Kim, Kyu-Heon; Jeon, Hyeong-Kyu

    2015-01-01

    The present study was performed to compare the mitochondrial genomes between 2 Spirometra tapeworms, Spirometra erinaceieuropaei and Spirometra decipiens (Cestoidea: Diphyllobothriidae), which larval stages are important etiological agents of sparganosis in humans. For each species, the full mitochondrial genome was amplified in 8 overlapping fragments using total genomic DNA purified from a single worm as the template. The mitochondrial genomes were 13,643 bp (S. erinaceieuropaei) and 13,641 bp (S. decipiens) in length and contained 36 genes; 12 protein-coding genes, 2 ribosomal RNA (rRNA, small and large subunits), and 22 transfer RNAs (tRNAs). The 12 protein-coding genes constituted 10,083 bp (S. erinaceieuropaei) and 10,086 bp (S. decipiens) of their respective mitochondrial genomes. The tRNA genes, ranging in length from 56 to 70 bp, were identified based on putative secondary structures such as the typical cloverleaf shape. A total of 23 intergenic sequences, varying from 1 to 204 bp in size, were interspersed in S. erinaceieuropaei (total, 504 bp) and S. decipiens (total, 496 bp) mtDNA. The 12 protein-coding genes of S. erinaceieuropaei and S. decipiens differed by 12.4%, whereas the overall difference in mtDNA sequence between S. erinaceieuropaei and S. decipiens was 12.9%. Thus, from the standpoint of the mitochondrial genome, S. decipiens represents a valid species that can be distinguished from S. erinaceieuropaei. PMID:26323844

  7. Limpets of the genus Cellana (Patellogastropoda) from Pakistan, North Arabian Sea: species identification based on DNA sequencing.

    PubMed

    Zafar, Fatima Hayat Shaheen; Ayub, Zarrien; Begum, Samar; Siddiqui, Ghazala; Roberts, David

    2016-07-01

    The true limpets are found in the intertidal zone of the rocky shores of Pakistan, North Arabian Sea. Partial sequence of the mitochondrial cytochrome oxidase I was used to estimate the degree of genetic differentiation among the morphological forms of Cellana, which were considered as three separate species earlier in Pakistan. The study revealed that the three morphs of Cellana on COI sequence generated a single haplotype and matched with the COI sequence of Cellana karachiensis. This point out the phenotypic plasticity between the proposed species. PMID:26065851

  8. Phylogeny, species limits, and biogeography of the Brazilian lizards of the genus Eurolophosaurus (Squamata: Tropiduridae) as inferred from mitochondrial DNA sequences.

    PubMed

    Passoni, José Carlos; Benozzati, Maria Lúcia; Rodrigues, Miguel Trefaut

    2008-02-01

    Phylogenetic relationships and divergence times for 10 populations of the three recognized "species" of Brazilian lizards of genus Eurolophosaurus were estimated from 1229bp of cyt b, COI, 12S, and 16S rRNA mitochondrial gene segments. Eurolophosaurus is monophyletic and the basal split within the genus separates E. divaricatus from a clade comprising E. amathites and E. nanuzae. Three populations of E. divaricatus, which occurs along the western bank of Rio São Francisco, were consistently grouped together. On the east bank of the river, E. amathites and E. nanuzae from state of Bahia were recovered as the sister group of E. nanuzae populations from state of Minas Gerais. The paraphyly of E. nanuzae and the high divergence levels among populations of E. divaricatus strongly suggest that species limits in Eurolophosaurus should be revised. Even considering an extreme evolutionary rate of 2.8% sequence divergence per million years for the four gene segments analyzed together, E. divaricatus would have separated from the two other species by at least 5.5my ago, and E. amathites from E. nanuzae populations from Bahia and Minas Gerais, respectively, by 1.5 and 3.5my. The paleolacustrine hypothesis and changes in the course of the river potentially explain faunal divergence in the area, but divergences are much older than previously admitted. PMID:18082430

  9. Identification and characterization of the mitochondrial targeting sequence and mechanism in human citrate synthase.

    PubMed

    Cheng, Tsung-Lin; Liao, Ching-Chun; Tsai, Wen-Hui; Lin, Chin-Chih; Yeh, Chin-Wei; Teng, Chiao-Fang; Chang, Wen-Tsan

    2009-08-01

    Citrate synthase (CS), the first and rate-limiting enzyme of the tricarboxylic acid (TCA) cycle, plays a decisive role in regulating energy generation of mitochondrial respiration. Most mitochondrial proteins are synthesized in the cytoplasm as preproteins with an amino (N)-terminal mitochondrial targeting sequence (MTS) that directs mitochondria-specific sorting of the preprotein. However, the MTS and targeting mechanism of the human CS protein are not fully characterized. The human CS gene is a single nuclear gene which transcribes into two mRNA variants, isoform a (CSa) and b (CSb), by alternative splicing of exon 2. CSa encodes 466 amino acids, including a putative N-terminal MTS, while CSb expresses 400 residues with a shorter N terminus, lacking the MTS. Our results indicated that CSa is localized in the mitochondria and the N-terminal 27 amino acids, including a well-conserved RXY downward arrow (S/A) motif (the RHAS sequence), can efficiently target the enhanced green fluorescent protein (EGFP) into the mitochondria. Furthermore, site-directed mutagenesis analysis of the conserved basic amino acids and serine/threonine residues revealed that the R9 residue is essential but all serine/threonine residues are dispensable in the mitochondrial targeting function. Moreover, RNA interference (RNAi)-mediated gene silencing of the preprotein import receptors, including TOM20, TOM22, and TOM70, showed that all three preprotein import receptors are required for transporting CSa into the mitochondria. In conclusion, we have experimentally identified the mitochondrial targeting sequence of human CSa and elucidated its targeting mechanism. These results provide an important basis for the study of mitochondrial dysfunction due to aberrant CSa trafficking. PMID:19479947

  10. Complete mitochondrial genome of a hybrid strain of the domesticated silkworm (Qiufeng × Baiyu).

    PubMed

    Li, Fengbo; Zhang, Huixian; Liu, Peigang; Wang, Yongqiang; Meng, Zhiqi

    2016-05-01

    The hybrid strain of the domesticated silkworm (Qiufeng × Baiyu) is one of the most popular commercial silkworm varieties in China. In this study, we reported its complete mitochondrial genome sequence for the first time. The 15,680 bp long genome contains 37 genes (13 protein-coding genes [PCGs], 2 rRNA genes, and 22 tRNA genes) and 1 major non-coding A + T-rich region, with the typical arrangement found in Lepidoptera. All PCGs started with typical ATN codons except for COI, which began with CGA. Eleven PCGs have complete stop codons, whereas COI and COII end with a single T. The 495 bp long A + T-rich region harbors the conserved sequence features typically found in lepidopteran insects. The complete mitochondrial genome sequence of Qiufeng × Baiyu provides an important data source for further study on the mechanism of silkworm domestication. PMID:25319289

  11. Complete mitochondrial DNA sequence of marble goby, Oxyeleotris marmorata (Bleeker, 1852).

    PubMed

    Xu, Yiping; Hu, Yonglai; Bao, Baolong; Gong, Xiaoling

    2016-01-01

    Marble goby, Oxyeleotris marmorata (Bleeker) is a large-scale invasive goby in China. In this study, the mitochondrial genome of marble goby was firstly determined. The entire mtDNA sequence was 16,556 bp in length with 13 protein-coding genes, 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and control region (CR). Its mitochondrial genome has the common features with those of other bony fishes with respect to gene arrangement, base composition, and tRNA structures. PMID:24845442

  12. Mutation eliminating mitochondrial leader sequence of methylmalonyl-CoA mutase causes muto methylmalonic acidemia.

    PubMed Central

    Ledley, F D; Jansen, R; Nham, S U; Fenton, W A; Rosenberg, L E

    1990-01-01

    Methylmalonyl-CoA mutase (EC 5.4.99.2) is a mitochondrial matrix enzyme whose activity is deficient in the inherited disorder methylmalonic acidemia. Previous studies on primary fibroblast cell lines from patients with methylmalonic acidemia have delineated a variety of biochemical phenotypes underlying this disorder. One cell line with primary mutase apoenzyme deficiency exhibited a particularly unusual phenotype; it expressed an abnormally small and unstable immunoreactive protein, which was not imported by mitochondria. We now report cloning and sequencing of the cDNA encoding this mutant protein. The mutation is a single base change, a cytosine----thymine transition, which introduces an amber termination codon at position 17 within the mitochondrial leader sequence. The immunoreactive protein produced by these cells reflects translation from AUG codons downstream from this termination codon and, hence, lacks a mitochondrial leader peptide. This mutation represents a complex prototype for a class of mutations in which absence of the mitochondrial targeting sequence leads to absence of a functioning gene product. Images PMID:1970180

  13. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-C6.

    PubMed

    Xu, Le; Wang, Shuai; Fan, Xiao; Xu, Dong; Zhang, Xiaowen; Miao, Yu; Ye, Naihao

    2016-09-01

    The complete mitochondrial sequence (37 657 bp) of the Saccharina sp. ye-C6 was obtained from the assembled and annotated genome data sequenced by Illumina sequencing technology (KT271760). The circular genome contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA), and 25 transfer RNA (tRNA) genes. Base composition of genome is A (28.41%), T (36.29%), C (14.72%), and G (20.58%). Through a phylogenetic analysis based on the mitochondrial genomes of brown algae, we found that Saccharina sp. ye-C6 and Saccharina japonica are the most closely related species and strongly supports their close phylogenetic affinity. PMID:26403617

  14. Resolution of the African hominoid trichotomy by use of a mitochondrial gene sequence

    SciTech Connect

    Ruvolo, M.; Disotell, T.R.; Allard, M.W. ); Brown, W.M. ); Honeycutt, R.L. )

    1991-02-15

    Mitochondrial DNA sequences encoding the cytochrome oxidase subunit II gene have been determined for five primate species, siamang (Hylobates syndactylus), lowland gorilla (Gorilla gorilla), pygmy chimpanzee (Pan paniscus), crab-eating macaque (Macaca fascicularis), and green monkey (Cercopithecus aethiops), and compared with published sequences of other primate and nonprimate species. Comparisons of cytochrome oxidase subunit II gene sequences provide clear-cut evidence from the mitochondrial genome for the separation of the African ape trichotomy into two evolutionary lineages, one leading to gorillas and the other to humans and chimpanzees. Several different tree-building methods support this same phylogenetic tree topology. The comparisons also yield trees in which a substantial length separates the divergence point of gorillas from that of humans and chimpanzees, suggesting that the lineage most immediately ancestral to humans and chimpanzees may have been in existence for a relatively long time.

  15. Sequencing and analysis of the complete mitochondrial genome of tundra shrew (Sorex tundrensis) from China.

    PubMed

    Xu, Chunzhu; Zhao, Shuai; Wu, Hualin; Wu, Shengyang; Zhang, Zhongwen; Wang, Bo; Dou, Huashan

    2016-07-01

    The complete mitogenome sequence of tundra shrew (Sorex tundrensis) was determined using long PCR. The genome was 17,444 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 23 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (32.9%), C (24.8%), T (29.0%), and G (13.3%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of tundra shrew. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. The three Sorex species formed a monophyletic group with the high bootstrap value (100 %) in all examinations. PMID:25812054

  16. Differentiating between monozygotic twins through next-generation mitochondrial genome sequencing.

    PubMed

    Wang, Zheng; Zhu, Ruxin; Zhang, Suhua; Bian, Yinnan; Lu, Daru; Li, Chengtao

    2015-12-01

    Monozygotic (MZ) twins, considered to be genetically identical, cannot be distinguished from one another by standard forensic DNA testing. A recent study employed whole genome sequencing to identify extremely rare mutations and reported that mutation analysis could be used to differentiate between MZ twins. Compared with nuclear DNA, mitochondrial DNA (mtDNA) has higher mutation rates; therefore, minor differences theoretically exist in MZ twins' mitochondrial genome (mtGenome). However, conventional Sanger-type sequencing (STS) is neither amenable to, nor feasible for, the detection of low-level sequence variants. The recent introduction of massively parallel sequencing (MPS) has the capability to sequence many targeted regions of multiple samples simultaneously with desirable depth of coverage. Thus, the aim of this study was to assess whether full mtGenome sequencing analysis can be used to differentiate between MZ twins. Ten sets of MZ twins provided blood samples that underwent extraction, quantification, mtDNA enrichment, library preparation, and ultra-deep sequencing. Point heteroplasmies were observed in eight sets of MZ twins, and a single nucleotide variant (nt15301) was detected in five sets of MZ twins. Thus, this study demonstrates that ultra-deep mtGenome sequencing could be used to differentiate between MZ twins. PMID:26327617

  17. Mitochondrial Sequence Variation in African-American Primary Open-Angle Glaucoma Patients

    PubMed Central

    Collins, David W.; Gudiseva, Harini V.; Trachtman, Benjamin T.; Jerrehian, Matthew; Gorry, Thomasine; Merritt III, William T.; Rhodes, Allison L.; Sankar, Prithvi S.; Regina, Meredith; Miller-Ellis, Eydie; O’Brien, Joan M.

    2013-01-01

    Primary open-angle glaucoma (POAG) is a major cause of blindness and results from irreversible retinal ganglion cell damage and optic nerve degeneration. In the United States, POAG is most prevalent in African-Americans. Mitochondrial genetics and dysfunction have been implicated in POAG, and potentially pathogenic sequence variations, in particular novel transversional base substitutions, are reportedly common in mitochondrial genomes (mtDNA) from POAG patient blood. The purpose of this study was to ascertain the spectrum of sequence variation in mtDNA from African-American POAG patients and determine whether novel nonsynonymous, transversional or other potentially pathogenic sequence variations are observed more commonly in POAG cases than controls. mtDNA from African-American POAG cases (n = 22) and age-matched controls (n = 22) was analyzed by deep sequencing of a single 16,487 base pair PCR amplicon by Ion Torrent, and candidate novel variants were validated by Sanger sequencing. Sequence variants were classified and interpreted using the MITOMAP compendium of polymorphisms. 99.8% of the observed variations had been previously reported. The ratio of novel variants to POAG cases was 7-fold lower than a prior estimate. Novel mtDNA variants were present in 3 of 22 cases, novel nonsynonymous changes in 1 of 22 cases and novel transversions in 0 of 22 cases; these proportions are significantly lower (p<.0005, p<.0004, p<.0001) than estimated previously for POAG, and did not differ significantly from controls. Although it is possible that mitochondrial genetics play a role in African-Americans’ high susceptibility to POAG, it is unlikely that any mitochondrial respiratory dysfunction is due to an abnormally high incidence of novel mutations that can be detected in mtDNA from peripheral blood. PMID:24146900

  18. Mitochondrial sequence variation in African-American primary open-angle glaucoma patients.

    PubMed

    Collins, David W; Gudiseva, Harini V; Trachtman, Benjamin T; Jerrehian, Matthew; Gorry, Thomasine; Merritt, William T; Rhodes, Allison L; Sankar, Prithvi S; Regina, Meredith; Miller-Ellis, Eydie; O'Brien, Joan M

    2013-01-01

    Primary open-angle glaucoma (POAG) is a major cause of blindness and results from irreversible retinal ganglion cell damage and optic nerve degeneration. In the United States, POAG is most prevalent in African-Americans. Mitochondrial genetics and dysfunction have been implicated in POAG, and potentially pathogenic sequence variations, in particular novel transversional base substitutions, are reportedly common in mitochondrial genomes (mtDNA) from POAG patient blood. The purpose of this study was to ascertain the spectrum of sequence variation in mtDNA from African-American POAG patients and determine whether novel nonsynonymous, transversional or other potentially pathogenic sequence variations are observed more commonly in POAG cases than controls. mtDNA from African-American POAG cases (n = 22) and age-matched controls (n = 22) was analyzed by deep sequencing of a single 16,487 base pair PCR amplicon by Ion Torrent, and candidate novel variants were validated by Sanger sequencing. Sequence variants were classified and interpreted using the MITOMAP compendium of polymorphisms. 99.8% of the observed variations had been previously reported. The ratio of novel variants to POAG cases was 7-fold lower than a prior estimate. Novel mtDNA variants were present in 3 of 22 cases, novel nonsynonymous changes in 1 of 22 cases and novel transversions in 0 of 22 cases; these proportions are significantly lower (p<.0005, p<.0004, p<.0001) than estimated previously for POAG, and did not differ significantly from controls. Although it is possible that mitochondrial genetics play a role in African-Americans' high susceptibility to POAG, it is unlikely that any mitochondrial respiratory dysfunction is due to an abnormally high incidence of novel mutations that can be detected in mtDNA from peripheral blood. PMID:24146900

  19. The complete mitochondrial genome of Haliotis laevigata (Gastropoda: Haliotidae) using MiSeq and HiSeq sequencing.

    PubMed

    Robinson, Nick A; Hall, Nathan E; Ross, Elizabeth M; Cooke, Ira R; Shiel, Brett P; Robinson, Andrew J; Strugnell, Jan M

    2016-01-01

    The mitochondrial genome of greenlip abalone, Haliotis laevigata, is reported. MiSeq and HiSeq sequencing of one individual was assembled to yield a single 16,545 bp contig. The sequence shares 92% identity to the H. rubra mitochondrial genome (a closely related species that hybridize with H. laevigata in the wild). The sequence will be useful for determining the maternal contribution to hybrid populations, for investigating population structure and stock-enhancement effectiveness. PMID:24660910

  20. The complete mitochondrial genome sequence of Oceanic whitetip shark, Carcharhinus longimanus (Carcharhiniformes: Carcharhinidae).

    PubMed

    Li, Weiwen; Dai, Xiaojie; Xu, Qianghua; Wu, Feng; Gao, Chunxia; Zhang, Yanbo

    2016-05-01

    The complete mitochondrial DNA sequence of Carcharhinus longimanus was determined and analyzed. The complete mtDNA genome sequence of C. longimanus was 16,706 bp in length. It contained 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and 2 non-conding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence information of C. longimanus can provide a useful data for further studies on molecular systematics, stock evaluation, taxonomic status and conservation genetics. PMID:25264845

  1. Ethnic variation in the mitochondrial targeting sequence polymorphism of MnSOD.

    PubMed

    Van Landeghem, G F; Tabatabaie, P; Kucinskas, V; Saha, N; Beckman, G

    1999-07-01

    In contrast to CuZn superoxide dismutase (SOD), only a very limited number of mutations have been described in MnSOD. One interesting example is a polymorphism (Ala-9Val) in the mitochondrial targeting sequence of this radical-scavenging enzyme. We have studied the Ala-9Val polymorphism in various ethnic groups by means of the oligonucleotide ligation assay. There were significant variations in this unique polymorphism between three different language groups: Baltic (Lithuanians), Finnic (Finns and Saamis) and Germanic (Swedes). The Ala frequency in an Asiatic population (Chinese) was significantly lower than in most European populations. This polymorphism may affect the mitochondrial targeting rate of MnSOD which may result in mitochondrial damage with implication in various late-onset neurological diseases. PMID:10436379

  2. Expression profiling of Drosophila mitochondrial genes via deep mRNA sequencing

    PubMed Central

    Torres, Tatiana Teixeira; Dolezal, Marlies; Schlötterer, Christian; Ottenwälder, Birgit

    2009-01-01

    Mitochondria play an essential role in several cellular processes. Nevertheless, very little is known about patterns of gene expression of genes encoded by the mitochondrial DNA (mtDNA). In this study, we used next-generation sequencing (NGS) for transcription profiling of genes encoded in the mitochondrial genome of Drosophila melanogaster and D. pseudoobscura. The analysis of males and females in both species indicated that the expression pattern was conserved between the two species, but differed significantly between both sexes. Interestingly, mRNA levels were not only different among genes encoded by separate transcription units, but also showed significant differences among genes located in the same transcription unit. Hence, mRNA abundance of genes encoded by mtDNA seems to be heavily modulated by post-transcriptional regulation. Finally, we also identified several transcripts with a noncanonical structure, suggesting that processing of mitochondrial transcripts may be more complex than previously assumed. PMID:19843606

  3. The complete sequence of mitochondrial genome of Wuyi Black pig (Sus Scrofa).

    PubMed

    Xiao, Dingfu; Hu, Xionggui; Chen, Yuguang; Gong, Zexiu; Chen, Li

    2016-05-01

    Wuyi Black pig is a native breed of Fujian province in China. It is the first time that the complete mitochondrial genome sequence of Wuyi Black pig is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,709 bp, which contains 2 ribosomal RNA genes, 22 tRNA genes, 13 PCGs and 1 control region (D-loop region). The total base composition of Wuyi Black pig mitochondrial genome is 34.67% for A, 26.20% for C, 25.81% for T and 13.33% for G, in the order A > C > T > G. The complete mitochondrial genome of Wuyi Black pig provides an important data in genetic mechanism and the evolution genomes. PMID:25208179

  4. The complete sequence of the mitochondrial genome of Longlin pig (Sus Scrofa).

    PubMed

    Hu, Xionggui; Xiao, Dingfu; Li, Wenping

    2016-05-01

    Longlin pig is a native breed of Fujian province in China. It is the first time that the complete mitochondrial genome sequence of Longlin pig is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,699 bp, which contains 1 control region (D-loop region), 2 ribosomal RNA genes, 13 PCGs and 22 tRNA genes. The total base composition of Longlin pig mitochondrial genome is 34.67% for A, 26.21% for C, 25.80% for T and 13.33% for G, in the order A>C>T>G. The complete mitochondrial genome of Longlin pig provides an important data in genetic mechanism and the evolution genomes. PMID:25259452

  5. MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites*

    PubMed Central

    Fukasawa, Yoshinori; Tsuji, Junko; Fu, Szu-Chin; Tomii, Kentaro; Horton, Paul; Imai, Kenichiro

    2015-01-01

    Mitochondria provide numerous essential functions for cells and their dysfunction leads to a variety of diseases. Thus, obtaining a complete mitochondrial proteome should be a crucial step toward understanding the roles of mitochondria. Many mitochondrial proteins have been identified experimentally but a complete list is not yet available. To fill this gap, methods to computationally predict mitochondrial proteins from amino acid sequence have been developed and are widely used, but unfortunately, their accuracy is far from perfect. Here we describe MitoFates, an improved prediction method for cleavable N-terminal mitochondrial targeting signals (presequences) and their cleavage sites. MitoFates introduces novel sequence features including positively charged amphiphilicity, presequence motifs, and position weight matrices modeling the presequence cleavage sites. These features are combined with classical ones such as amino acid composition and physico-chemical properties as input to a standard support vector machine classifier. On independent test data, MitoFates attains better performance than existing predictors in both detection of presequences and in predicting their cleavage sites. We used MitoFates to look for undiscovered mitochondrial proteins from 42,217 human proteins (including isoforms such as alternative splicing or translation initiation variants). MitoFates predicts 1167 genes to have at least one isoform with a presequence. Five-hundred and eighty of these genes were not annotated as mitochondrial in either UniProt or Gene Ontology. Interestingly, these include candidate regulators of parkin translocation to damaged mitochondria, and also many genes with known disease mutations, suggesting that careful investigation of MitoFates predictions may be helpful in elucidating the role of mitochondria in health and disease. MitoFates is open source with a convenient web server publicly available. PMID:25670805

  6. Species identification using genetic tools: the value of nuclear and mitochondrial gene sequences in whale conservation.

    PubMed

    Palumbi, S R; Cipriano, F

    1998-01-01

    DNA sequence analysis is a powerful tool for identifying the source of samples thought to be derived from threatened or endangered species. Analysis of mitochondrial DNA (mtDNA) from retail whale meat markets has shown consistently that the expected baleen whale in these markets, the minke whale, makes up only about half the products analyzed. The other products are either unregulated small toothed whales like dolphins or are protected baleen whales such as humpback, Bryde's, fin, or blue whales. Independent verification of such mtDNA identifications requires analysis of nuclear genetic loci, but this is technically more difficult than standard mtDNA sequencing. In addition, evolution of species-specific sequences (i.e., fixation of sequence differences to produce reciprocally monophyletic gene trees) is slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. When will use of nuclear sequences allow forensic DNA identification? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The "three-times rule" suggests that phylogenetic sorting at nuclear loci is likely to produce species-specific sequences when mitochondrial alleles are reciprocally monophyletic and the branches leading to the mtDNA sequences of a species are three times longer than the average difference observed within species. A preliminary test of the three-times rule, which depends on many assumptions about the species and genes involved, suggests that blue and fin whales should have species-specific sequences at most neutral nuclear loci, whereas humpback and fin whales should show species-specific sequences at fewer nuclear loci. Partial sequences of actin introns from these species confirm the predictions of the three-times rule and show that blue and fin whales are reciprocally monophyletic at this locus. These intron sequences are thus good tools for the identification of these species

  7. The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization

    PubMed Central

    Chesnick, Joby M.; Goff, Megan; Graham, James; Ocampo, Christopher; Lang, B. Franz; Seif, Elias; Burger, Gertraud

    2000-01-01

    This is the first report of a complete mitochondrial genome sequence from a photosynthetic member of the stramenopiles, the chrysophyte alga Chrysodidymus synuroideus. The circular-mapping mitochondrial DNA (mtDNA) of 34 119 bp contains 58 densely packed genes (all without introns) and five unique open reading frames (ORFs). Protein genes code for components of respiratory chain complexes, ATP synthase and the mitoribosome, as well as one product of unknown function, encoded in many other protist mtDNAs (YMF16). In addition to small and large subunit ribosomal RNAs, 23 tRNAs are mtDNA-encoded, permitting translation of all codons present in protein-coding genes except ACN (Thr) and CGN (Arg). The missing tRNAs are assumed to be imported from the cytosol. Comparison of the C.synuroideus mtDNA with that of other stramenopiles allowed us to draw conclusions about mitochondrial genome organization, expression and evolution. First, we provide evidence that mitochondrial ORFs code for highly derived, unrecognizable versions of ribosomal or respiratory genes otherwise ‘missing’ in a particular mtDNA. Secondly, the observed constraints in mitochondrial genome rearrangements suggest operon-based, co-ordinated expression of genes functioning in common biological processes. Finally, stramenopile mtDNAs reveal an unexpectedly low variability in genome size and gene complement, testifying to substantial differences in the tempo of mtDNA evolution between major eukaryotic lineages. PMID:10871400

  8. A mitochondrial DNA sequence is associated with abnormal pollen development in cytoplasmic male sterile bean plants.

    PubMed Central

    Johns, C; Lu, M; Lyznik, A; Mackenzie, S

    1992-01-01

    Cytoplasmic male sterility (CMS) in common bean is associated with the presence of a 3-kb unique mitochondrial sequence designated pvs. The pvs sequence encodes at least two open reading frames (297 and 720 bp in length) with portions derived from the chloroplast genome. Fertility restoration by the nuclear restorer gene Fr results in the loss of this transcriptionally active unique region. We examined the effect of CMS (pvs present) and fertility restoration by Fr (pvs absent) on the pattern of pollen development in bean. In the CMS line, pollen aborted in the tetrad stage late in microgametogenesis. Microspores maintained cytoplasmic connections throughout pollen development, indicating aberrant or incomplete cytokinesis. Pollen-specific events associated with pollen abortion and fertility restoration imply that a gametophytic factor or event may be involved in CMS. In situ hybridization experiments suggested that significant reduction or complete loss of the mitochondrial sterility-associated sequence occurred in fertile pollen of F2 populations segregating for fertility. These observations support a model of fertility restoration by the loss of a mitochondrial DNA sequence prior to or during microsporogenesis/gametogenesis. PMID:1498602

  9. Dog mitochondrial genome sequencing to enhance dog mtDNA discrimination power in forensic casework.

    PubMed

    Verscheure, Sophie; Backeljau, Thierry; Desmyter, Stijn

    2014-09-01

    A Belgian dog population sample and several population studies worldwide have confirmed that only a limited number of mtDNA control region haplotypes is observed in the majority of dogs. The high population frequency of these haplotypes negatively impacts both the exclusion probability of dog mtDNA analysis and the evidential value of a match with one of these haplotypes in casework. Variation within the mtDNA coding region was explored to improve the discrimination power of dog mtDNA analysis. In the current study, the entire mitochondrial genome of 161 dogs was sequenced applying a quality assured strategy and resulted in a total of 119 different mitochondrial genome sequences. Our research was focused on those dogs with the six most common control region haplotypes from a previous Belgian population study. We identified 33 informative SNPs that successfully divide the six most common control region haplotypes into 32 clusters of mitochondrial genome sequences. Determining the identity of these 33 polymorphic sites in addition to control region sequencing in case of a match with one of these 6 control region haplotypes could augment the exclusion probability of forensic dog mtDNA analysis from 92.5% to 97.5%. PMID:24905334

  10. Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing

    PubMed Central

    Calvo, Sarah E.; Compton, Alison G.; Hershman, Steven G.; Lim, Sze Chern; Lieber, Daniel S.; Tucker, Elena J.; Laskowski, Adrienne; Garone, Caterina; Liu, Shangtao; Jaffe, David B.; Christodoulou, John; Fletcher, Janice M.; Bruno, Damien L; Goldblatt, Jack; DiMauro, Salvatore; Thorburn, David R.; Mootha, Vamsi K.

    2012-01-01

    Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. While in research settings NGS has pinpointed causal alleles using segregation in large families, the key challenge for clinical diagnosis is application to single individuals. To explore its diagnostic utility, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease, who were refractory to traditional molecular diagnosis. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with over 100 causal genes identified to date. We performed “MitoExome” sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Since patients and controls harbored a comparable number of such heterozygous alleles, we could not prioritize dominant acting genes. However, patients showed a five-fold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23/42 (55%) patients harbored such recessive genes or pathogenic mtDNA variants. Firm diagnoses were enabled in 10 patients (24%) who had mutations in genes previously linked to disease. 13 patients (31%) had mutations in nuclear genes never linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by cDNA complementation and evidence from multiple patients, respectively. The results underscore the immediate potential and challenges of deploying NGS in clinical settings. PMID:22277967

  11. Comparative Sequence Analysis of the Non-Protein-Coding Mitochondrial DNA of Inbred Rat Strains

    PubMed Central

    Abhyankar, Avinash; Park, Hee-Bok; Tonolo, Giancarlo; Luthman, Holger

    2009-01-01

    The proper function of mammalian mitochondria necessitates a coordinated expression of both nuclear and mitochondrial genes, most likely due to the co-evolution of nuclear and mitochondrial genomes. The non-protein coding regions of mitochondrial DNA (mtDNA) including the D-loop, tRNA and rRNA genes form a major component of this regulated expression unit. Here we present comparative analyses of the non-protein-coding regions from 27 Rattus norvegicus mtDNA sequences. There were two variable positions in 12S rRNA, 20 in 16S rRNA, eight within the tRNA genes and 13 in the D-loop. Only one of the three neutrality tests used demonstrated statistically significant evidence for selection in 16S rRNA and tRNA-Cys. Based on our analyses of conserved sequences, we propose that some of the variable nucleotide positions identified in 16S rRNA and tRNA-Cys, and the D-loop might be important for mitochondrial function and its regulation. PMID:19997590

  12. Complete mitochondrial genome sequence of the Eastern gorilla (Gorilla beringei) and implications for african ape biogeography.

    PubMed

    Das, Ranajit; Hergenrother, Scott D; Soto-Calderón, Iván D; Dew, J Larry; Anthony, Nicola M; Jensen-Seaman, Michael I

    2014-01-01

    The Western and Eastern species of gorillas (Gorilla gorilla and Gorilla beringei) began diverging in the mid-Pleistocene, but in a complex pattern with ongoing gene flow following their initial split. We sequenced the complete mitochondrial genomes of 1 Eastern and 1 Western gorilla to provide the most accurate date for their mitochondrial divergence, and to analyze patterns of nucleotide substitutions. The most recent common ancestor of these genomes existed about 1.9 million years ago, slightly more recent than that of chimpanzee and bonobo. We in turn use this date as a calibration to reanalyze sequences from the Eastern lowland and mountain gorilla subspecies to estimate their mitochondrial divergence at approximately 380000 years ago. These dates help frame a hypothesis whereby populations became isolated nearly 2 million years ago with restricted maternal gene flow, followed by ongoing male migration until the recent past. This process of divergence with prolonged hybridization occurred against the backdrop of the African Pleistocene, characterized by intense fluctuations in temperature and aridity, while at the same time experiencing tectonic uplifting and consequent shifts in the drainage of major river systems. Interestingly, this same pattern of introgression following divergence and discrepancies between mitochondrial and nuclear loci is seen in fossil hominins from Eurasia, suggesting that such processes may be common in hominids and that living gorillas may provide a useful model for understanding isolation and migration in our extinct relatives. PMID:25189777

  13. Complete Mitochondrial Genome Sequence of the Eastern Gorilla (Gorilla beringei) and Implications for African Ape Biogeography

    PubMed Central

    Das, Ranajit; Hergenrother, Scott D.; Soto-Calderón, Iván D.; Dew, J. Larry; Anthony, Nicola M.

    2014-01-01

    The Western and Eastern species of gorillas (Gorilla gorilla and Gorilla beringei) began diverging in the mid-Pleistocene, but in a complex pattern with ongoing gene flow following their initial split. We sequenced the complete mitochondrial genomes of 1 Eastern and 1 Western gorilla to provide the most accurate date for their mitochondrial divergence, and to analyze patterns of nucleotide substitutions. The most recent common ancestor of these genomes existed about 1.9 million years ago, slightly more recent than that of chimpanzee and bonobo. We in turn use this date as a calibration to reanalyze sequences from the Eastern lowland and mountain gorilla subspecies to estimate their mitochondrial divergence at approximately 380000 years ago. These dates help frame a hypothesis whereby populations became isolated nearly 2 million years ago with restricted maternal gene flow, followed by ongoing male migration until the recent past. This process of divergence with prolonged hybridization occurred against the backdrop of the African Pleistocene, characterized by intense fluctuations in temperature and aridity, while at the same time experiencing tectonic uplifting and consequent shifts in the drainage of major river systems. Interestingly, this same pattern of introgression following divergence and discrepancies between mitochondrial and nuclear loci is seen in fossil hominins from Eurasia, suggesting that such processes may be common in hominids and that living gorillas may provide a useful model for understanding isolation and migration in our extinct relatives. PMID:25189777

  14. A specific isoform of poly(ADP-ribose) glycohydrolase is targeted to the mitochondrial matrix by a N-terminal mitochondrial targeting sequence

    SciTech Connect

    Whatcott, Clifford J.; Meyer-Ficca, Mirella L.; Meyer, Ralph G.; Jacobson, Myron K.

    2009-12-10

    Poly(ADP-ribose) polymerases (PARPs) convert NAD to polymers of ADP-ribose that are converted to free ADP-ribose by poly(ADP-ribose) glycohydrolase (PARG). The activation of the nuclear enzyme PARP-1 following genotoxic stress has been linked to release of apoptosis inducing factor from the mitochondria, but the mechanisms by which signals are transmitted between nuclear and mitochondrial compartments are not well understood. The study reported here has examined the relationship between PARG and mitochondria in HeLa cells. Endogenous PARG associated with the mitochondrial fraction migrated in the range of 60 kDa. Transient transfection of cells with PARG expression constructs with amino acids encoded by exon 4 at the N-terminus was targeted to the mitochondria as demonstrated by subcellular fractionation and immunofluorescence microscopy of whole cells. Deletion and missense mutants allowed identification of a canonical N-terminal mitochondrial targeting sequence consisting of the first 16 amino acids encoded by PARG exon 4. Sub-mitochondrial localization experiments indicate that this mitochondrial PARG isoform is targeted to the mitochondrial matrix. The identification of a PARG isoform as a component of the mitochondrial matrix raises several interesting possibilities concerning mechanisms of nuclear-mitochondrial cross talk involved in regulation of cell death pathways.

  15. The complete mitochondrial genome sequence of Neovison vison (Carnivora: Mustelidae).

    PubMed

    Sun, Wei-Li; Wang, Shao-Jing; Wang, Zhuo; Liu, Han-Lu; Zhong, Wei; Yang, Ya-Han; Li, Guang-Yu

    2016-05-01

    The phylogenetic and taxonomic position of the American mink Neovison vison have long been unclear. In this paper, the complete mitogenome of N. vison was sequenced and characterized. The total length was 16,594 bp and typically consists of 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNA, a large control region (CR) and a light-strand replication origin (OL). Gene contents, locations, and arrangements were identical to those of typical vertebrate. The overall base composition is 33.6%, 25.4%, 27.8% and 13.3% for A, C, T and G, respectively, with a moderate bias on AT content (61.4%). This result is expected to provide useful molecular data and contribute to further taxonomic and phylogenetic studies of Mustelidae and Carnivora. PMID:25319300

  16. The complete mitochondrial genome sequence of Aesopia cornuta (Pleuronectiformes: Soleidae).

    PubMed

    Wang, Shu-Ying; Shi, Wei; Wang, Zhong-Ming; Gong, Li; Kong, Xiao-Yu

    2015-02-01

    Aesopia cornuta belongs to the family Soleidae of Pleuronectiformes, and the morphological characters are much similar to those of Zebrias. In this article, we sequenced, characterized, and compared the complete mitogenome of A. cornuta for the first time. The genome is 16,737 base pairs in length, and is typically consist of 37 genes, including 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA, as well as a putative L-strand replication origin and a putative control region. The gene organization is identical to that of typical bony fishes. The overall base composition is 29.1, 28.3, 26.8 and 15.8% for C, A, T and G, respectively, with a slight AT bias of 55.1%. This result is expected to contribute to understanding the systematic evolution of the genus Aesopia and further taxonomic and phylogenetic studies of Soleidae and Pleuronectiformes. PMID:23789774

  17. The complete mitochondrial genome sequence of Eudocimus ruber (Pelecaniformes:Threskiornithidae).

    PubMed

    Chang, Liao; He, Shiyang; Zhang, Jianbo; Zhang, Qian; Li, Shengbin

    2016-07-01

    The Eudocimus ruber (Scarlet ibis) belongs to the bird order Pelecaniformes. Here, we sequenced the mitochondrial genome of E. ruber. The complete mitochondrial genome of E. ruber is 16 697 bp in length and contains 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and a non-coding control region. Consistent with other sequenced birds, most genes are encoded on the heavy strand, except for ND6 and 8 tRNA genes. The overall base composition of the E. ruber is 30.8% A, 30.8% C, 13.8%G and 24.6% T. The molecular-based phylogenetic tree suggested that E. ruber has close affinities with birds from family Threskiornithidae as expected. PMID:26099973

  18. Sequencing and analysis of the complete mitochondrial genome of Aedes albopictus (Diptera: Culicidae) in China.

    PubMed

    Zhang, Hengduan; Xing, Dan; Wang, Gang; Li, Chunxiao; Zhao, Tongyan

    2016-07-01

    The complete sequence of the mitochondrial genome of the Aedes albopictus (Diptera: Culicidae) is presented using traditional Sanger sequencing. Its mitogenome are 16,660 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding A + T rich region. As in other insects, most mitochondrial genes are encoded on the heavy strand, except for ND5, ND4, ND4L, ND1, two rRNA and eight tRNA genes, which are encoded on the light strand. The overall base composition on heavy strand was as follows - A: 40.1%, G: 8.2%, C: 11.9%, T: 39.8% and the A + T content 79.9%. The results of phylogenetic analyzes showed that the Ae. albopictus has closed relationship with the family Culicidae and order Diptera. PMID:26114325

  19. The complete mitochondrial genome sequence of Erpobdella octoculata (Hirudinea: Arhynchobdellida: Erpobdellidae).

    PubMed

    Xu, Yun-Ling; Nie, Jing

    2016-05-01

    Erpobdella octoculata (Linnaeus, 1758; Hirudinea: Arhynchobdellida: Erpobdellidae) is a very common and morphologically variable macrophagous predators of aquatic invertebrates. Here we determined the complete mitochondrial DNA (mtDNA) sequence of this species, as the first representative of the suborder Erpobdelliformes. This genome is 14,407 bp in length with an A + T content of 71.55%, containing 37 typical animal mitochondrial genes and a non-coding region (NCR). It has high AT content and the same gene arrangement pattern as those of typical annelids. The complete mtDNA sequence of E. octoculata provides useful genetic markers for identification, ecological and evolutionary studies of leeches. PMID:25329287

  20. Complete mitochondrial genome sequence of the hedgehog seahorse Hippocampus spinosissimus Weber, 1933 (Gasterosteiformes:Syngnathidae).

    PubMed

    Liu, Shuaishuai; Zhang, Yanhong; Wang, Changming; Lin, Qiang

    2016-07-01

    The complete mitochondrial genome sequence of the hedgehog seahorse Hippocampus spinosissimus was first determined in this article. The total length of H. spinosissimus mitogenome is 16 527 bp and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The gene order and composition of H. spinosissimus were similar to those of most other vertebrates. The overall base composition of H. spinosissimus is 32.1% A, 30.3% T, 14.9% G and 22.7% C, with a slight A + T-rich feature (62.4%). Phylogenetic analyses based on complete mitochondrial genome sequence showed that H. spinosissimus has a close genetic relationship to H. ingens and H. kuda. PMID:26364951

  1. Mitochondrial genome sequence of Egyptian swift Rock Pigeon (Columba livia breed Egyptian swift).

    PubMed

    Li, Chun-Hong; Shi, Wei; Shi, Wan-Yu

    2015-06-01

    The Egyptian swift Rock Pigeon is a breed of fancy pigeon developed over many years of selective breeding. In this work, we report the complete mitochondrial genome sequence of Egyptian swift Rock Pigeon. The total length of the mitogenome was 17,239 bp and its overall base composition was estimated to be 30.2% for A, 24.0% for T, 31.9% for C and 13.9% for G, indicating an A-T (54.2%)-rich feature in the mitogenome. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region (D-loop region). The complete mitochondrial genome sequence of Egyptian swift Rock Pigeon would serve as an important data set of the germplasm resources for further study. PMID:24438285

  2. The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida.

    PubMed

    Patra, Ajit Kumar; Kwon, Yong Min; Kang, Sung Gyun; Fujiwara, Yoshihiro; Kim, Sang-Jin

    2016-04-01

    The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions. PMID:26776396

  3. The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts.

    PubMed

    Xue, Jia-Yu; Liu, Yang; Li, Libo; Wang, Bin; Qiu, Yin-Long

    2010-02-01

    Plants have large and complex mitochondrial genomes in comparison to other eukaryotes. In bryophytes, the mitochondrial genomes exhibit a mixed mode of conservative and dynamic evolution. Here, we sequenced the complete mitochondrial genome from hornwort Phaeoceros laevis, to investigate the level of conservation in mitochondrial genome evolution within hornworts. The circular molecule consists of 209,482 base pairs and represents the largest known mitochondrial genome of bryophytes. It contains 30 protein genes, 3 rRNA genes, and 21 tRNA genes, with 34 cis-spliced group II introns disrupting 16 protein genes. There are 11 pseudogenes in this genome, and nine of them are shared with the other fully sequenced hornwort chondriome from Megaceros aenigmaticus, a distant relative of P. laevis. These pseudogenes were likely formed during an early stage of hornwort evolution. The two hornwort chondriomes differ by four inversions and translocations, seven genes, and four introns in the genome structure and organization. At the sequence level, they are very similar, with the identity values ranging mostly from 80 to 95% in intergenic spacers, introns, and exons. These data indicate that mitochondrial genome evolution in hornworts is less conservative than in liverworts, but has not reached the dynamic level as seen in seed plants. PMID:19998039

  4. Complete mitochondrial genome sequence of Melipona scutellaris, a Brazilian stingless bee.

    PubMed

    Pereira, Ulisses de Padua; Bonetti, Ana Maria; Goulart, Luiz Ricardo; Santos, Anderson Rodrigues Dos; Oliveira, Guilherme Correa de; Cuadros-Orellana, Sara; Ueira-Vieira, Carlos

    2016-09-01

    Melipona scutellaris is a Brazilian stingless bee species and a highly important native pollinator besides its use in rational rearing for honey production. In this study, we present the whole mitochondrial DNA sequence of M. scutellaris from a haploid male. The mitogenome has a size of 14,862 bp and harbors 13 protein-coding genes (PCGs), 2 rRNA genes and 21 tRNA genes. PMID:25703850

  5. Complete mitochondrial DNA sequence of the Eastern keelback mullet Liza affinis.

    PubMed

    Gong, Xiaoling; Zhu, Wenjia; Bao, Baolong

    2016-05-01

    Eastern keelback mullet (Liza affinis) inhabits inlet waters and estuaries of rivers. In this paper, we initially determined the complete mitochondrial genome of Liza affinis. The entire mtDNA sequence is 16,831 bp in length, including 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and 1 putative control region. Its order and numbers of genes are similar to most bony fishes. PMID:25423506

  6. Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

    PubMed Central

    2011-01-01

    Background The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits. Results The nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively. Conclusions Whereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non

  7. The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences.

    PubMed

    Matsubara, Mioko; Komatsu, Miéko; Araki, Takeyoshi; Asakawa, Shuichi; Yokobori, Shin-ichi; Watanabe, Kimitsuna; Wada, Hiroshi

    2005-09-01

    One of the most important issues in asteroid phylogeny is the phylogenetic status of Paxillosida. This group lacks an anus and suckers on the tube feet in adults and does not develop the brachiolaria stage in early development. Two controversial hypotheses have been proposed for the phylogenetic status of Paxillosida, i.e., Paxillosida is primitive or rather specialized in asteroids. In this study, we determined the complete mitochondrial DNA nucleotide sequences from two paxillosidans (Astropecten polyacanthus and Luidia quinaria) and one forcipulatidan (Asterias amurensis). The mitochondrial genomes of the three asteroids were identical with respect to gene order and transcription direction, and were identical to the previously reported mitochondrial genomes of Asterina pectinifera (Valvatida) and Pisaster ochraceus (Forcipulatida) in this respect. Therefore, the comparison of genome structures was uninformative for the purposes of asteroid phylogeny. However, molecular phylogenetic analyses based on the amino acid sequences and the nucleotide sequences from the five asteroids supported the monophyly of the clade that included the two paxillosidans and Asterina. This suggests that the paxillosidan characters are secondarily derived ones. PMID:15878829

  8. The architecture and complete sequence of mitochondrial genome of an assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae).

    PubMed

    Li, Hu; Gao, Jianyu; Liu, Haiyu; Liu, Hui; Liang, Aiping; Zhou, Xuguo; Cai, Wanzhi

    2011-01-01

    The 16, 470 bp nucleotide sequence of the mitochondrial genome (mitogenome) of an assassin bug from the reduviid subfamily Harpactorinae, Agriosphodrus dohrni, has been revealed. The entire genome encodes for two ribosomal RNA genes (rrnL and rrnS), 22 transfer RNA (tRNA) genes, 13 protein-coding genes, and a control region. The nucleotide composition is biased toward adenine and thymine (A+T = 72.2%). Comparative analysis with two other reduviid species Triatoma dimidiata and Valentia hoffmanni, exhibited highly conserved genome architectures including genome contents, gene order, nucleotide composition, codon usage, amino acid composition, as well as genome asymmetry. All protein-coding genes use standard mitochondrial initiation codons (methionine and isoleucine), except that nad1 starts with GTG. All tRNAs have the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA(Ser(AGN)) forms a simple loop. Secondary structure comparisons of the two mitochondrial ribosomal subunits among sequenced assassin bugs show that the sequence and structure of rrnL is more conservative than that of rrnS. The presence of structural elements in the control region is also discussed, with emphasis on their implications in the regulation of replication and/or transcription of the reduviid mitogenome. The phylogenetic analyses indicated that within Reduviidae, Harpactorinae is a sister group to the Salyavatinae + Triatominae clade. PMID:21750648

  9. Sequencing and analysis of the complete mitochondrial genome of Gloydius saxatilis (Squamata: Viperidae: Crotalinae).

    PubMed

    Xu, Chunzhu; Xie, Fei; Liu, Yichen; Zhao, Shuai; Wang, Yongsheng; Ma, Teng; Zhao, Tianqing

    2016-07-01

    The mitochondrial genome sequence of Gloydius saxatilis is analyzed and presented for the public for the first time. The genome was 17,218 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 control regions. The overall base composition was A (32.3%), C (28.9%), T (25.8%), and G (13.0%). The base compositions presented clearly the A-C skew, which was most obviously in the protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of G. saxatilis. Mitochondrial genomes analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the thirteen Crotalinae species. It appeared that no less than two major phyletic lineages were present in Crotalinae. The main clades within the Crotalinae supported are: A clade including the Protobothrops. A clade (G. brevicaudus, G. ussuriensis, G. intermedius, G. saxatilis) with the Ovophis as the sister taxon to Protobothrops and was supported by bootstrap values of 88%. The four Gloydius species formed a paraphyletic group with the high bootstrap value (100%) in all examinations. PMID:25806581

  10. Phylogenetic study and barcoding of the blood cockle, Tegillarca granosa, found on the west coast of peninsular Malaysia using the COI gene.

    PubMed

    Chee, S Y; Devakie, M N; Siti Azizah, M N

    2011-01-01

    Blood cockles are among the most economically important brackish water invertebrates found in Malaysia. However, our knowledge of blood cockle phylogeny and systematics is rudimentary, especially for the species Tegillarca granosa. It is unclear, for instance, whether the cockles occurring on the west coast of peninsular Malaysia constitute a single species, or multiple, phylogenetically distinct species. We performed the first DNA molecular phylogenetic analysis of T. granosa to distinguish it from other related species found in other parts of the world and to create a DNA database for the species. An approximately 585-nucleotide fragment of the mitochondrial DNA (cytochrome oxidase I, COI) was sequenced for 150 individual cockles, representing 10 populations: three from the north, four from the central part and three from the southern part of peninsular Malaysia. Phylogenetic analyses of the resulting dataset yielded tree topologies that not only showed the relationship between T. granosa and its closest relatives but its position in the evolutionary tree. Three mitochondrial clades were evident, each containing an individual genus. Using the mutation rate of the COI gene, the divergence time between T. granosa and its closest related species was estimated to be 460 thousand years ago. This study provides a phylogenetic framework for this ecologically prominent and commercially important cockle species. PMID:21732288

  11. The complete mitochondrial genome sequence of Hemibagrus nemurus (Siluriformes: Bagridae).

    PubMed

    Wu, Yu-Peng; He, Qiu-Sheng; Xie, Jian-Lin; Guo, Xiao-Fang; Li, Hong-Yan

    2016-05-01

    Hemibagrus nemurus (Valenciennes, 1840) is a kind of tropical freshwater catfish which is native to Asian waters. It is economically valued for its importance in fisheries and aquaculture. At present, there exist some confusion in species identification in Bagridae. In this paper, we sequenced and characterize the complete mitogenome of H. nemurus. The genome was 16,526 bp in length, and typically consists of 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNA, 1 origin of replication on the light-strand (OL) and a single large control region (CR). The gene organization is identical to that of a typical bony fish. The overall base composition was 31.5%, 26.6%, 26.7%, and 15.2% for A, T, C, and G, respectively, with a slight bias on AT content (58.1%). This result is expected to provide useful molecular data and contribute to further taxonomic and phylogenetic studies of Hemibagrus and Bagridae. PMID:25319306

  12. The complete mitochondrial genome sequence of Alopex lagopus (Caniformia: Canidae).

    PubMed

    Sun, Wei-Li; Liu, Han-Lu; Zhong, Wei; Wang, Zhuo; Li, Guang-Yu

    2016-09-01

    The phylogenetic and taxonomic positions of the blue fox (Alopex lagopus) have long been unclear. In this study, we determined and described the complete mitogenome sequence of A. lagopus for the first time, which is 16,629 bp in length and contains 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 origin of replication on the light-strand and a putative control region. The overall base composition is A: 31.3%, T: 27.8%, C: 26.1% and G: 14.8%, with a slight AT bias (59.1%). Most of them have TAA as the stop codon, except ND2 uses TAG, ND4 uses AGG, Cytb uses AGA and COX3 and ND3 use an incomplete stop codon TA. This information could not only contribute to provide useful molecular data for the species identification, but also to further taxonomic and phylogenetic studies of Alopex and Canidae. PMID:25630723

  13. Species boundaries of Gulf of Mexico vestimentiferans (Polychaeta, Siboglinidae) inferred from mitochondrial genes

    NASA Astrophysics Data System (ADS)

    Pia Miglietta, Maria; Hourdez, Stephane; Cowart, Dominique A.; Schaeffer, Stephen W.; Fisher, Charles

    2010-11-01

    At least six morphospecies of vestimentiferan tubeworms are associated with cold seeps in the Gulf of Mexico (GOM). The physiology and ecology of the two best-studied species from depths above 1000 m in the upper Louisiana slope (Lamellibrachia luymesi and Seepiophila jonesi) are relatively well understood. The biology of one rare species from the upper slope (escarpiid sp. nov.) and three morphospecies found at greater depths in the GOM (Lamellibrachia sp. 1, L. sp. 2, and Escarpia laminata) are not as well understood. Here we address species distributions and boundaries of cold-seep tubeworms using phylogenetic hypotheses based on two mitochondrial genes. Fragments of the mitochondrial large ribosomal subunit rDNA (16S) and cytochrome oxidase subunit I (COI) genes were sequenced for 167 vestimentiferans collected from the GOM and analyzed in the context of other seep vestimentiferans for which sequence data were available. The analysis supported five monophyletic clades of vestimentiferans in the GOM. Intra-clade variation in both genes was very low, and there was no apparent correlation between the within-clade diversity and collection depth or location. Two of the morphospecies of Lamellibrachia from different depths in the GOM could not be distinguished by either mitochondrial gene. Similarly, E. laminata could not be distinguished from other described species of Escarpia from either the west coast of Africa or the eastern Pacific using COI. We suggest that the mitochondrial COI and 16S genes have little utility as barcoding markers for seep vestimentiferan tubeworms.

  14. The complete mitochondrial genome sequence of the Gracile shrew mole, Uropsilus gracilis (Soricomorpha: Talpidae).

    PubMed

    Tu, Feiyun; Fan, Zhenxin; Chen, Shunde; Yin, Yonghua; Li, Peng; Zhang, Xiuyue; Liu, Shaoying; Yue, Bisong

    2012-10-01

    The Gracile shrew mole (Uropsilus gracilis) belongs to the family Talpidae, which distributes in southwestern China, extending to northern Myanmar. In this study, the complete mitochondrial genome of U. gracilis was sequenced. It was determined to be of 16,533 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of U. gracilis and other 12 insectivores were used for phylogenetic analysis. Phylogenetic trees were constructed by using Bayesian and maximum likelihood methods, which showed that U. gracilis was clustered together with U. soricipes, and Urotrichus should be prior to Galemys. PMID:22920311

  15. Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences.

    PubMed

    Lanave, C; Liuni, S; Licciulli, F; Attimonelli, M

    2000-01-01

    The AMmtDB database (http://bio-www.ba.cnr.it:8000/srs6/ ) has been updated by collecting the multi-aligned sequences of Chordata mitochondrial genes coding for proteins and tRNAs. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually. PMID:10592208

  16. 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

    2014-01-01

    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. PMID:24782088

  17. Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: an ultra-large metazoan mitochondrial genome.

    PubMed

    Liu, Yun-Guo; Kurokawa, Tadahide; Sekino, Masashi; Tanabe, Toru; Watanabe, Kazuhito

    2013-03-01

    The complete mitochondrial (mt) genome of the ark shell Scapharca broughtonii was determined using long PCR and a genome walking sequencing strategy with genus-specific primers. The S. broughtonii mt genome (GenBank accession number AB729113) contained 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 2 ribosomal RNA genes, and 42 transfer tRNA genes, in a length of 46,985 nucleotides for the size of mtDNA with only one copy of the heteroplasmic tandem repeat (HTR) unit. Moreover the S. broughtonii mt genome shows size variation; these genomes ranged in size from about 47 kb to about 50 kb because of variation in the number of repeat sequences in the non-coding region. The mt-genome of S. broughtonii is, to date, the longest reported metazoan mtDNA sequence. Sequence duplication in non-coding region and the formation of HTR arrays were two of the factors responsible for the ultra-large size of this mt genome. All the tRNA genes were found within the S. broughtonii mt genome, unlike the other bivalves usually lacking one or more tRNA genes. Twelve additional specimens were used to analyze the patterns of tandem repeat arrays by PCR amplification and agarose electrophoresis. Each of the 12 specimens displayed extensive heteroplasmy and had 8-10 length variants. The motifs of the HTR arrays are about 353-362 bp and the number of repeats ranges from 1 to 11. PMID:23291309

  18. When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae)

    PubMed Central

    Haarto, Antti; Ståhls, Gunilla

    2014-01-01

    Abstract The northern European taxa of genus Melanostoma Schiner, 1860 (Syrphidae, Diptera) are revised. A longstanding question concerning the number of Melanostoma taxa occurring in northern Europe prompted us to contrast and compare their morphological and molecular variability. Particular uncertainty concerned the putative existence of a sibling species of Melanostoma mellinum, and the identity of the taxon Melanostoma dubium in northern Europe due to existence of morphologically similar dark forms of M. mellinum in the northern parts of its distributional range. Partial sequences of two DNA markers, the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI-3') and the nuclear second internal transcribed spacer (ITS2) were analysed separately under parsimony. The obtained COI-3'gene fragment showed taxon-specific haplotypes and haplotypes that were shared among the taxa. The ITS2 sequences presented genotypes unique to each species, and congruence with our independently established taxonomic entities. Based on congruent signal of the ITS2 sequences and study of morphological characters we establish the presence of four taxa in northern Europe: Melanostoma mellium (= M. dubium nec auctt., syn. n.), M. certum sp. n. (= M. dubium auctt.), M. mellarium stat. n. (= M. mellinum auctt. partim) and M. scalare. Lectotype designations were made for Musca mellina, Syrphus mellarius and Melanostoma mellinum var. melanatus. The following synonymies were established: Melanostoma mellarium = Melanostoma melanatum syn. n.; Melanostoma mellinum = Scaeva dubia syn. n., Melanostoma tschernovi syn. n., and Melanostoma clausseni syn. n. Morphological circumscriptions of the taxa and an identification key are presented. PMID:25152670

  19. Complete mitochondrial genome sequences of the three pelagic chaetognaths Sagitta nagae, Sagitta decipiens and Sagitta enflata.

    PubMed

    Miyamoto, Hiroomi; Machida, Ryuji J; Nishida, Shuhei

    2010-03-01

    The complete nucleotide sequences of the mitochondrial genomes were determined for the three pelagic chaetognaths, Sagitta nagae, Sagitta decipiens, and Sagitta enflata. The mitochondrial genomes of these species which were 11,459, 11,121, and 12,631bp in length, respectively, contained 14 genes (11 protein-coding genes, one transfer RNA gene, and two ribosomal RNA genes), and were found to have lost 23 genes that are present in the typical metazoan mitochondrial genome. The same mitochondrial genome contents have been reported from the benthic chaetognaths belonging to the family Spadellidae, Paraspadella gotoi and Spadella cephaloptera. Within the phylum Chaetognatha, Sagitta and Spadellidae are distantly related, suggesting that the gene loss occurred in the ancestral species of the phylum. The gene orders of the three Sagitta species are markedly different from those of the other non-Chaetognatha metazoans. In contrast to the region with frequent gene rearrangements, no gene rearrangements were observed in the gene cluster encoding COII-III, ND1-3, srRNA, and tRNA(met). Within this conserved gene cluster, gene rearrangements were not observed in the three Sagitta species or between the Sagitta and Spadellidae species. The gene order of this cluster was also assumed to be the ancestral state of the phylum. PMID:20374943

  20. The Complete DNA Sequence of the Mitochondrial Genome of a ``living Fossil,'' the Coelacanth (Latimeria Chalumnae)

    PubMed Central

    Zardoya, R.; Meyer, A.

    1997-01-01

    The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3' end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNAs, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship. PMID:9215903

  1. Optimization of primer specific filter metrics for the assessment of mitochondrial DNA sequence data

    PubMed Central

    CURTIS, PAMELA C.; THOMAS, JENNIFER L.; PHILLIPS, NICOLE R.; ROBY, RHONDA K.

    2011-01-01

    Filter metrics are used as a quick assessment of sequence trace files in order to sort data into different categories, i.e. High Quality, Review, and Low Quality, without human intervention. The filter metrics consist of two numerical parameters for sequence quality assessment: trace score (TS) and contiguous read length (CRL). Primer specific settings for the TS and CRL were established using a calibration dataset of 2817 traces and validated using a concordance dataset of 5617 traces. Prior to optimization, 57% of the traces required manual review before import into a sequence analysis program, whereas after optimization only 28% of the traces required manual review. After optimization of primer specific filter metrics for mitochondrial DNA sequence data, an overall reduction of review of trace files translates into increased throughput of data analysis and decreased time required for manual review. PMID:21171863

  2. Sequencing strategy of mitochondrial HV1 and HV2 DNA with length heteroplasmy.

    PubMed

    Rasmussen, E M; Sørensen, E; Eriksen, B; Larsen, H J; Morling, N

    2002-10-01

    We describe a method to obtain reliable mitochondrial DNA (mtDNA) sequences downstream of the homopolymeric stretches with length heteroplasmy in the sequencing direction. The method is based on the use of junction primers that bind to a part of the homopolymeric stretch and the first 2-4 bases downstream of the homopolymeric region. This junction primer method gave clear and unambiguous results using samples from 21 individuals with length heteroplasmy in the hypervariable regions HV1, HV2 or both. The method is of special value for forensic casework, because sequencing of both strands of an mtDNA region is preferable in order to reduce ambiguities in sequence determination. PMID:12372693

  3. Mitochondrial DNA control region sequences study in Saraiki population from Pakistan.

    PubMed

    Hayat, Sikandar; Akhtar, Tanveer; Siddiqi, Muhammad Hassan; Rakha, Allah; Haider, Naeem; Tayyab, Muhammad; Abbas, Ghazanfar; Ali, Azam; Bokhari, Syed Yassir Abbas; Tariq, Muhammad Akram; Khan, Fazle Majid

    2015-03-01

    The analysis of mitochondrial DNA (mtDNA) control region was carried in 85 unrelated Sariki individuals living in the different provinces of Pakistan. DNA was extracted from blood preserved in EDTA vacutainers. Hypervariable regions (HV1, HV2 & HV3) were PCR amplified and sequenced. Sequencing results were aligned and compared with revised Cambridge reference sequence (rCRS). The sequencing results showed presence of total 63 different haplotypes, 58 of them are unique and 05 are common haplotypes shared by more than one individual. The most common haplotype observed was (W6) with a frequency 12.9% of population sample. The Saraiki population was detected with genetic diversity (0.9570) and power of discrimination (0.9458). This study will be beneficial for forensic casework. PMID:25465675

  4. Statistical validation of the identification of tuna species: bootstrap analysis of mitochondrial DNA sequences.

    PubMed

    Terol, Javier; Mascarell, Rosario; Fernandez-Pedrosa, Victoria; Pérez-Alonso, Manuel

    2002-02-27

    Sequencing of the mitochondrial cytochrome b gene has been used to differentiate three tuna species: Thunnus albacares (yellowfin tuna), Thunnus obesus (bigeye tuna), and Katsuwonus pelamis (skipjack). A PCR amplified 528 bp fragment from 30 frozen samples and a 171 bp fragment from 26 canned samples of the three species were analyzed to determine the intraspecific variation and the positions with diagnostic value. Polymorphic sites between the species that did not present intraspecific variation were given a diagnostic value. The genetic distance between the sequences was calculated, and a phylogenetic tree was constructed, showing that the sequences belonging to the same species clustered together. The bootstrap test of confidence was used to determine the statistical validation of the species assignation, allowing for the first time a quantification of the certainty of the species assignation. The bootstrap values obtained from these results indicate that the sequencing of the cytochrome b fragments allows a correct species assignation with a probability > or =95%. PMID:11853465

  5. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

    PubMed Central

    Hahn, Christoph; Bachmann, Lutz; Chevreux, Bastien

    2013-01-01

    We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim. PMID:23661685

  6. Establishing the pangolin mitochondrial D-loop sequences from the confiscated scales.

    PubMed

    Hsieh, Hsing-Mei; Lee, James Chun-I; Wu, Jane-Hong; Chen, Chao-An; Chen, Yen-Jean; Wang, Guan-Bang; Chin, Shih-Chien; Wang, Lih-Chiann; Linacre, Adrian; Tsai, Li-Chin

    2011-08-01

    Pangolin scales are encountered in traditional East Asian medicines (TEAM) and the ever increasing demand for these scales has escalated the decline in the numbers of these mammals. The identification of protected pangolin species is necessary to enforce international and national legislation as well as assist with conservation measures. There is limited morphological feature on a pangolin scale thus requiring DNA analysis as a means of identification. We report on the isolation of DNA from pangolin scales and a strategy for obtaining the full length of the mitochondrial D-loop, being 1159 bp. Primer sets creating five overlapping amplicons were designed to amplify sections of this mitochondrial DNA locus. DNA from the blood stain of nineteen Formosan pangolins (Manis pentadactyla pentadactyla) along with 145 scale samples that were suspected to have come from pangolins, was amplified and sequenced; leading to a total of 91 D-loop sequences being obtained. The 19 Formosan pangolin sequences produced 5 haplotypes and 72 of the 145 seized scales provided useable sequence classified as a further 38 haplotypes. The D-loop sequences from those scales suspected to be from a pangolin had a higher similarity to any of the 19 samples taken from M. p. pentadactyla compared to a D-loop sequence from Manis tetradactyla (the only pangolin D-loop sequence in GenBank, NC_004027). These 43 haplotypes were used to establish a local database for the D-loop sequence of pangolins and add to the data of Manis sp. held on GenBank. The PCR amplification strategy development in this study could be used in forensic DNA identification of scales suspected to be from protected pangolin species. PMID:20638354

  7. Evidence for frequent and tissue-specific sequence heteroplasmy in human mitochondrial DNA.

    PubMed

    Naue, Jana; Hörer, Steffen; Sänger, Timo; Strobl, Christina; Hatzer-Grubwieser, Petra; Parson, Walther; Lutz-Bonengel, Sabine

    2015-01-01

    Mitochondrial point heteroplasmy is a common event observed not only in patients with mitochondrial diseases but also in healthy individuals. We here report a comprehensive investigation of heteroplasmy occurrence in human including the whole mitochondrial control region from nine different tissue types of 100 individuals. Sanger sequencing was used as a standard method and results were supported by cloning, minisequencing, and massively parallel sequencing. Only 12% of all individuals showed no heteroplasmy, whereas 88% showed at least one heteroplasmic position within the investigated tissues. In 66% of individuals up to 8 positions were affected. The highest relative number of heteroplasmies was detected in muscle and liver (79%, 69%), followed by brain, hair, and heart (36.7%-30.2%). Lower percentages were observed in bone, blood, lung, and buccal cells (19.8%-16.2%). Accumulation of position-specific heteroplasmies was found in muscle (positions 64, 72, 73, 189, and 408), liver (position 72) and brain (partial deletion at position 71). Deeper analysis of these specific positions in muscle revealed a non-random appearance and position-specific dependency on age. MtDNA heteroplasmy frequency and its potential functional importance have been underestimated in the past and its occurrence is ubiquitous and dependent at least on age, tissue, and position-specific mutation rates. PMID:25526677

  8. Complete mitochondrial genome sequence and gene organization of Chinese indigenous chickens with phylogenetic considerations.

    PubMed

    Zhao, F P; Fan, H Y; Li, G H; Zhang, B K

    2016-01-01

    In this study, we sequenced the complete mitochondrial DNA of Chinese indigenous Jinhu Black-bone and Rugao chickens. The two chicken mitochondrial genomes were deposited in GenBank under accession Nos. KP742951 and KR347464, respectively. The complete mitochondrial genomes of Jinhu Black-bone and Rugao chickens were sequenced and found to span 16,785 and 16,786 bp, respectively, and consisted of 22 tRNA genes, two rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and one control region (D-loop). The majority of genes were positioned on the H-strand, and the ND6 and eight tRNA genes were found to be encoded on the L-strand. The mitogenomes showed a similar gene order to that of the published Gallus gallus genome, as neither included a control region. The overall base composition of the genome of the two chickens was A = 30.22/30.28%, G = 13.57/13.49%, T = 23.74/23.76%, and C = 32.48/32.48%. Nucleotide skewness of the coding strands of the two chicken genomes (AT-skew = 0.12, GC-skew = -0.41) was biased towards T and G. Phylogenetic analysis revealed 29 subspecies, and the molecular genetic relationship among the 29 subspecies was identical to that of traditional taxonomy. PMID:27421002

  9. The complete mitochondrial genome sequence of Garrulax ocellatus (Aves, Passeriformes, Timaliidae).

    PubMed

    Zhou, Yanyan; Qi, Yu; Xu, Huailiang; Huan, Zongjin; Li, Diyan; Xie, Meng; Ni, Qingyong; Zhang, Mingwang; Yao, Yongfang

    2016-07-01

    Timaliidae, generally known as the babblers, includes about 275 species in 50 genera. We sequenced the complete mitochondrial genome of Garrulax ocellatus, and it was determined to be 17,828 bp in length, containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNAsfer (tRNA) genes, and 2 control regions. The complete mitochondrial genome contained 15.24% G, 23.02% T, 33.13% C, and 28.61% A, which was similar to other Passeriformes mitochondrial genomes. There are eight tRNA genes and one PCG (ND6) encoded on the L-strand, and other PCGs were encoded on the H-strand. All genes were closely assembled and only 17 intergenic spacers were observed. In total, the spacers were 99 bp in length, and there were seven pairs of genes overlapping sequences of 30 bp in length. Phylogenetic relationship could provide useful information for the further study on the species taxonomic. PMID:26152349

  10. [Sequencing and analysis of the complete mitochondrial genome of the King Cobra, Ophiophagus hannah (Serpents: Elapidae)].

    PubMed

    Chen, Nian; Lai, Xiao-Ping

    2010-07-01

    We obtained the complete mitochondrial genome of King Cobra(GenBank accession number: EU_921899) by Ex Taq-PCR, TA-cloning and primer-walking methods. This genome is very similar to other vertebrate, which is 17 267 bp in length and encodes 38 genes (including 13 protein-coding, 2 ribosomal RNA and 23 transfer RNA genes) and two long non-coding regions. The duplication of tRNA-Ile gene forms a new mitochondrial gene rearrangement model. Eight tRNA genes and one protein genes were transcribed from L strand, and the other genes were transcribed genes from H strand. Genes on the H strand show a fairly similar content of Adenosine and Thymine respectively, whereas those on the L strand have higher proportion of A than T. Combined rDNA sequence data (12S+16S rRNA) were used to reconstruct the phylogeny of 21 snake species for which complete mitochondrial genome sequences were available in the public databases. This large data set and an appropriate range of outgroup taxa demonstrated that Elapidae is more closely related to colubridae than viperidae, which supports the traditional viewpoints. PMID:20650853

  11. Phylogenetic relationships of bears (the Ursidae) inferred from mitochondrial DNA sequences.

    PubMed

    Zhang, Y P; Ryder, O A

    1994-12-01

    The phylogenetic relationships among some bear species are still open questions. We present here mitochondrial DNA sequences of D-loop region, cytochrome b, 12S rRNA, tRNA(Pro), and tRNA(Thr) genes from all bear species and the giant panda. A series of evolutionary trees with concordant topology has been derived based on the combined data set of all of the mitochondrial DNA sequences, which may have resolved the evolutionary relationships of all bear species: the ancestor of the spectacled bear diverged first, followed by the sloth bear; the brown bear and polar bear are sister taxa relative to the Asiatic black bear; the closest relative of the American black bear is the sun bear. Primers for forensic identification of the giant panda and bears are proposed. Analysis of these data, in combination with data from primates and antelopes, suggests that relative substitutional rates between different mitochondrial DNA regions may vary greatly among different taxa of the vertebrates. PMID:7697192

  12. Recombination by sequence repeats with formation of suppressive or residual mitochondrial DNA in Neurospora

    SciTech Connect

    Almasan, A.; Mishra, N.C. )

    1991-09-01

    Recombination junctions of several Neurospora mitochondrial DNA (mtDNA) mutants and their revertants were identified. Their nucleotide sequences and putative secondary structures were determined in order to understand the nature of the elements involved in intramolecular recombination. Multiple deletions, involving the same portion of Neurospora mtDNA, were identified in six independently isolated mutants. A 9-nucleotide repeat element, CCCCNCCCC, was found to be involved in these and other Neurospora mitochondrial recombination events. The repeat elements were clustered as hot spots on the Neurospora mtDNA and were associated with palindromic DNA sequences. The palindromes have a potential to generate hairpin structures. A much lower free energy of the putative hairpins at the 5{prime} end of the recombination site, and the possible formation of non-B-DNA structure by polypyrimidine tracks, may be important in the initiation of recombination. Using PCR, the authors found low levels of a specific mitochondrial deletion in certain Neurospora mutants. Their presence in low amounts in a population with a much larger number of normal mtDNA is unexpected. Contrary to earlier belief, this finding supports the view that deleted, smaller DNA molecules are not always suppressive relative to normal mtDNAs.

  13. [Sequence variation of mitochondrial cytochrome b gene and phylogenetic relationships among twelve species of Charadriiformes].

    PubMed

    Chen, Xiao-Fang; Wang, Xiang; Yuan, Xiao-Dong; Tang, Min-Qian; Li, Yu-Xiang; Guo, Yu-Mei; Li, Qing-Wei

    2003-05-01

    Studies of the phylogenetic relationships of the Charadriiformes have been largely based on conservative morphological characters. During the past 10 years, many studies on the evolutionary biology of birds adopted phylogenetic information obtained from mitochondrial DNA, but few work on the Charadriiformes has been reported to date. Therefore, phylogenetic relationships and classification of the Charadriiformes remains controversial. In this study, we try to shed light on these relationships via DNA sequence analysis of the mitochondrial Cyt b gene in 12 species of Charadriiformes. It was a preliminary study of the origin and evolution of the species by using nucleotide sequence data. Using the well-known PCR techniques, the complete mitochondrial Cyt b gene sequences were amplified and sequenced respectively from Charadrius mongolus, Charadrius alexandrinus, Numenius madagascariensis, Numenius arquat, Numenius phaeopus, Tringa totanus, Tringa glareola, Xenus cineres, Arenaria interpres, Calidris tenuirostris, Recurvirostra avosetts and Haematopus ostralensis. The 1143 bp long DNA sequences of the gene from these species were obtained, in which 381 variable sites were identified without insertions or deletions. The nucleic acid sequence variation of the mitochondrial Cyt b gene was 5.16%-16.01% among these species. Phylogenetic trees constructed using the NJ method, MP method and ML method with Ciconia ciconia as the outgroup indicate that the 12 species of Charadriiformes examined in this study are clustered in two major clades. The first clade includes T. totanus, T. glareola, A. interpres, C. tenuirostris, X. cineres, N. madagascariensis, N. arquata and N. phaeopus. The second one includes C. mongolus, C. alexandrinus, R. avosetts and H. ostralensis. Our molecular data show that the phylogenetic relationships among species of Scolopacidae are consistent with the classification based on morphological studies; R. avosetts and H. ostralensis are relatively closer

  14. Mitochondrial intronic open reading frames in Podospora: Mobility and consecutive exonic sequence variations

    SciTech Connect

    Sellem, C.H.; Rossignol, M.; Belcour, L.

    1996-06-01

    The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optical sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes. 46 refs., 5 figs., 2 tabs.

  15. 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

  16. Complete mitochondrial genome DNA sequence for two ophiuroids and a holothuroid: the utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny.

    PubMed

    Scouras, Andrea; Beckenbach, Karen; Arndt, Allan; Smith, Michael J

    2004-04-01

    The complete mitochondrial genome sequences have been determined for the holothuroid Cucumaria miniata and two ophiuroid species Ophiopholis aculeata and Ophiura lütkeni. In addition, the nucleotide sequence of the mitochondrial protein-coding genes for the asteroid Pisaster ochraceus has been completed. Maximum-likelihood and LogDet distance analyses of concatenated protein-coding sequences produced a series of trees that did not conclusively support generally accepted models of echinoderm phylogeny. The ophiuroid data consistently demonstrated accelerated nucleotide divergence rates and lack of stationarity. This confounds the phylogenetic analyses. Molecular investigations using individual protein-coding gene alignments demonstrated that the cytochrome b gene exhibits the least deviation in rate and stationarity and generated some trees consistent with proposed echinoderm phylogenies. Phylogenies based on echinoderm mitochondrial gene rearrangements also proved problematic because of extensive variation in gene order between and within classes. A comparison of the two distinctive ophiuroid mitochondrial gene orders supports the hypothesis that O. lütkeni has a more derived mitochondrial gene order versus O. aculeata. The variation in the echinoderm mitochondrial gene maps reinforces the limitations of the application of mitochondrial gene rearrangements as a global phylogenetic tool. PMID:15019608

  17. Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements.

    PubMed

    Kumazawa, Yoshinori; Endo, Hideki

    2004-04-30

    The mitochondrial genome of the Komodo dragon (Varanus komodoensis) was nearly completely sequenced, except for two highly repetitive noncoding regions. An efficient sequencing method for squamate mitochondrial genomes was established by combining the long polymerase chain reaction (PCR) technology and a set of reptile-oriented primers designed for nested PCR amplifications. It was found that the mitochondrial genome had novel gene arrangements in which genes from NADH dehydrogenase subunit 6 to proline tRNA were extensively shuffled with duplicate control regions. These control regions had 99% sequence similarity over 700 bp. Although snake mitochondrial genomes are also known to possess duplicate control regions with nearly identical sequences, the location of the second control region suggested independent occurrence of the duplication on lineages leading to snakes and the Komodo dragon. Another feature of the mitochondrial genome of the Komodo dragon was the considerable number of tandem repeats, including sequences with a strong secondary structure, as a possible site for the slipped-strand mispairing in replication. These observations are consistent with hypotheses that tandem duplications via the slipped-strand mispairing may induce mitochondrial gene rearrangements and may serve to maintain similar copies of the control region. PMID:15449544

  18. MITOCHONDRIAL GENE SEQUENCES AMONG DIFFERENT GEOGRAPHICAL ISOLATES OF SCHISTOSOMA JAPONICUM IN YUNNAN PROVINCE, CHINA.

    PubMed

    Jia, Xue-Mei; Li, Cui-Ying; Li, Mei; Zeng, Jin; Zheng, Su-Yue; Li, Fei

    2016-05-01

    In order to evaluate differentiate genetic differences among Schistosoma japonicum isolates from Dali Ancient City, Xizhou and Yongsheng County, Yunnan Province, China, mitochondrial col, cytb, nd1, nd6, and nd4l were PCR amplified and sequenced, revealing nucleotide difference(s) among these strains of 8, 1, 5, 4, and 0, respectively. Phylogenetic analysis showed that S. japonicum from the three different geographical locations of Yunnan Province were clustered genetically together and were more similar to S. malayensis and S. mekongi than S. haematobium or S. mansoni. For intra-species differentiation purposes, Schistosoma mitochondrial col, nd1, and nd6 are better genetic markers than cytb and nd41. PMID:27405120

  19. The complete mitochondrial genome sequence of Eimeria innocua (Eimeriidae, Coccidia, Apicomplexa).

    PubMed

    Hafeez, Mian Abdul; Vrba, Vladimir; Barta, John Robert

    2016-07-01

    The complete mitochondrial genome of Eimeria innocua KR strain (Eimeriidae, Coccidia, Apicomplexa) was sequenced. This coccidium infects turkeys (Meleagris gallopavo), Bobwhite quails (Colinus virginianus), and Grey partridges (Perdix perdix). Genome organization and gene contents were comparable with other Eimeria spp. infecting galliform birds. The circular-mapping mt genome of E. innocua is 6247 bp in length with three protein-coding genes (cox1, cox3, and cytb), 19 gene fragments encoding large subunit (LSU) rRNA and 14 gene fragments encoding small subunit (SSU) rRNA. Like other Apicomplexa, no tRNA was encoded. The mitochondrial genome of E. innocua confirms its close phylogenetic affinities to Eimeria dispersa. PMID:26099978

  20. [Complete sequence and gene organization of the Tibetan chicken mitochondrial genome].

    PubMed

    Tong, Xiao-Mei; Liang, Yu; Wang, Wei; Xu, Shu-Qing; Zheng, Xiao-Guang; Wang, Jian; Yu, Jun

    2006-07-01

    Using PCR amplification, sequencing and assembling, we obtained the complete mitochondrial genome of Tibetan chicken. The complete mitochondrial genome was 16 783 bp in length. It contained 37 genes (13 protein coding genes, 2 rRNA, 22 tRNA) and a control region. The deduced restriction map revealed a unique pattern of Dra I restriction in Tibetan chicken. Phylogenetic trees based on the D-loop locus and the 13 protein coding genes by Neighbor-joining and Maximum Parsimony analysis indicated that the red junglefowl was the direct ancestor of Tibetan chicken and Tibetan chicken was closest to white leghorn and white plymouth rock, although the evolution of Tibetan chicken appeared to be relatively independent from them. A possible explanation is that the ancestor of Tibetan chicken lived in a relatively isolated environment after entering into the high altitude area and developed unique genetic characters. PMID:16825161

  1. A mitochondrial genome sequence of a hominin from Sima de los Huesos.

    PubMed

    Meyer, Matthias; Fu, Qiaomei; Aximu-Petri, Ayinuer; Glocke, Isabelle; Nickel, Birgit; Arsuaga, Juan-Luis; Martínez, Ignacio; Gracia, Ana; de Castro, José María Bermúdez; Carbonell, Eudald; Pääbo, Svante

    2014-01-16

    Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene. One of these sites, the 'Sima de los Huesos' ('pit of bones'), has yielded the world's largest assemblage of Middle Pleistocene hominin fossils, consisting of at least 28 individuals dated to over 300,000 years ago. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene. PMID:24305051

  2. Molecular systematics of the genus Sigmodon: results from mitochondrial and nuclear gene sequences

    PubMed Central

    Henson, Dallas D.; Bradley, Robert D.

    2010-01-01

    Phylogenetic relationships within the genus Sigmodon Say and Ord, 1825 were examined using sequence data from multiple gene regions, including exon 1 of the nuclear-encoded interphotoreceptor retinoid binding protein, intron 7 of the nuclear beta-fibrinogen gene, and the mitochondrial cytochrome b gene from 27 individuals representing 11 species of Sigmodon. Nuclear genes were analyzed independently, combined with each other, and combined with the mitochondrial data. Topologies were constructed using parsimony and Bayesian methods, with nodal support provided by bootstrap and posterior probability values. All analyses recovered four independent clades (I–IV), each representing unique species groups: hispidus, fulviventer, peruanus, and alstoni. The analyses from the combined data also provided support for relationships previously proposed within those species groups. PMID:20407590

  3. Characterization of the complete mitochondrial genomes from Polycladida (Platyhelminthes) using next-generation sequencing.

    PubMed

    Aguado, M Teresa; Grande, Cristina; Gerth, Michael; Bleidorn, Christoph; Noreña, Carolina

    2016-01-10

    The complete mitochondrial genomes of three polycladids, the acotylean Hoploplana elisabelloi and the cotyleans Enchiridium sp. and Prosthiostomum siphunculus have been assembled with high coverage from Illumina sequencing data. The mt genomes contain 36 genes including 12 of the 13 protein-coding genes characteristic for metazoan mitochondrial genomes, two ribosomal RNA genes, and 22 transfer RNA genes. Gene annotation, gene order, genetic code, start and stop codons and codon bias have been identified. In comparison with the well investigated parasitic Neodermata, our analysis reveals a great diversity of gene orders within Polycladida and Platyhelminthes in general. By analyzing representative genomes of the main groups of Platyhelminthes we explored the phylogenetic relationships of this group. The phylogenetic analyses strongly supported the monophyly of Polycladida, and based on a small taxon sampling suggest the monophyly of Acotylea and Cotylea. PMID:26325071

  4. Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences.

    PubMed

    Meyer, A; Kocher, T D; Basasibwaki, P; Wilson, A C

    1990-10-11

    Lake Victoria, together with its satellite lakes, harbours roughly 200 endemic forms of cichlid fishes that are classified as 'haplochromines' and yet the lake system is less than a million years old. This 'flock' has attracted attention because of the possibility that it evolved within the lake from one ancestral species and that biologists are thus presented with a case of explosive evolution. Within the past decade, however, morphology has increasingly emphasized the view that the flock may be polyphyletic. We sequenced up to 803 base pairs of mitochondrial DNA from 14 representative Victorian species and 23 additional African species. The flock seems to be monophyletic, and is more akin to that from Lake Malawi than to species from Lake Tanganyika; in addition, it contains less genetic variation than does the human species, and there is virtually no sharing of mitochondrial DNA types among species. These results confirm that the founding event was recent. PMID:2215680

  5. Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: further evidence of rodent paraphyly.

    PubMed

    Reyes, A; Pesole, G; Saccone, C

    1998-05-01

    The complete mitochondrial genome of the fat dormouse, Glis glis, has been sequenced (16,602 bp). A total of 23 complete mitochondrial mammalian genomes have been taken into account for phylogenetic reconstruction. Phylogenetic analyses were performed with parsimony, distance (stationary Markov model), and maximum-likelihood methods. In all cases, data strongly support the paraphyly of rodents, with dormouse and guinea pig in a different clade from rat and mouse, reaching bootstrap values of 95%. Rodent monophyly and the existence of Glires (Rodentia and Lagomorpha) are weakly supported, with maximum bootstrap values of 11% and 8.6%, respectively. This result agrees with the analyses of isochore patterns in the nuclear genome and the B2 and B2-like retroposons, which show a close relationship between dormice and guinea pigs rather than between dormice and rats and mice. PMID:9580978

  6. Complete sequence and gene organization of the mitochondrial genome of Asio flammeus (Strigiformes, strigidae).

    PubMed

    Zhang, Yanan; Song, Tao; Pan, Tao; Sun, Xiaonan; Sun, Zhonglou; Qian, Lifu; Zhang, Baowei

    2016-07-01

    The complete sequence of the mitochondrial genome was determined for Asio flammeus, which is distributed widely in geography. The length of the complete mitochondrial genome was 18,966 bp, containing 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes (PCGs), and 1 non-coding region (D-loop). All the genes were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The D-loop of A. flammeus contained many tandem repeats of varying lengths and repeat numbers. The molecular-based phylogeny showed that our species acted as the sister group to A. capensis and the supported Asio was the monophyletic group. PMID:25980662

  7. The complete mitochondrial genome sequence and gene organization of Tridentiger trigonocephalus (Gobiidae: Gobionellinae) with phylogenetic consideration.

    PubMed

    Wei, Hongqing; Ma, Hongyu; Ma, Chunyan; Zhang, Fengying; Wang, Wei; Chen, Wei; Ma, Lingbo

    2016-09-01

    The complete mitochondrial genome plays an important role in studies of genome-level characteristics and phylogenetic relationships. Here we determined the complete mitogenome sequence of Tridentiger trigonocephalus (Perciformes, Gobiidae), and discovered its phylogenetic relationship. This circular genome was 16 662 bp in length, and consisted of 37 typical genes, including 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The gene order of T. trigonocephalus mitochondrial genome was identical to those observed in most other vertebrates. Of 37 genes, 28 were encoded by heavy strand, while the others were encoded by light strand. The phylogenetic tree constructed by 13 concatenated protein-coding genes showed that T. trigonocephalus was closest to T. bifasciatus, and then to T. barbatus among the 20 species within suborder Gobioidei. This work should facilitate the studies on population genetic diversity, and molecular evolution in Gobioidei fishes. PMID:26370266

  8. Heteroplasmic substitutions in the entire mitochondrial genomes of human colon cells detected by ultra-deep 454 sequencing.

    PubMed

    Skonieczna, Katarzyna; Malyarchuk, Boris; Jawień, Arkadiusz; Marszałek, Andrzej; Banaszkiewicz, Zbigniew; Jarmocik, Paweł; Borcz, Marcelina; Bała, Piotr; Grzybowski, Tomasz

    2015-03-01

    Mitochondrial DNA (mtDNA) heteroplasmy has been widely described from clinical, evolutionary and analytical points of view. Historically, the majority of studies have been based on Sanger sequencing. However, next-generation sequencing technologies are now being used for heteroplasmy analysis. Ultra-deep sequencing approaches provide increased sensitivity for detecting minority variants. However, a phylogenetic a posteriori analysis revealed that most of the next-generation sequencing data published to date suffers from shortcomings. Because implementation of new technologies in clinical, population, or forensic studies requires proper verification, in this paper we present a direct comparison of ultra-deep 454 and Sanger sequencing for the detection of heteroplasmy in complete mitochondrial genomes of normal colon cells. The spectrum of heteroplasmic mutations is discussed against the background of mitochondrial DNA variability in human populations. PMID:25465762

  9. The Mitochondrial Genomes of Aquila fasciata and Buteo lagopus (Aves, Accipitriformes): Sequence, Structure and Phylogenetic Analyses

    PubMed Central

    Jiang, Lan; Chen, Juan; Wang, Ping; Ren, Qiongqiong; Yuan, Jian; Qian, Chaoju; Hua, Xinghong; Guo, Zhichun; Zhang, Lei; Yang, Jianke; Wang, Ying; Zhang, Qin; Ding, Hengwu; Bi, De; Zhang, Zongmeng; Wang, Qingqing; Chen, Dongsheng; Kan, Xianzhao

    2015-01-01

    The family Accipitridae is one of the largest groups of non-passerine birds, including 68 genera and 243 species globally distributed. In the present study, we determined the complete mitochondrial sequences of two species of accipitrid, namely Aquila fasciata and Buteo lagopus, and conducted a comparative mitogenome analysis across the family. The mitogenome length of A. fasciata and B. lagopus are 18,513 and 18,559 bp with an A + T content of 54.2% and 55.0%, respectively. For both the two accipitrid birds mtDNAs, obvious positive AT-skew and negative GC-skew biases were detected for all 12 PCGs encoded by the H strand, whereas the reverse was found in MT-ND6 encoded by the L strand. One extra nucleotide‘C’is present at the position 174 of MT-ND3 gene of A. fasciata, which is not observed at that of B. lagopus. Six conserved sequence boxes in the Domain II, named boxes F, E, D, C, CSBa, and CSBb, respectively, were recognized in the CRs of A. fasciata and B. lagopus. Rates and patterns of mitochondrial gene evolution within Accipitridae were also estimated. The highest dN/dS was detected for the MT-ATP8 gene (0.32493) among Accipitridae, while the lowest for the MT-CO1 gene (0.01415). Mitophylogenetic analysis supported the robust monophyly of Accipitriformes, and Cathartidae was basal to the balance of the order. Moreover, we performed phylogenetic analyses using two other data sets (two mitochondrial loci, and combined nuclear and mitochondrial loci). Our results indicate that the subfamily Aquilinae and all currently polytypic genera of this subfamily are monophyletic. These two novel mtDNA data will be useful in refining the phylogenetic relationships and evolutionary processes of Accipitriformes. PMID:26295156

  10. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication

    PubMed Central

    2011-01-01

    Background DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets. Results In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (Equus przewalski) using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago. Conclusions Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the time depth of the

  11. Cytogenetic and Sequence Analyses of Mitochondrial DNA Insertions in Nuclear Chromosomes of Maize

    PubMed Central

    Lough, Ashley N.; Faries, Kaitlyn M.; Koo, Dal-Hoe; Hussain, Abid; Roark, Leah M.; Langewisch, Tiffany L.; Backes, Teresa; Kremling, Karl A. G.; Jiang, Jiming; Birchler, James A.; Newton, Kathleen J.

    2015-01-01

    The transfer of mitochondrial DNA (mtDNA) into nuclear genomes is a regularly occurring process that has been observed in many species. Few studies, however, have focused on the variation of nuclear-mtDNA sequences (NUMTs) within a species. This study examined mtDNA insertions within chromosomes of a diverse set of Zea mays ssp. mays (maize) inbred lines by the use of fluorescence in situ hybridization. A relatively large NUMT on the long arm of chromosome 9 (9L) was identified at approximately the same position in four inbred lines (B73, M825, HP301, and Oh7B). Further examination of the similarly positioned 9L NUMT in two lines, B73 and M825, indicated that the large size of these sites is due to the presence of a majority of the mitochondrial genome; however, only portions of this NUMT (∼252 kb total) were found in the publically available B73 nuclear sequence for chromosome 9. Fiber-fluorescence in situ hybridization analysis estimated the size of the B73 9L NUMT to be ∼1.8 Mb and revealed that the NUMT is methylated. Two regions of mtDNA (2.4 kb and 3.3 kb) within the 9L NUMT are not present in the B73 mitochondrial NB genome; however, these 2.4-kb and 3.3-kb segments are present in other Zea mitochondrial genomes, including that of Zea mays ssp. parviglumis, a progenitor of domesticated maize. PMID:26333837

  12. DNA barcoding of Oryx leucoryx using the mitochondrial cytochrome C oxidase gene.

    PubMed

    Elmeer, K; Almalki, A; Mohran, K A; Al-Qahtani, K N; Almarri, M

    2012-01-01

    The massive destruction and deterioration of the habitat of Oryx leucoryx and illegal hunting have decimated Oryx populations significantly, and now these animals are almost extinct in the wild. Molecular analyses can significantly contribute to captive breeding and reintroduction strategies for the conservation of this endangered animal. A representative 32 identical sequences used for species identification through BOLD and GenBank/NCBI showed maximum homology 96.06% with O. dammah, which is a species of Oryx from Northern Africa, the next closest species 94.33% was O. gazella, the African antelope. DNA barcode sequences of the mitochondrial cytochrome C oxidase (COI) gene were determined for O. leucoryx; identification through BOLD could only recognize the genus correctly, whereas the species could not be identified. This was due to a lack of sequence data for O. leucoryx on BOLD. Similarly, BLAST analysis of the NCBI data base also revealed no COI sequence data for the genus Oryx. PMID:22535389

  13. mit-o-matic: a comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets.

    PubMed

    Vellarikkal, Shamsudheen Karuthedath; Dhiman, Heena; Joshi, Kandarp; Hasija, Yasha; Sivasubbu, Sridhar; Scaria, Vinod

    2015-04-01

    The human mitochondrial genome has been reported to have a very high mutation rate as compared with the nuclear genome. A large number of mitochondrial mutations show significant phenotypic association and are involved in a broad spectrum of diseases. In recent years, there has been a remarkable progress in the understanding of mitochondrial genetics. The availability of next-generation sequencing (NGS) technologies have not only reduced sequencing cost by orders of magnitude but has also provided us good quality mitochondrial genome sequences with high coverage, thereby enabling decoding of a number of human mitochondrial diseases. In this study, we report a computational and experimental pipeline to decipher the human mitochondrial DNA variations and examine them for their clinical correlation. As a proof of principle, we also present a clinical study of a patient with Leigh disease and confirmed maternal inheritance of the causative allele. The pipeline is made available as a user-friendly online tool to annotate variants and find haplogroup, disease association, and heteroplasmic sites. The "mit-o-matic" computational pipeline represents a comprehensive cloud-based tool for clinical evaluation of mitochondrial genomic variations from NGS datasets. The tool is freely available at http://genome.igib.res.in/mitomatic/. PMID:25677119

  14. Phylogeny and genetic diversity of Bridgeoporus nobilissimus inferred using mitochondrial and nuclear rDNA sequences

    USGS Publications Warehouse

    Redberg, G.L.; Hibbett, D.S.; Ammirati, J.F., Jr.; Rodriguez, R.J.

    2003-01-01

    The genetic diversity and phylogeny of Bridgeoporus nobilissimus have been analyzed. DNA was extracted from spores collected from individual fruiting bodies representing six geographically distinct populations in Oregon and Washington. Spore samples collected contained low levels of bacteria, yeast and a filamentous fungal species. Using taxon-specific PCR primers, it was possible to discriminate among rDNA from bacteria, yeast, a filamentous associate and B. nobilissimus. Nuclear rDNA internal transcribed spacer (ITS) region sequences of B. nobilissimus were compared among individuals representing six populations and were found to have less than 2% variation. These sequences also were used to design dual and nested PCR primers for B. nobilissimus-specific amplification. Mitochondrial small-subunit rDNA sequences were used in a phylogenetic analysis that placed B. nobilissimus in the hymenochaetoid clade, where it was associated with Oxyporus and Schizopora.

  15. Sequence polymorphism of mitochondrial DNA in Japanese individuals from Gifu Prefecture.

    PubMed

    Nagai, Atsushi; Nakamura, Isao; Shiraki, Futoru; Bunai, Yasuo; Ohya, Isao

    2003-03-01

    Sequence polymorphisms of the hypervariable region HV1 in mitochondrial DNA (mtDNA) were analyzed in a sample of 137 unrelated Japanese individuals living in Gifu Prefecture (central region of Japan) using polymerase chain reaction amplification and direct sequencing. Eighty-two different haplotypes resulting from 81 variable sites were found in the mtDNA HV1 region between positions 16061 and 16450. The most frequent haplotype (16223T, 16362C) was shared by ten individuals. The genetic diversity and the genetic identity were 0.985 and 0.022, respectively. The C-stretch region located around position 16189 was observed in 23.4% of this population sample. Sequence heteroplasmy at the position 16103 (A/G) was found in one individual. PMID:12935592

  16. Sequence polymorphism of the mitochondrial DNA hypervariable regions I and II in 205 Singapore Malays.

    PubMed

    Wong, Hang Yee; Tang, June S W; Budowle, Bruce; Allard, Marc W; Syn, Christopher K C; Tan-Siew, Wai Fun; Chow, Shui Tse

    2007-01-01

    Mitochondrial DNA sequences of the hypervariable regions HV1 and HV2 were analyzed in 205 unrelated ethnic Malays residing in Singapore as an initial effort to generate a database for forensic identification purposes. Sequence polymorphism was detected using PCR and direct sequencing analysis. A total of 152 haplotypes was found containing 152 polymorphisms. Out of the 152 haplotypes, 115 were observed only once and 37 types were seen in multiple individuals. The most common haplotype (16223T, 16295T, 16362C, 73G, 146C, 199C, 263G, and 315.1C) was shared by 7 (3.41%) individuals, two haplotypes were shared by 4 individuals, seven haplotypes were shared by 3 individuals, and 27 haplotypes by 2 individuals. Haplotype diversity and random match probability were estimated to be 0.9961% and 0.87%, respectively. PMID:17150401

  17. The complete mitochondrial genome sequence of Southwellina hispida supports monophyly of Palaeacanthocephala (Acanthocephala: Polymorphida).

    PubMed

    Gazi, Mohiuddin; Kim, Jiyeon; Park, Joong-Ki

    2015-08-01

    Acanthocephala is a relatively small, but distinct obligate parasitic group that includes 4 classes: Archiacanthocephala, Palaeacanthocephala, Polyacanthocephala, and Eoacanthocephala. The phylogenetic relationships of acanthocephalans are mainly based on nuclear ribosomal genes. In this study, we determined the complete mitochondrial genome sequence of Southwellina hispida (Palaeacanthocephala: Polymorphida), and used this genome sequence along with other platyzoan species (including syndermatan groups) to assess its phylogenetic position within Acanthocephala. The S. hispida mtDNA is a 14,742 bp circular molecule that contains 36 genes (lacking atp8) encoded in the same direction. Phylogenetic analyses of amino acid sequences for 12 protein-coding genes suggested palaeacanthocephalan species to be monophyletic, and this group to be sister to Eoacanthocephala. These results confirm other morphological and molecular data supporting palaeacanthocephalan monophyly. PMID:25656507

  18. Sequence and organization of the complete mitochondrial genome of the marsh tit Poecile palustris (Aves: Paridae).

    PubMed

    Day, John C; Broughton, Richard K; Hinsley, Shelley A

    2016-09-01

    The complete mitochondrial genome of the marsh tit Poecile palustris (Linnaeus, 1758) was sequenced using a combined Illumina and Sanger sequencing approach. Using the known sequence of Poecile atricapillus Linnaeus, 1766 (Paridae) homologous NGS reads were identified and assembled. The genome is 16,824 bp in length and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. Gene order resembles that of the standard avian gene order. The base composition of the genome is A (29.15%), T (22.50%), C (33.61%) and G (14.73%). The control region between tRNA(Glu) and tRNA(Phe) is composed of 1240 bp with no obvious repetitive motifs. PMID:25845385

  19. Mitochondrial genome sequences of landsnails Aegista diversifamilia and Dolicheulota formosensis (Gastropoda: Pulmonata: Stylommatophora).

    PubMed

    Huang, Chih-Wei; Lin, Si-Min; Wu, Wen-Lung

    2016-07-01

    The first mitochondrial genome sequences of Aegista and Dolicheulota belonging to Bradybaenidae are described in this report. Mitogenomic sequences were generated from Illumina paired-end sequencing. The complete mitogenome of Aegista diversifamilia was 14,039 bp in length and nearly complete mitogenome of Dolicheulota formosensis was 14,237 bp. Both mitogenomes consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. Most genes were overlapped with neighboring genes that the overlapping regions ranged from 2 to 64 bp in A. diversifamilia and from 1 to 45 bp in D. formosensis. Novel gene arrangement, tRNA-Tyr-ND3-tRNA-Trp, was identified in A. diversifamilia, whereas D. formosensis showed identical gene order to other Bradybaenidae mitogenomes. Maximum likelihood phylogenetic tree suggested Aegista as a sister clade to Euhadra and Dolicheulota. Bradybaenidae is monophyly sister clade to Camaenidae. PMID:26094989

  20. Preliminary study on mitochondrial 16S rRNA gene sequences and phylogeny of flatfishes (Pleuronectiformes)

    NASA Astrophysics Data System (ADS)

    You, Feng; Liu, Jing; Zhang, Peijun; Xiang, Jianhai

    2005-09-01

    A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR and sequenced to show the molecular systematics of Pleuronectiformes for comparison with related gene sequences of other 6 flatfish downloaded from GenBank. Phylogenetic analysis based on genetic distance from related gene sequences of 10 flatfish showed that this method was ideal to explore the relationship between species, genera and families. Phylogenetic trees set-up is based on neighbor-joining, maximum parsimony and maximum likelihood methods that accords to the general rule of Pleuronectiformes evolution. But they also resulted in some confusion. Unlike data from morphological characters, P. olivaceus clustered with K. bicoloratus, but P. cinnamomeus did not cluster with P. olivaceus, which is worth further studying.

  1. Complete sequence and characterization of mitochondrial and chloroplast genome of Chlorella variabilis NC64A.

    PubMed

    Orsini, Massimiliano; Costelli, Cristina; Malavasi, Veronica; Cusano, Roberto; Concas, Alessandro; Angius, Andrea; Cao, Giacomo

    2016-09-01

    The complete nucleotide sequences of the mitochondrial (mtDNA) and chloroplast (cpDNA) genomes of Chlorella variabilis NC64A (Trebouxiophyceae) have been determined in this study (GenBank accession no. KP271968 and KP271969, respectively). The mt genome assembles as a circle of 78,500 bp and contains 62 genes, including 32 protein-coding, 27 tRNA and 3 rRNA genes. The overall GC content is 28.2%, while the coding sequence is 34%. The cp genome forms a circle of 124,793 bp, containing 114 genes, including 79 protein-coding, 32 tRNA and 3 rRNA genes. The overall GC content is 33,9%, while the coding sequence is 50%. PMID:25690053

  2. A high-throughput Sanger strategy for human mitochondrial genome sequencing

    PubMed Central

    2013-01-01

    Background A population reference database of complete human mitochondrial genome (mtGenome) sequences is needed to enable the use of mitochondrial DNA (mtDNA) coding region data in forensic casework applications. However, the development of entire mtGenome haplotypes to forensic data quality standards is difficult and laborious. A Sanger-based amplification and sequencing strategy that is designed for automated processing, yet routinely produces high quality sequences, is needed to facilitate high-volume production of these mtGenome data sets. Results We developed a robust 8-amplicon Sanger sequencing strategy that regularly produces complete, forensic-quality mtGenome haplotypes in the first pass of data generation. The protocol works equally well on samples representing diverse mtDNA haplogroups and DNA input quantities ranging from 50 pg to 1 ng, and can be applied to specimens of varying DNA quality. The complete workflow was specifically designed for implementation on robotic instrumentation, which increases throughput and reduces both the opportunities for error inherent to manual processing and the cost of generating full mtGenome sequences. Conclusions The described strategy will assist efforts to generate complete mtGenome haplotypes which meet the highest data quality expectations for forensic genetic and other applications. Additionally, high-quality data produced using this protocol can be used to assess mtDNA data developed using newer technologies and chemistries. Further, the amplification strategy can be used to enrich for mtDNA as a first step in sample preparation for targeted next-generation sequencing. PMID:24341507

  3. Sequence-specific modification of mitochondrial DNA using a chimeric zinc finger methylase

    PubMed Central

    Minczuk, Michal; Papworth, Monika A.; Kolasinska, Paulina; Murphy, Michael P.; Klug, Aaron

    2006-01-01

    We used engineered zinc finger peptides (ZFPs) to bind selectively to predetermined sequences in human mtDNA. Surprisingly, we found that engineered ZFPs cannot be reliably routed to mitochondria by using only conventional mitochondrial targeting sequences. We here show that addition of a nuclear export signal allows zinc finger chimeric enzymes to be imported into human mitochondria. The selective binding of mitochondria-specific ZFPs to mtDNA was exemplified by targeting the T8993G mutation, which causes two mitochondrial diseases, neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP) and also maternally inherited Leigh's syndrome. To develop a system that allows the monitoring of site-specific alteration of mtDNA we combined a ZFP with the easily assayed DNA-modifying activity of hDNMT3a methylase. Expression of the mutation-specific chimeric methylase resulted in the selective methylation of cytosines adjacent to the mutation site. This is a proof of principle that it is possible to target and alter mtDNA in a sequence-specific manner by using zinc finger technology. PMID:17170133

  4. A functional test of Neandertal and modern human mitochondrial targeting sequences

    SciTech Connect

    Gralle, Matthias; Schaefer, Ingo; Seibel, Peter; Paeaebo, Svante

    2010-11-26

    Research highlights: {yields} Two mutations in mitochondrial targeting peptides occurred during human evolution, possibly after Neandertals split off from modern human lineage. {yields} The ancestral and modern human versions of these two targeting peptides were tested functionally for their effects on localization and cleavage rate. {yields} In spite of recent evolution, and to the contrary of other mutations in targeting peptides, these mutations had no visible effects. -- Abstract: Targeting of nuclear-encoded proteins to different organelles, such as mitochondria, is a process that can result in the redeployment of proteins to new intracellular destinations during evolution. With the sequencing of the Neandertal genome, it has become possible to identify amino acid substitutions that occurred on the modern human lineage since its separation from the Neandertal lineage. Here we analyze the function of two substitutions in mitochondrial targeting sequences that occurred and rose to high frequency recently during recent human evolution. The ancestral and modern versions of the two targeting sequences do not differ in the efficiency with which they direct a protein to the mitochondria, an observation compatible with the neutral theory of molecular evolution.

  5. Sequencing and analysis of the complete mitochondrial genome of Amur minnow from China.

    PubMed

    Zhao, Shuai; Han, Xiaomin; Xu, Chunzhu

    2016-07-01

    The complete mitogenome sequence of Amur minnow (Rhynchocypris lagowskii) was determined using long PCR. The genome was 16,594 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The overall base composition of the heavy strand is A (28.60%), C (26.32%), T (27.40%), and G (17.68%). The control region was 927 bp in length and the A + T content of the region was 63.32%. The extended termination-associated sequence domain, the central conserved domain, and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur minnow. Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 15 Cyprinidae species. It appeared that no less than two major phyletic lineages were present in Leuciscinae. The main clades within the Leuciscinae supported are: A clade is the Tribolodon. A clade (Rhynchocypris) with the Oreoleuciscus as the sister taxon to Tribolodon was supported by bootstrap values of 49%. The five different geographical populations of the R. lagowskii formed a paraphyletic group with the high bootstrap value (45%) in all examinations. PMID:26029880

  6. Mitochondrial genome sequence of Paramisgurnus dabryanus from the Yellow River estuary: implication for Cobitidae phylogeny.

    PubMed

    Zhu, Ming; Liu, Feng

    2016-07-01

    Paramisgurnus dabryanus Sauvage (Cobitidae, Cypriniformes) is a native large-scale loach widely distributed in main inland freshwater systems of China. The complete mitochondrial genome sequence of P. dabryanus from the Yellow River (YR) estuary was characterized in the present study. The circular mitogenome is 16 570 bp in size and contains two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes. The overall A + T content is 56.64% in the range of other Cobitidae studied. The mitogenome of P. dabryanus YR has an overall nucleotide sequence identity of 96.9% with that from Zhejiang, and 89.2% with that from Hubei. All the Misgurnus and Paramisgurnus species were clustered into two Misgurnus/Paramisgurnus complex clades with high bootstrap values based on the whole mitogenome sequences. The mitochondrial phylogenomic analysis indicates that the relationships in Cobitidae are inconsistent with the current classification system and taxonomic revision is required on the basis of molecular phylogeny and morphology. PMID:26162049

  7. Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing

    PubMed Central

    Just, Rebecca S.; Irwin, Jodi A.; Parson, Walther

    2015-01-01

    Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Well vetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10–20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method. PMID:26009256

  8. Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing.

    PubMed

    Just, Rebecca S; Irwin, Jodi A; Parson, Walther

    2015-09-01

    Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Well vetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10-20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method. PMID:26009256

  9. The complete mitochondrial genome sequence of Triplophysa anterodorsalis (Teleostei, Balitoridae, Nemacheilinae).

    PubMed

    Que, Yan-fu; Liao, Xiao-lin; Xu, Dong-mei; Yang, Zhi; Tang, Hui-yuan; Zhu, Bin

    2016-01-01

    Triplophysa anterodorsalis is an endemic fish in the upper stream of the Yangtze River, Jinsha River and its tributaries. However, wild populations of T. anterodorsalis declined sharply due to cascade hydropower stations constructed successively in the Jinsha River during the past decades. In the present study, the complete mitochondrial DNA genome sequence of T. anterodorsalis was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial genome sequence of T. anterodorsalis is a circular molecule of 16,567 bp in size. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of T. anterodorsalis is 27.37% A, 25.68% C, 18.37% G, and 28.57% T, with a relatively a relatively high A + T content (55.94%). The results could provide useful data for studies on genetic structure and diversity and rational resource conservation in T. anterodorsalis. PMID:24919506

  10. Phylogenetic analysis of oryx species using partial sequences of mitochondrial rRNA genes.

    PubMed

    Khan, H A; Arif, I A; Al Farhan, A H; Al Homaidan, A A

    2008-01-01

    We conducted a comparative evaluation of 12S rRNA and 16S rRNA genes of the mitochondrial genome for molecular differentiation among three oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) with respect to two closely related outgroups, addax and roan. Our findings showed the failure of 12S rRNA gene to differentiate between the genus Oryx and addax, whereas a 342-bp partial sequence of 16S rRNA accurately grouped all five taxa studied, suggesting the utility of 16S rRNA segment for molecular phylogeny of oryx at the genus and possibly species levels. PMID:19048493

  11. Molecular dating of the diversification of Phyllostominae bats based on nuclear and mitochondrial DNA sequences.

    PubMed

    Hoffmann, Federico G; Hoofer, Steven R; Baker, Robert J

    2008-11-01

    Times of divergence among the three tribes included within the subfamily Phyllostominae were estimated using a Bayesian approach to infer dates of divergence based on mitochondrial and nuclear sequence data. The subfamily Phyllostominae is particularly attractive for such analysis, as it is one of the few groups of bats to have fossil specimens. Our molecular time analyses suggest that diversification among tribes and genera of phyllostomine bats occurred during the Early to Mid-Miocene, and was coincident with diversification events in two co distributed taxa: Caviomorph rodents and New World monkeys. PMID:18727956

  12. The complete mitochondrial genome sequence of Squalidus japonicus coreanus (Teleostei, Cypriniformes, Cyprinidae).

    PubMed

    Eon Park, Chang; Park, Gun-Seok; Kwak, Yunyoung; Kim, Min-Chul; Kim, Kgu-Hwan; Park, Hee Cheon; Shin, Jae-Ho

    2016-09-01

    The short-barbel gudgeon Squalidus japonicus coreanus (Teleostei, Cypriniformes, Cyprinidae) is a subspecies of S. japonicus, and is endemic to Korea. The complete mitochondrial genome sequence consisted of 16 597 base pairs (bp) encoding 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and two non-coding regions. The overall base composition of S. japonicus coreanus was G + C: 47.4% and A + T: 52.6%, apparently with a slight AT bias. Phylogenetic analysis showed that S. japonicus coreanus was closely related to Pungtungia herzi. PMID:26329666

  13. Complete mitochondrial DNA sequence and phylogenic analysis of Oxyeleotris lineolatus (Perciformes, Eleotridae).

    PubMed

    Zang, Xue; Yin, Danqing; Wang, Ruoran; Yin, Shaowu; Tao, Panfeng; Chen, Jiawei; Zhang, Guosong

    2016-07-01

    In this study, the mitochondrial genome of Oxyeleotris lineolatus was first determined. The length of entire mtDNA sequence was 16,522 bp with (A + T) content of 53.81%, and it contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. The gene order and the orientation are similar to some typical fish species. The data will provide useful molecular information for phylogenetic studies concerning O. lineolatus and its related species. PMID:26016879

  14. Sequence analysis and mapping of a novel human mitochondrial ATP synthase subunit 9 cDNA (ATP5G3)

    SciTech Connect

    Yan, W.L.; Gusella, J.F. |; Haines, J.L. |

    1994-11-15

    The authors describe the cloning, sequence analysis, and chromosomal mapping of a novel mitochondrial ATP synthase subunit 9 cDNA, P3. Subunit 9 transports protons across the inner mitochondrial membrane to the F{sub 1}-ATPase protruding on the matrix side, resulting in the generation of ATP. Sequence analysis of the P3 cDNA reveals only 80% identity with the human subunit 9 genes P1 and P2 in the DNA sequence encoding the mature protein identical to P1 and P2. The predicted sequence of the P3 leader peptide differs from the P1 and P2 leaders, but retains the {open_quotes}RFS{close_quotes} motif critical for mitochondrial import and maturation. The P3 gene (ATP5G3) maps to chromosome 2. 8 refs., 1 fig., 1 tab.

  15. Complete Sequence of the Mitochondrial DNA of the Annelid Worm Lumbricus Terrestris

    PubMed Central

    Boore, J. L.; Brown, W. M.

    1995-01-01

    We have determined the complete nucleotide (nt) sequence of the mitochondrial genome of an oligochaete annelid, the earthworm Lumbricus terrestris. This genome contains the 37 genes typical of metazoan mitochondrial DNA (mtDNA), including ATPase8, which is missing from some invertebrate mtDNAs. ATPase8 is not immediately upstream of ATPase6, a condition found previously only in the mtDNA of snails. All genes are transcribed from the same DNA strand. The largest noncoding region is 384 nt and is characterized by several homopolymer runs, a tract of alternating TA pairs, and potential secondary structures. All protein-encoding genes either overlap the adjacent downstream gene or end at an abbreviated stop codon. In Lumbricus mitochondria, the variation of the genetic code that is typical of most invertebrate mitochondrial genomes is used. Only the codon ATG is used for translation initiation. Lumbricus mtDNA is A + T rich, which appears to affect the codon usage pattern. The DHU arm appears to be unpaired not only in tRNA(ser(AGN)), as is typical for metazoans, but perhaps also in tRNA(ser(UCN)), a condition found previously only in a chiton and among nematodes. Relating the Lumbricus gene organization to those of other major protostome groups requires numerous rearrangements. PMID:8536978

  16. Phylogenetic relationships of three hymenolepidid species inferred from nuclear ribosomal and mitochondrial DNA sequences.

    PubMed

    Okamoto, M; Agatsuma, T; Kurosawa, T; Ito, A

    1997-12-01

    Three hymenolepidid tapeworms, Hymenolepis diminuta, H. nana and H. microstoma, are commonly maintained in laboratory rodents and used in many experimental model systems of tapeworm infections. We examined partial sequences from the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene and nuclear ribosomal internal transcribed spacer 2 (ITS2) sequences to infer phylogenetic relationships of the 3 hymenolepidid species. Parts of the CO1 gene and ITS2 were amplified by PCR and sequenced directly. The CO1 gene sequence obtained was the same in length (391 bp) among all specimens. In the case of ITS2, however, several insertions and deletions were detected (671-741 bp) not only among species but also between an American isolate and a Japanese isolate of H. diminuta. Percentage nucleotide differences between H. diminuta and H. microstoma, or H. diminuta and H. nana were 16.6-18.2% for the CO1 gene and 21.3-22.9% for ITS2. The differences in both sequences between H. microstoma and H. nana were about 14%. Phylogenetic trees inferred from both of the nucleotide sequences showed similar topology, and suggest that H. diminuta may have diverged from the common ancestral line the earliest, and that H. nana is closer to H. microstoma than to H. diminuta. PMID:9488878

  17. Underlying Data for Sequencing the Mitochondrial Genome with the Massively Parallel Sequencing Platform Ion Torrent™ PGM™

    PubMed Central

    2015-01-01

    Background Massively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by sequencing millions of DNA fragments simultaneously. Compared with Sanger sequencing, MPS also can reduce labor and cost on a per nucleotide basis and indeed on a per sample basis. In this study, whole genomes of human mitochondria (mtGenome) were sequenced on the Personal Genome Machine (PGMTM) (Life Technologies, San Francisco, CA), the out data were assessed, and the results were compared with data previously generated on the MiSeqTM (Illumina, San Diego, CA). The objectives of this paper were to determine the feasibility, accuracy, and reliability of sequence data obtained from the PGM. Results 24 samples were multiplexed (in groups of six) and sequenced on the at least 10 megabase throughput 314 chip. The depth of coverage pattern was similar among all 24 samples; however the coverage across the genome varied. For strand bias, the average ratio of coverage between the forward and reverse strands at each nucleotide position indicated that two-thirds of the positions of the genome had ratios that were greater than 0.5. A few sites had more extreme strand bias. Another observation was that 156 positions had a false deletion rate greater than 0.15 in one or more individuals. There were 31-98 (SNP) mtGenome variants observed per sample for the 24 samples analyzed. The total 1237 (SNP) variants were concordant between the results from the PGM and MiSeq. The quality scores for haplogroup assignment for all 24 samples ranged between 88.8%-100%. Conclusions In this study, mtDNA sequence data generated from the PGM were analyzed and the output evaluated. Depth of coverage variation and strand bias were identified but generally were infrequent and did not impact reliability of variant calls. Multiplexing of samples was demonstrated which can improve throughput and reduce cost per sample analyzed

  18. A reexamination of the phylogenetic position of Callimico (primates) incorporating new mitochondrial DNA sequence data.

    PubMed

    Pastorini, J; Forstner, M R; Martin, R D; Melnick, D J

    1998-07-01

    The New World monkeys are divided into two main groups, Callitrichidae and Cebidae. Callimico goeldii shares traits with both the Cebidae and the Callitrichidae. Recent morphological phyletic studies generally place Callimico as the most basal member of the Callitrichidae. In contrast, genetic studies (immunological, restriction fragment, and sequence data) have consistently placed Callimico somewhere within the Callitrichidae, not basal to this clade. A DNA sequence data set from the terminal 236 codons of the mitochondrial ND4 gene and the tRNA(His), tRNA(Ser), and tRNA(Leu) genes was generated to clarify the position of Callimico. The sequences of 887 base pairs were analyzed by maximum-parsimony, neighbor-joining, and maximum-likelihood methods. The results of these various methods are generally congruent and place Callimico within the Callitrichidae between the marmosets (Callithrix and Cebuella) and the tamarins (Saguinus and Leontopithecus). Combined analyses of all suitable nuclear and mitochondrial gene sequences confirm the position of Callimico between the marmosets and the tamarins. As available molecular evidence indicates that Callimico is more closely related to the marmosets than to the tamarins, a reconsideration of the morphological evidence in light of the consensus tree from DNA sequence analyses is warranted. The marmosets and tamarins share four morphological characters (loss of the third molar, loss of the hypocone, reduced body size, reproductive twinning). Dwarfism may have evolved repeatedly among the Callitrichidae. It is well-known that the loss of a character can occur many times independently. The reproduction of marmosets and tamarins is extremely specialized and it is difficult to imagine that this complex and unique twinning system evolved separately in marmosets and tamarins. However, it is possible that a secondary reversal to single offspring took place in Callimico. PMID:9664694

  19. Illumina next-generation sequencing reveals the complete mitochondrial genome of Psenopsis anomala (Perciformes: Centrolophidae) with phylogenetic consideration.

    PubMed

    Chen, Huapu; Che, Zhiwei; Li, Jiantao; Dai, Mingli; Xiang, Ling; Deng, Siping; Zhu, Chunhua; Huang, Hai; Li, Guangli

    2016-09-01

    Using Illumina next-generation sequencing (NGS), the complete mitochondrial genome of the Psenopsis anomala was sequenced in the present study. The mitochondrial genome of P. anomala is 16,528 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The structure about gene order and composition of P. anomala mitochondrial genome is similar to those of most other vertebrates. The nucleotide compositions of the light strand in descending order is 29.18% of T, 27.97% of G, 27.06% of A, and 15.79% of C. With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, other mitochondrial genes are encoded on the heavy strand. The phylogenetic analysis by maximum-likelihood (ML) method shown that the Psenopsis anomala was closer to Peprilus triacanthus in the phylogenetic relationship. PMID:25974666

  20. Mitochondrial DNA Sequence and Lack of Response to Anoxia in the Annual Killifish Austrofundulus limnaeus

    PubMed Central

    Wagner, Josiah T.; Herrejon Chavez, Florisela; Podrabsky, Jason E.

    2016-01-01

    The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, understanding the unique properties of A. limnaeus mitochondria is of great interest. In this work, we describe the first complete mitochondrial genome (mtgenome) sequence of a single adult A. limnaeus individual and compare both coding and non-coding regions to several other closely related fish mtgenomes. Mitochondrial features were predicted using MitoAnnotator and polyadenylation sites were predicted using RNAseq mapping. To estimate the responsiveness of A. limnaeus mitochondria to anoxia treatment, we measure relative mitochondrial DNA copy number and total citrate synthase activity in both relatively anoxia-tolerant and anoxia-sensitive embryonic stages. Our cross-species comparative approach identifies unique features of ND1, ND5, ND6, and ATPase-6 that may facilitate the unique phenotype of A. limnaeus embryos. Additionally, we do not find evidence for mitochondrial degradation or biogenesis during anoxia/reoxygenation treatment in A. limnaeus embryos, suggesting that anoxia-tolerant mitochondria do not respond to anoxia in a manner similar to anoxia-sensitive mitochondria.

  1. All 37 Mitochondrial Genes of Aphid Aphis craccivora Obtained from Transcriptome Sequencing: Implications for the Evolution of Aphids

    PubMed Central

    Li, Hu; Cai, Wanzhi

    2016-01-01

    The availability of mitochondrial genome data for Aphididae, one of the economically important insect pest families, in public databases is limited. The advent of next generation sequencing technology provides the potential to generate mitochondrial genome data for many species timely and cost-effectively. In this report, we used transcriptome sequencing technology to determine all the 37 mitochondrial genes of the cowpea aphid, Aphis craccivora. This method avoids the necessity of finding suitable primers for long PCRs or primer-walking amplicons, and is proved to be effective in obtaining the whole set of mitochondrial gene data for insects with difficulty in sequencing mitochondrial genome by PCR-based strategies. Phylogenetic analyses of aphid mitochondrial genome data show clustering based on tribe level, and strongly support the monophyly of the family Aphididae. Within the monophyletic Aphidini, three samples from Aphis grouped together. In another major clade of Aphididae, Pterocomma pilosum was recovered as a potential sister-group of Cavariella salicicola, as part of Macrosiphini. PMID:27314587

  2. All 37 Mitochondrial Genes of Aphid Aphis craccivora Obtained from Transcriptome Sequencing: Implications for the Evolution of Aphids.

    PubMed

    Song, Nan; Zhang, Hao; Li, Hu; Cai, Wanzhi

    2016-01-01

    The availability of mitochondrial genome data for Aphididae, one of the economically important insect pest families, in public databases is limited. The advent of next generation sequencing technology provides the potential to generate mitochondrial genome data for many species timely and cost-effectively. In this report, we used transcriptome sequencing technology to determine all the 37 mitochondrial genes of the cowpea aphid, Aphis craccivora. This method avoids the necessity of finding suitable primers for long PCRs or primer-walking amplicons, and is proved to be effective in obtaining the whole set of mitochondrial gene data for insects with difficulty in sequencing mitochondrial genome by PCR-based strategies. Phylogenetic analyses of aphid mitochondrial genome data show clustering based on tribe level, and strongly support the monophyly of the family Aphididae. Within the monophyletic Aphidini, three samples from Aphis grouped together. In another major clade of Aphididae, Pterocomma pilosum was recovered as a potential sister-group of Cavariella salicicola, as part of Macrosiphini. PMID:27314587

  3. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences

    SciTech Connect

    Macey, J. Robert; Papenfuss, Theodore J.; Kuehl, Jennifer V.; Fourcade, H. Matthew; Boore, Jeffrey L.

    2004-05-19

    Complete mitochondrial genomic sequences are reported from 12 members in the four families of the reptile group Amphisbaenia. Analysis of 11,946 aligned nucleotide positions (5,797 informative) produces a robust phylogenetic hypothesis. The family Rhineuridae is basal and Bipedidae is the sister taxon to the Amphisbaenidae plus Trogonophidae. Amphisbaenian reptiles are surprisingly old, predating the breakup of Pangaea 200 million years before present, because successive basal taxa (Rhineuridae and Bipedidae) are situated in tectonic regions of Laurasia and nested taxa (Amphisbaenidae and Trogonophidae) are found in Gondwanan regions. Thorough sampling within the Bipedidae shows that it is not tectonic movement of Baja California away from the Mexican mainland that is primary in isolating Bipes species, but rather that primary vicariance occurred between northern and southern groups. Amphisbaenian families show parallel reduction in number of limbs and Bipes species exhibit parallel reduction in number of digits. A measure is developed for comparing the phylogenetic information content of various genes. A synapomorphic trait defining the Bipedidae is a shift from the typical vertebrate mitochondrial gene arrangement to the derived state of trnE and nad6. In addition, a tandem duplication of trnT and trnP is observed in B. biporus with a pattern of pseudogene formation that varies among populations. The first case of convergent rearrangement of the mitochondrial genome among animals demonstrated by complete genomic sequences is reported. Relative to most vertebrates, the Rhineuridae has the block nad6, trnE switched in order with cob, trnT, trnP, as they are in birds.

  4. Genetic differentiation in pointing dog breeds inferred from microsatellites and mitochondrial DNA sequence.

    PubMed

    Parra, D; Méndez, S; Cañón, J; Dunner, S

    2008-02-01

    Recent studies presenting genetic analysis of dog breeds do not focus specifically on genetic relationships among pointing dog breeds, although hunting was among the first traits of interest when dogs were domesticated. This report compares histories with genetic relationships among five modern breeds of pointing dogs (English Setter, English Pointer, Epagneul Breton, Deutsch Drahthaar and German Shorthaired Pointer) collected in Spain using mitochondrial, autosomal and Y-chromosome information. We identified 236 alleles in autosomal microsatellites, four Y-chromosome haplotypes and 18 mitochondrial haplotypes. Average F(ST) values were 11.2, 14.4 and 13.1 for autosomal, Y-chromosome microsatellite markers and mtDNA sequence respectively, reflecting relatively high genetic differentiation among breeds. The high gene diversity observed in the pointing breeds (61.7-68.2) suggests contributions from genetically different individuals, but that these individuals originated from the same ancestors. The modern English Setter, thought to have arisen from the Old Spanish Pointer, was the first breed to cluster independently when using autosomal markers and seems to share a common maternal origin with the English Pointer and German Shorthaired Pointer, either via common domestic breed females in the British Isles or through the Old Spanish Pointer females taken to the British Isles in the 14th and 16th centuries. Analysis of mitochondrial DNA sequence indicates the isolation of the Epagneul Breton, which has been formally documented, and shows Deutsch Drahthaar as the result of crossing the German Shorthaired Pointer with other breeds. Our molecular data are consistent with historical documents. PMID:18254732

  5. Detection of Ultra-Rare Mitochondrial Mutations in Breast Stem Cells by Duplex Sequencing

    PubMed Central

    Ahn, Eun Hyun; Hirohata, Kensen; Kohrn, Brendan F.; Fox, Edward J.; Chang, Chia-Cheng; Loeb, Lawrence A.

    2015-01-01

    Long-lived adult stem cells could accumulate non-repaired DNA damage or mutations that increase the risk of tumor formation. To date, studies on mutations in stem cells have concentrated on clonal (homoplasmic) mutations and have not focused on rarely occurring stochastic mutations that may accumulate during stem cell dormancy. A major challenge in investigating these rare mutations is that conventional next generation sequencing (NGS) methods have high error rates. We have established a new method termed Duplex Sequencing (DS), which detects mutations with unprecedented accuracy. We present a comprehensive analysis of mitochondrial DNA mutations in human breast normal stem cells and non-stem cells using DS. The vast majority of mutations occur at low frequency and are not detectable by NGS. The most prevalent point mutation types are the C>T/G>A and A>G/T>C transitions. The mutations exhibit a strand bias with higher prevalence of G>A, T>C, and A>C mutations on the light strand of the mitochondrial genome. The overall rare mutation frequency is significantly lower in stem cells than in the corresponding non-stem cells. We have identified common and unique non-homoplasmic mutations between non-stem and stem cells that include new mutations which have not been reported previously. Four mutations found within the MT-ND5 gene (m.12684G>A, m.12705C>T, m.13095T>C, m.13105A>G) are present in all groups of stem and non-stem cells. Two mutations (m.8567T>C, m.10547C>G) are found only in non-stem cells. This first genome-wide analysis of mitochondrial DNA mutations may aid in characterizing human breast normal epithelial cells and serve as a reference for cancer stem cell mutation profiles. PMID:26305705

  6. Coptotermes gestroi (Isoptera: Rhinotermitidae) in Brazil: possible origins inferred by mitochondrial cytochrome oxidase II gene sequences.

    PubMed

    Martins, C; Fontes, L R; Bueno, O C; Martins, V G

    2010-09-01

    The Asian subterranean termite, Coptotermes gestroi, originally from northeast India through Burma, Thailand, Malaysia, and the Indonesian archipelago, is a major termite pest introduced in several countries around the world, including Brazil. We sequenced the mitochondrial COII gene from individuals representing 23 populations. Phylogenetic analysis of COII gene sequences from this and other studies resulted in two main groups: (1) populations of Cleveland (USA) and four populations of Malaysia and (2) populations of Brazil, four populations of Malaysia, and one population from each of Thailand, Puerto Rico, and Key West (USA). Three new localities are reported here, considerably enlarging the distribution of C. gestroi in Brazil: Campo Grande (state of Mato Grosso do Sul), Itajaí (state of Santa Catarina), and Porto Alegre (state of Rio Grande do Sul). PMID:20924414

  7. The complete mitochondrial genome sequence of Acentrogobius sp. (Gobiiformes: Gobiidae) and phylogenetic studies of Gobiidae.

    PubMed

    Yang, Qiu-Hua; Lin, Qi; He, Li-Bin; Huang, Rui-Fang; Lin, Ke-Bing; Ge, Hui; Wu, Jian-Shao; Zhou, Chen

    2016-07-01

    At present, few morphological descriptions are available for Acentrogobius species and there exist some confused issues on the species classification and phylogeny. In this study, we first determined and described the complete mitochondrial genome of Acentrogobius sp. The complete mitogenome sequence is 17 083 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and a light-strand replication origin (OL). The overall base composition is 28.9% A, 26.2% T, 28.5% C, and 16.4% G, with a slight AT bias (55.1%). To furthermore validate the new determined sequences, phylogenetic trees involving all the Gobiidae species available in GenBank database were constructed. These results are expected to provide useful molecular data for species identification and further phylogenetic studies of Gobiiformes. PMID:26152347

  8. The complete mitochondrial genome sequence of the blue sheep, Pseudois nayaur nayaur (Cetartiodactyla: Caprinae).

    PubMed

    Jiang, Li-Chun; Tan, Shuai; Peng, Rui; Zou, Fang-Dong

    2015-01-01

    The blue sheep (Pseudois nayaur nayaur) belongs to the subfamily Caprinae, and is distributed in the Qinghai-Tibet Plateau and peripheral mountains of China. In this study, the complete mitochondrial genome of P. n. nayaur was sequenced. It was determined to be of 16,700 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of P. n. nayaur and other 29 caprine species were used for phylogenetic analysis. Phylogenetic trees were reconstructed by Bayesian and maximum likelihood methods, and it suggested that P. n. nayaur was the sister group of P. schaeferi and P. nayaur, and also indicated a close relationship of genus Pseudois with genus Capra. PMID:24409917

  9. Phylogenetic Relationships among Asian species of Petaurista (Rodentia, Sciuridae), Inferred from Mitochondrial Cytochrome b Gene Sequences.

    PubMed

    Oshida, T; Lin, L K; Masuda, R; Yoshida, M C

    2000-01-01

    To elucidate the phylogenetic relationships among four species belonging to the genus Petaurista (P. alborufus castaneus, P. alborufus lena, P. leucogenys leucogenys, P. leucogenys nikkonis, P. petaurista melanotus, and P. philippensis grandis), we investigated the partial sequences (1,068 bp) of the mitochondrial cytochrome b gene for these giant flying squirrels. Phylogenetic trees (NJ, MP, and ML trees) constructed from cytochrome b sequences indicated that P. leucogenys was grouped independently with other species, and that P. philippensis was most closely related to P. petaurista with 99-100% bootstrap values. In addition, two subspecies of P. alborufus did not form a single clade: P. alborufus castaneus from China was most distantly related to the other species, whereas P. alborufus lena from Taiwan was closely related to P. petaurista and P. philippensis with 82-90% bootstrap values. This result suggests that it is reasonable to regard P. alborufus lena as a distinct species from P. alborufus castaneus. PMID:18494567

  10. Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences

    PubMed Central

    Lanave, Cecilia; Liuni, Sabino; Licciulli, Flavio; Attimonelli, Marcella

    2000-01-01

    The AMmtDB database (http://bio-www.ba.cnr.it:8000/srs6/ ) has been updated by collecting the multi-aligned sequences of Chordata mitochondrial genes coding for proteins and tRNAs. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user’s operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually. PMID:10592208

  11. Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences.

    PubMed

    Lanave, Cecilia; Licciulli, Flavio; De Robertis, Mariateresa; Marolla, Alessandra; Attimonelli, Marcella

    2002-01-01

    The AMmtDB database (http://bighost.area.ba.cnr.it/mitochondriome) has been updated by collecting the multi-aligned sequences of Chordata and Invertebrata mitochondrial genes coding for proteins and tRNAs. Links to the multi-aligned mtDNA intraspecies variants, collected in VarMmtDB at the Mitochondriome web site, have been introduced. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually. PMID:11752285

  12. Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences

    PubMed Central

    Lanave, Cecilia; Licciulli, Flavio; De Robertis, Mariateresa; Marolla, Alessandra; Attimonelli, Marcella

    2002-01-01

    The AMmtDB database (http://bighost.area.ba.cnr.it/mitochondriome) has been updated by collecting the multi-aligned sequences of Chordata and Invertebrata mitochondrial genes coding for proteins and tRNAs. Links to the multi-aligned mtDNA intraspecies variants, collected in VarMmtDB at the Mitochondriome web site, have been introduced. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user’s operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually. PMID:11752285

  13. The complete mitochondrial genome sequence of the Korean hare (Lepus coreanus).

    PubMed

    Yu, Jeong-Nam; Chung, Chul-Un; Kwak, Myounghai

    2015-02-01

    The complete mitogenome of the Korean hare (Lepus coreanus) was determined by the long and accurate polymerase chain reaction and primer-walking methods. The mitogenome of the Korean hare is 17,472 bp in length and contains sequences that encode 13 protein genes, 22 tRNAs, 2 rRNAs and a noncoding control region. The mitogenome is arranged in an identical order to that found in most other vertebrates. All mitochondrial genes are encoded on the heavy strand, except for eight tRNA genes and the ND6 gene. The control region contains putative termination associated elements, conserved sequence blocks and short and long tandem repeats motifs. PMID:23883283

  14. The complete mitochondrial genome sequence of the spider habronattus oregonensis reveals rearranged and extremely truncated tRNAs

    SciTech Connect

    Masta, Susan E.; Boore, Jeffrey L.

    2004-01-31

    We sequenced the entire mitochondrial genome of the jumping spider Habronattus oregonensis of the arachnid order Araneae (Arthropoda: Chelicerata). A number of unusual features distinguish this genome from other chelicerate and arthropod mitochondrial genomes. Most of the transfer RNA gene sequences are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. At least nine of the tRNA sequences lack the potential to form TYC arm stem pairings, and instead are inferred to have TV-replacement loops. Furthermore, sequences that could encode the 3' aminoacyl acceptor stems in at least 10 tRNAs appear to be lacking, because fully paired acceptor stems are not possible and because the downstream sequences instead encode adjacent genes. Hence, these appear to be among the smallest known tRNA genes. We postulate that an RNA editing mechanism must exist to restore the 3' aminoacyl acceptor stems in order to allow the tRNAs to function. At least seven tRN As are rearranged with respect to the chelicerate Limulus polyphemus, although the arrangement of the protein-coding genes is identical. Most mitochondrial protein-coding genes of H. oregonensis have ATN as initiation codons, as commonly found in arthropod mtDNAs, but cytochrome oxidase subunit 2 and 3 genes apparently use UUG as an initiation codon. Finally, many of the gene sequences overlap one another and are truncated. This 14,381 bp genome, the first mitochondrial genome of a spider yet sequenced, is one of the smallest arthropod mitochondrial genomes known. We suggest that post transcriptional RNA editing can likely maintain function of the tRNAs while permitting the accumulation of mutations that would otherwise be deleterious. Such mechanisms may have allowed for the minimization of the spider mitochondrial genome.

  15. Application of mitochondrial DNA sequence analysis in the forensic identification of Chinese sika deer subspecies.

    PubMed

    Wu, Hua; Wan, Qiu-Hong; Fang, Sheng-Guo; Zhang, Shu-Yan

    2005-03-10

    As a direct and indirect consequence of human activities, only two subspecies, Cervus nippon sinchuanicus and Cervus nippon kopschi, currently subsist in the wild of China. However, a large population of Cervus nippon hortulorum and Cervus nippon nippon is raised in order to gain deer parts for Chinese traditional medicine. According to Chinese Wild Animal Conservation Law, hunting, capturing and trading of the wild sika deer are strictly banned, however, raising and trading of the domestic individual are permitted. Thus, it is very necessary to identify the subspecies of sika deer in China in forensic tests. In our study, we used mitochondrial DNA control region sequence analysis and phylogenetic analysis to identify the subspecies of sika deer. Mitochondrial DNA control region sequences analysis revealed that two haplotypes came from the unknown samples. One is the same as the haplotype that came from the samples of wild population of C. n. kopschi. Phylogenetic analysis indicated that the two haplotypes of unknown samples clustered with the haplotypes of C. n. kopschi, and had significant difference from the haplotypes of the other subspecies. These results together revealed that the unknown samples came from two individuals that belong to the wild population of C. n. kopschi living in the Qinglingfeng State Natural Reserve of Zhejiang province. Therefore, the results provide forensic evidence of illegal wild animal hunting. PMID:15639603

  16. The complete mitochondrial genome sequence of the Xizang Plateau frog, Nanorana parkeri (Anura: Dicroglossidae).

    PubMed

    Jiang, Lichun; Ruan, Qiping; Chen, Wei

    2016-09-01

    The Xizang Plateau frog (Nanorana parkeri) belongs to the family Dicroglossidae, which distributes in southern and eastern Xizang, southern-most Qinghai in China, high elevations of north-central Nepal, Himalayan Bhutan, northeastern Kashmir and India. In this study, the complete mitochondrial genome of N. parkeri was sequenced. The mitogenome was 17,837 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a non-coding control region (CR). As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. The overall base composition of the N. parkeri is A: 27.7 % A, T: 30.1 % T, C: 26.6% and G: 15.6%. The alignment of the Nanorana species CRs exhibited high genetic variability and rich A + T content. In comparison with the mtDNA sequences typical of vertebrates, a tandem duplication of the tRNA(Met) gene and a rearrangement of the tRNA(Thr), tRNA(Pro) and tRNA(Leu) (CUN) genes were found. The complete mitogenome of N. parkeri can provided an important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species. PMID:25758045

  17. Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences.

    PubMed

    Sercundes, Michelle Klein; Valadas, Samantha Yuri Oshiro Branco; Keid, Lara Borges; Oliveira, Tricia Maria Ferreira Souza; Ferreira, Helena Lage; Vitor, Ricardo Wagner de Almeida; Gregori, Fábio; Soares, Rodrigo Martins

    2016-01-01

    Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG), Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genus Hammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well. PMID:27007245

  18. Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman.

    PubMed

    Coia, V; Cipollini, G; Anagnostou, P; Maixner, F; Battaggia, C; Brisighelli, F; Gómez-Carballa, A; Destro Bisol, G; Salas, A; Zink, A

    2016-01-01

    The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps - putatively in genetic continuity with the Tyrolean Iceman-and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp. PMID:26764605

  19. Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples.

    PubMed

    Parson, Walther; Huber, Gabriela; Moreno, Lilliana; Madel, Maria-Bernadette; Brandhagen, Michael D; Nagl, Simone; Xavier, Catarina; Eduardoff, Mayra; Callaghan, Thomas C; Irwin, Jodi A

    2015-03-01

    Though shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, DNA testing has historically focused on the recovery of just about 600 base pairs of the mitochondrial DNA control region. Here, we describe our success in recovering complete mitochondrial genome (mtGenome) data (∼16,569bp) from single shed hairs. By employing massively parallel sequencing (MPS), we demonstrate that particular hair samples yield DNA sufficient in quantity and quality to produce 2-3kb mtGenome amplicons and that entire mtGenome data can be recovered from hair extracts even without PCR enrichment. Most importantly, we describe a small amplicon multiplex assay comprised of sixty-two primer sets that can be routinely applied to the compromised hair samples typically encountered in forensic casework. In all samples tested here, the MPS data recovered using any one of the three methods were consistent with the control Sanger sequence data developed from high quality known specimens. Given the recently demonstrated value of complete mtGenome data in terms of discrimination power among randomly sampled individuals, the possibility of recovering mtGenome data from the most compromised and limited evidentiary material is likely to vastly increase the utility of mtDNA testing for hair evidence. PMID:25438934

  20. Complete mitochondrial DNA sequences of Saccostrea mordax and Saccostrea cucullata: genome organization and phylogeny analysis.

    PubMed

    Volatiana, Josie Ancella; Fang, Shasha; Kinaro, Zachary Omambia; Liu, Xiao

    2016-07-01

    Classified in the phylum mollusks, oysters are bivalves which are found in estuaries and coastal zones. Because of their plastic shell, mitochondrial DNA analysis of this species becomes an interesting field, necessary to investigate their phylogenetic and evolution of relations. In our study, two oyster species: Saccostrea mordax and Saccostrea cucullata from Indian Ocean (Madagascar) were investigated. The complete sequence of Saccostrea mordax (16 512 bp) and Saccostrea cucullata (16 396 bp) were described and determined, with their mitogenomes deposited in the GenBank with accession number KP769562 and KP967577 respectively. Both mitochondrial genome sequences contained 12 protein-coding genes, 23 tRNAs, and two rRNAs, all encoded in the same heavy strand. High levels of similarity in the gene arrangement of the two Saccostrea species were evident. The phylogenetic analysis shows a closer relationship between the two Saccostrea species and confirms the strong relationship within Saccostrea, Crassostrea and Ostrea genus in taxonomy of Ostreidae family. PMID:26226596

  1. Complete Sequence and Gene Organization of the Mitochondrial Genome of the Land Snail Albinaria Coerulea

    PubMed Central

    Hatzoglou, E.; Rodakis, G. C.; Lecanidou, R.

    1995-01-01

    The complete sequence (14,130 bp) of the mitochondrial DNA (mtDNA) of the land snail Albinaria coerulea was determined. It contains 13 protein, two rRNA and 22 tRNA genes. Twenty-four of these genes are encoded by one and 13 genes by the other strand. The gene arrangement shares almost no similarities with that of two other molluscs for which the complete gene content and arrangement are known, the bivalve Mytilus edulis and the chiton Katharina tunicata; the protein and rRNA gene order is similar to that of another terrestrial gastropod, Cepaea nemoralis. Unusual features include the following: (1) the absence of lengthy noncoding regions (there are only 141 intergenic nucleotides interspersed at different gene borders, the longest intergenic sequence being 42 nucleotides), (2) the presence of several overlapping genes (mostly tRNAs), (3) the presence of tRNA-like structures and other stem and loop structures within genes. An RNA editing system acting on tRNAs must necessarily be invoked for posttranscriptional extension of the overlapping tRNAs. Due to these features, and also because of the small size of its genes (e.g., it contains the smallest rRNA genes among the known coelomates), it is one of the most compact mitochondrial genomes known to date. PMID:7498775

  2. A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis)

    PubMed Central

    Hou, Wan-ru; Chen, Yu; Wu, Xia; Hu, Jin-chu; Peng, Zheng-song; Yang, Jung; Tang, Zong-xiang; Zhou, Cai-Quan; Li, Yu-ming; Yang, Shi-kui; Du, Yu-jie; Kong, Ling-lu; Ren, Zheng-long; Zhang, Huai-yu; Shuai, Su-rong

    2007-01-01

    We obtained the complete mitochondrial genome of U.thibetanus mupinensis by DNA sequencing based on the PCR fragments of 18 primers we designed. The results indicate that the mtDNA is 16 868 bp in size, encodes 13 protein genes, 22 tRNA genes, and 2 rRNA genes, with an overall H-strand base composition of 31.2% A, 25.4% C, 15.5% G and 27.9% T. The sequence of the control region (CR) located between tRNA-Pro and tRNA-Phe is 1422 bp in size, consists of 8.43% of the whole genome, GC content is 51.9% and has a 6bp tandem repeat and two 10bp tandem repeats identified by using the Tandem Repeats Finder. U. thibetanus mupinensis mitochondrial genome shares high similarity with those of three other Ursidae: U. americanus (91.46%), U. arctos (89.25%) and U. maritimus (87.66%). PMID:17205108

  3. Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman

    PubMed Central

    Coia, V.; Cipollini, G.; Anagnostou, P.; Maixner, F.; Battaggia, C.; Brisighelli, F.; Gómez-Carballa, A; Destro Bisol, G.; Salas, A.; Zink, A.

    2016-01-01

    The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps – putatively in genetic continuity with the Tyrolean Iceman—and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp. PMID:26764605

  4. Sequencing and analysis of complete mitochondrial genome of Apodemus draco (Rodentia: Arvicolinae).

    PubMed

    Wei, Haixue; Jia, Qiang; Li, Fengjun; Liu, Yongcheng; Chen, Shunde; Yong, Bin

    2016-07-01

    The genus Apodemus are the most common small rodents in fields. They are also one of the best species for biogeographic study and understanding the environmental changes. In this study, the complete mitochondrial genome sequence of Apodemus draco is determined. The mitogenome is 16 220 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region, with a base composition of 35.1% A, 29.0% T, 23.8% C and 12.1% G. The nucleotide sequence data of 12 heavy-strand protein-coding genes of Apodemus draco and other 23 rodents were used for mitochondrial genome phylogenetic analyses. The monophyly of the genus Apodemus was well supported with sister to the genus Mus. Bayesian analysis also suggested that Apodemus draco was a sister to Apodemus latronum. The present study may facilitate further investigation of the molecular evolution and biogeographic study of the genus Apodemus. PMID:27158789

  5. Analysis of mixtures using next generation sequencing of mitochondrial DNA hypervariable regions

    PubMed Central

    Kim, Hanna; Erlich, Henry A.; Calloway, Cassandra D.

    2015-01-01

    Aim To apply massively parallel and clonal sequencing (next generation sequencing or NGS) to the analysis of forensic mixed samples. Methods A duplex polymerase chain reaction (PCR) assay targeting the mitochondrial DNA (mtDNA) hypervariable regions I/II (HVI/HVII) was developed for NGS analysis on the Roche 454 GS Junior instrument. Eight sets of multiplex identifier-tagged 454 fusion primers were used in a combinatorial approach for amplification and deep sequencing of up to 64 samples in parallel. Results This assay was shown to be highly sensitive for sequencing limited DNA amounts ( ~ 100 mtDNA copies) and analyzing contrived and biological mixtures with low level variants ( ~ 1%) as well as “complex” mixtures (≥3 contributors). PCR artifact “hybrid” sequences generated by jumping PCR or template switching were observed at a low level (<2%) in the analysis of mixed samples but could be eliminated by reducing the PCR cycle number. Conclusion This study demonstrates the power of NGS technologies targeting the mtDNA HVI/HVII regions for analysis of challenging forensic samples, such as mixtures and specimens with limited DNA. PMID:26088845

  6. Complete mitochondrial DNA sequences of six snakes: phylogenetic relationships and molecular evolution of genomic features.

    PubMed

    Dong, Songyu; Kumazawa, Yoshinori

    2005-07-01

    Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNALeu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences. PMID:16007493

  7. Mitochondrial genome sequences and comparative genomics ofPhytophthora ramorum and P. sojae

    SciTech Connect

    Martin, Frank N.; Douda, Bensasson; Tyler, Brett M.; Boore,Jeffrey L.

    2007-01-01

    The complete sequences of the mitochondrial genomes of theoomycetes of Phytophthora ramorum and P. sojae were determined during thecourse of their complete nuclear genome sequencing (Tyler, et al. 2006).Both are circular, with sizes of 39,314 bp for P. ramorum and 42,975 bpfor P. sojae. Each contains a total of 37 identifiable protein-encodinggenes, 25 or 26 tRNAs (P. sojae and P. ramorum, respectively)specifying19 amino acids, and a variable number of ORFs (7 for P. ramorum and 12for P. sojae) which are potentially additional functional genes.Non-coding regions comprise approximately 11.5 percent and 18.4 percentof the genomes of P. ramorum and P. sojae, respectively. Relative to P.sojae, there is an inverted repeat of 1,150 bp in P. ramorum thatincludes an unassigned unique ORF, a tRNA gene, and adjacent non-codingsequences, but otherwise the gene order in both species is identical.Comparisons of these genomes with published sequences of the P. infestansmitochondrial genome reveals a number of similarities, but the gene orderin P. infestans differs in two adjacent locations due to inversions.Sequence alignments of the three genomes indicated sequence conservationranging from 75 to 85 percent and that specific regions were morevariable than others.

  8. The phylogeny of Mediterranean tortoises and their close relativesbased on complete mitochondrial genome sequences from museumspecimens

    SciTech Connect

    Parham, James F.; Macey, J. Robert; Papenfuss, Theodore J.; Feldman, Chris R.; Turkozan, Oguz; Polymeni, Rosa; Boore, Jeffrey

    2005-04-29

    As part of an ongoing project to generate a mitochondrial database for terrestrial tortoises based on museum specimens, the complete mitochondrial genome sequences of 10 species and a {approx}14 kb sequence from an eleventh species are reported. The sampling of the present study emphasizes Mediterranean tortoises (genus Testudo and their close relatives). Our new sequences are aligned, along with those of two testudinoid turtles from GenBank, Chrysemys picta and Mauremys reevesii, yielding an alignment of 14,858 positions, of which 3,238 are parsimony informative. We develop a phylogenetic taxonomy for Testudo and related species based on well-supported, diagnosable clades. Several well-supported nodes are recovered, including the monophyly of a restricted Testudo, T. kleinmanni + T. marginata (the Chersus clade), and the placement of the enigmatic African pancake tortoise (Malacochersustornieri) within the predominantly Palearctic greater Testudo group (Testudona tax. nov.). Despite the large amount of sequence reported, there is low statistical support for some nodes within Testudona and Sowe do not propose names for those groups. A preliminary and conservative estimation of divergence times implies a late Miocene diversification for the testudonan clade (6-12 million years ago), matching their first appearance in the fossil record. The multi-continental distribution of testudonan turtles can be explained by the establishment of permanent connections between Europe, Africa, and Asia at this time. The arrival of testudonan turtles to Africa occurred after one or more initial tortoise invasions gave rise to the diverse (>25 species) 'Geochelone complex.'Two unusual genomic features are reported for the mtDNA of one tortoise, M. tornieri: (1) nad4 has a shift of reading frame that we suggest is resolved by translational frameshifting of the mRNA on the ribosome during protein synthesis and (2) there are two copies of the control region and trnF, with the latter

  9. Complete DNA Sequence of the Mitochondrial Genome of the Black Chiton, Katharina Tunicata

    PubMed Central

    Boore, J. L.; Brown, W. M.

    1994-01-01

    The DNA sequence of the 15,532-base pair (bp) mitochondrial DNA (mtDNA) of the chiton Katharina tunicata has been determined. The 37 genes typical of metazoan mtDNA are present: 13 for protein subunits involved in oxidative phosphorylation, 2 for rRNAs and 22 for tRNAs. The gene arrangement resembles those of arthropods much more than that of another mollusc, the bivalve Mytilus edulis. Most genes abut directly or overlap, and abbreviated stop codons are inferred for four genes. Four junctions between adjacent pairs of protein genes lack intervening tRNA genes; however, at each of these junctions there is a sequence immediately adjacent to the start codon of the downstream gene that is capable of forming a stem-and-loop structure. Analysis of the tRNA gene sequences suggests that the D arm is unpaired in tRNA(ser(AGN)), which is typical of metazoan mtDNAs, and also in tRNA(ser(UCN)), a condition found previously only in nematode mtDNAs. There are two additional sequences in Katharina mtDNA that can be folded into structures resembling tRNAs; whether these are functional genes is unknown. All possible codons except the stop codons TAA and TAG are used in the protein-encoding genes, and Katharina mtDNA appears to use the same variation of the mitochondrial genetic code that is used in Drosophila and Mytilus. Translation initiates at the codons ATG, ATA and GTG. A + T richness appears to have affected codon usage patterns and, perhaps, the amino acid composition of the encoded proteins. A 142-bp non-coding region between tRNA(glu) and CO3 contains a 72-bp tract of alternating A and T. PMID:7828825

  10. Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor

    SciTech Connect

    Sheard, Laura B; Tan, Xu; Mao, Haibin; Withers, John; Ben-Nissan, Gili; Hinds, Thomas R; Kobayashi, Yuichi; Hsu, Fong-Fu; Sharon, Michal; Browse, John; He, Sheng Yang; Rizo, Josep; Howe, Gregg A; Zheng, Ning

    2011-11-07

    Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. The F-box protein CORONATINE INSENSITIVE 1 (COI1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JAZ proteins. Despite its importance, the mechanism of jasmonate perception remains unclear. Here we present structural and pharmacological data to show that the true Arabidopsis jasmonate receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone (3R,7S)-jasmonoyl-l-isoleucine (JA-Ile) with high specificity. High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved {alpha}-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. In addition, we identify a third critical component of the jasmonate co-receptor complex, inositol pentakisphosphate, which interacts with both COI1 and JAZ adjacent to the ligand. Our results unravel the mechanism of jasmonate perception and highlight the ability of F-box proteins to evolve as multi-component signalling hubs.

  11. Jasmonate perception by inositol phosphate-potentiated COI1-JAZ co-receptor

    PubMed Central

    Sheard, Laura B.; Tan, Xu; Mao, Haibin; Withers, John; Ben-Nissan, Gili; Hinds, Thomas R.; Kobayashi, Yuichi; Hsu, Fong-Fu; Sharon, Michal; Browse, John; He, Sheng Yang; Rizo, Josep; Howe, Gregg A.; Zheng, Ning

    2010-01-01

    Jasmonates (JAs) are a family of plant hormones that regulate plant growth, development, and responses to stress. The F-box protein CORONATINE-INSENSITIVE 1 (COI1) mediates JA signaling by promoting hormone-dependent ubiquitination and degradation of transcriptional repressor JAZ proteins. Despite its importance, the mechanism of JA perception remains unclear. Here we present structural and pharmacological data to show that the true JA receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone, (3R,7S)-jasmonoyl-L-isoleucine (JA-Ile), with high specificity. High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved α-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. In addition, we identify a third critical component of the JA co-receptor complex, inositol pentakisphosphate, which interacts with both COI1 and JAZ adjacent to the ligand. Our results unravel the mechanism of JA perception and highlight the ability of F-box proteins to evolve as multi-component signaling hubs. PMID:20927106

  12. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.

    PubMed

    Dabney, Jesse; Knapp, Michael; Glocke, Isabelle; Gansauge, Marie-Theres; Weihmann, Antje; Nickel, Birgit; Valdiosera, Cristina; García, Nuria; Pääbo, Svante; Arsuaga, Juan-Luis; Meyer, Matthias

    2013-09-24

    Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp. PMID:24019490

  13. Complete sequence and characterization of the Silurus lanzhouensis (Siluriformes: Siluridae) mitochondrial genome.

    PubMed

    Lian, Zong-Qiang; Wu, Xu-Dong; Xiao, Wei; Sai, Qing-Yun; Gun, Shuang-Bao

    2016-07-01

    The complete mitochondrial DNA (mtDNA) sequence of Silurus lanzhouensis was constructed from whole-genome Illumina sequencing data. The 16 523 bp circular genome comprises typical mtDNA components. All 13 protein-coding genes (PCGs) are initiated by an ATG except for COX1, which uses GTG. Some PCGs harbor TAG (ND2 and ND3) or an incomplete stop codon T (COX2, ND4, and CYTB), while others use TAA as their stop codon. 12S rRNA and 16S rRNA secondary structures are composed of four domains with 45 helices and six domains with 54 helices, respectively. All tRNAs are predicted to fold into the expected typical cloverleaf secondary structure except tRNA-Ser((AGN)). The largest intergenic spacer sequence was predicted to be the origin of light-strand replication. Eight conserved sequences were identified in the control region (CR). This complete S. lanzhouensis mitogenome provides useful data for further studies on molecular systematics, taxonomic status, stock evaluation, and conservation genetics. PMID:26171872

  14. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

    PubMed Central

    Dabney, Jesse; Knapp, Michael; Glocke, Isabelle; Gansauge, Marie-Theres; Weihmann, Antje; Nickel, Birgit; Valdiosera, Cristina; García, Nuria; Pääbo, Svante; Arsuaga, Juan-Luis; Meyer, Matthias

    2013-01-01

    Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp. PMID:24019490

  15. Belgian canine population and purebred study for forensics by improved mitochondrial DNA sequencing.

    PubMed

    Desmyter, Stijn; Gijsbers, Leonie

    2012-01-01

    In canine population studies for forensics, the mitochondrial DNA is profiled by sequencing the two hyper variable regions, HV1 and HV2 of the control region. In a first effort to create a Belgian population database some samples showed partially poor sequence quality. We demonstrated that a nuclear pseudogene was co-amplified with the mtDNA control region. Using a new combination of primers this adverse result was no longer observed and sequencing quality was improved. All former samples with poor sequence data were reanalyzed. Furthermore, the forensic canine population study was extended to 208 breed and mixed dogs. In total, 58 haplotypes were identified, resulting in an exclusion capacity of 0.92. The profile distribution of the Belgian population sample was not significantly different from those observed in population studies of three other countries. In addition to the total population study 107 Belgian registered pedigree dogs of six breeds were profiled. Per breed, the obtained haplotypes were supplemented with those from population and purebred studies. The combined data revealed that some haplotypes were more or less prominent present in particular dog breeds. The statistically significant differences in haplotype distribution between breeds and population sample can have consequences on mtDNA databasing and matching probabilities in forensics. PMID:21489897

  16. A pedigree-based study of mitochondrial D-loop DNA sequence variation among Arabian horses.

    PubMed

    Bowling, A T; Del Valle, A; Bowling, M

    2000-02-01

    Through DNA sequence comparisons of a mitochondrial D-loop hypervariable region, we investigated matrilineal diversity for Arabian horses in the United States. Sixty-two horses were tested. From published pedigrees they traced in the maternal line to 34 mares acquired primarily in the mid to late 19th century from nomadic Bedouin tribes. Compared with the reference sequence (GenBank X79547), these samples showed 27 haplotypes with altogether 31 base substitution sites within 397 bp of sequence. Based on examination of pedigrees from a random sampling of 200 horses in current studbooks of the Arabian Horse Registry of America, we estimated that this study defined the expected mtDNA haplotypes for at least 89% of Arabian horses registered in the US. The reliability of the studbook recorded maternal lineages of Arabian pedigrees was demonstrated by haplotype concordance among multiple samplings in 14 lines. Single base differences observed within two maternal lines were interpreted as representing alternative fixations of past heteroplasmy. The study also demonstrated the utility of mtDNA sequence studies to resolve historical maternity questions without access to biological material from the horses whose relationship was in question, provided that representatives of the relevant female lines were available for comparison. The data call into question the traditional assumption that Arabian horses of the same strain necessarily share a common maternal ancestry. PMID:10690354

  17. Nucleotide Sequence and Gene Organization of the Starfish Asterina Pectinifera Mitochondrial Genome

    PubMed Central

    Asakawa, S.; Himeno, H.; Miura, K. I.; Watanabe, K.

    1995-01-01

    The 16,260-bp mitochondrial DNA (mtDNA) from the starfish Asterina pectinifera has been sequenced. The genes for 13 proteins, two rRNAs and 22 tRNAs are organized in an extremely economical fashion, similar to those of other animal mtDNAs, with some of the genes overlapping each other. The gene organization is the same as that for another echinoderm, sea urchin, except for the inversion of a 4.6-kb segment that contains genes for two proteins, 13 tRNAs and the 16S rRNA. Judging from the organization of the protein coding genes, mammalian mtDNAs resemble the sea urchin mtDNA more than that of the starfish. The region around the 3' end of the 12S rRNA gene of the starfish shows a high similarity with those for vertebrates. This region encodes a possible stem and loop structure; similar potential structures occur in this region of vertebrate mtDNAs and also in nonmitochondrial small subunit rRNA. A similar stem and loop structure is also found at the 3' end of the 16S rRNA genes in A. pectinifera, in another starfish Pisaster ochraceus, in vertebrates and in Drosophila, but not in sea urchins. The full sequence data confirm the presumption that AGA/AGG, AUA and AAA codons, respectively, code for serine, isoleucine, and asparagine in the starfish mitochondria, and that AGA/AGG codons are read by tRNA(GCU)(Ser), which possesses a truncated dihydrouridine arm, that was previously suggested from a partial mtDNA sequence. The structural characteristics of tRNAs and possible mechanisms for the change in the mitochondrial genetic code are also discussed. PMID:7672576

  18. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser

    PubMed Central

    2011-01-01

    Background Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the genome are debated issues. Insertion sites match with chromosomal breaks, revealing that micro-deletions usually occurring at non-homologous end joining loci become reduced in presence of NumtS. Some NumtS are involved in recombination events leading to fragment duplication. Moreover, NumtS are polymorphic, a feature that renders them candidates as population markers. Finally, they are a cause of contamination during human mtDNA sequencing, leading to the generation of false heteroplasmies. Results Here we present RHNumtS.2, the most exhaustive human NumtSome catalogue annotating 585 NumtS, 97% of which were here validated in a European individual and in HapMap samples. The NumtS complete dataset and related features have been made available at the UCSC Genome Browser. The produced sequences have been submitted to INSDC databases. The implementation of the RHNumtS.2 tracks within the UCSC Genome Browser has been carried out with the aim to facilitate browsing of the NumtS tracks to be exploited in a wide range of research applications. Conclusions We aimed at providing the scientific community with the most exhaustive overview on the human NumtSome, a resource whose aim is to support several research applications, such as studies concerning human structural variation, diversity, and disease, as well as the detection of false heteroplasmic mtDNA variants. Upon implementation of the NumtS tracks, the application of the BLAT program on the UCSC Genome Browser has now become an additional tool to check for heteroplasmic artefacts, supported by data available through the NumtS tracks. PMID:22013967

  19. The first complete mitochondrial genome sequences of Amblypygi (Chelicerata: Arachnida) reveal conservation of the ancestral arthropod gene order.

    PubMed

    Fahrein, Kathrin; Masta, Susan E; Podsiadlowski, Lars

    2009-05-01

    Amblypygi (whip spiders) are terrestrial chelicerates inhabiting the subtropics and tropics. In morphological and rRNA-based phylogenetic analyses, Amblypygi cluster with Uropygi (whip scorpions) and Araneae (spiders) to form the taxon Tetrapulmonata, but there is controversy regarding the interrelationship of these three taxa. Mitochondrial genomes provide an additional large data set of phylogenetic information (sequences, gene order, RNA secondary structure), but in arachnids, mitochondrial genome data are missing for some of the major orders. In the course of an ongoing project concerning arachnid mitochondrial genomics, we present the first two complete mitochondrial genomes from Amblypygi. Both genomes were found to be typical circular duplex DNA molecules with all 37 genes usually present in bilaterian mitochondrial genomes. In both species, gene order is identical to that of Limulus polyphemus (Xiphosura), which is assumed to reflect the putative arthropod ground pattern. All tRNA gene sequences have the potential to fold into structures that are typical of metazoan mitochondrial tRNAs, except for tRNA-Ala, which lacks the D arm in both amblypygids, suggesting the loss of this feature early in amblypygid evolution. Phylogenetic analysis resulted in weak support for Uropygi being the sister group of Amblypygi. PMID:19448726

  20. Mitochondrial DNA control region sequence variation in migraine headache and cyclic vomiting syndrome.

    PubMed

    Wang, Qingxue; Ito, Masamichi; Adams, Kathleen; Li, B U K; Klopstock, Thomas; Maslim, Audrey; Higashimoto, Tomoyasu; Herzog, Juergen; Boles, Richard G

    2004-11-15

    Migraine headache is a very common condition affecting about 10% of the population that results in substantial morbidity and economic loss. The two most common variants are migraine with (MA) and without (MO) aura. Often considered to be a migraine-like variant, cyclic vomiting syndrome (CVS) is a predominately childhood condition characterized by severe, discrete episodes of nausea, vomiting, and lethargy. Disease-associated mitochondrial DNA (mtDNA) sequence variants are suggested in common migraine and CVS based upon a strong bias towards the maternal inheritance of disease, and several other factors. Temporal temperature gradient gel electrophoresis (TTGE) followed by cyclosequencing and RFLP was used to screen almost 90% of the mtDNA, including the control region (CR), for heteroplasmy in 62 children with CVS and neuromuscular disease (CVS+) and in 95 control subjects. One or two rare mtDNA-CR heteroplasmic sequence variants were found in six CVS+ and in zero control subjects (P = 0.003). These variants comprised 6 point and 2 length variants in hypervariable regions 1 and 2 (HV1 and HV2, both part of the mtDNA-CR), one half of which were clustered in the nt 16040-16188 segment of HV1 that includes the termination associated sequence (TAS), a functional location important in the regulation of mtDNA replication. Based upon our findings, sequencing and statistical analysis looking for homoplasmic nucleotide changes was performed in HV1 among 30 CVS+, 30 randomly-ascertained CVS (rCVS), 18 MA, 32 MO, and 35 control haplogroup H cases. Within the nt 16040-16188 segment, homoplasmic sequence variants were three-fold more common relative to control subjects in both CVS groups (P = 0.01 combined data) and in MO (P = 0.02), but not in MA (P = 0.5 vs. control subjects and 0.02 vs. MO). No group differences were noted in the remainder of HV1. We conclude that sequence variation in this small "peri-TAS" segment is associated with CVS and MO, but not MA. These variants

  1. Phylogenetic studies of two Anas platyrhynchos (Anatini: Anatinae) in Hunan province of China based on complete mitochondrial DNA sequences.

    PubMed

    He, Xi; Lin, Qian; Cao, Rong; Yuan, Ya-Ting; Pan, Di-Zi; Yun, Long; Zhang, Shi-Rui; Hou, De-Xing

    2016-07-01

    In this study, we cloned and sequenced the complete mitochondrial DNAs of Chinese duck, Anas platyrhynchos, population from two different areas of Hunan province in China. The Anas platyrhynchos breed Linwu duck (LW) sample was taken from the Linwu county of Chenzhou city, and the Anas platyrhynchos breed Youxian duck (YX) sample was taken from the Youxian county of Zhuzhou city. The lengths of their complete mitochondrial genome were 16,604 bp (LW) and 16,606 bp (YX), respectively. The organization of the two Anas platyrhynchos breed mitochondrial genomes was similar to those reported from other duck mitochondrial genomes. Phylogenetic analyses using N-J computational algorithms showed that the analyzed species are divided into four major clades: Anatinae, Anserinae, Dendrocygninae and Anseranatidae. Also, the Linwu duck and Youxian duck have highly similar phylogenetic relationship. PMID:26057008

  2. DNA sequence of the Xenopus laevis mitochondrial heavy and light strand replication origins and flanking tRNA genes.

    PubMed Central

    Wong, J F; Ma, D P; Wilson, R K; Roe, B A

    1983-01-01

    We have determined the primary structure of the two regions of the Xenopus laevis mitochondrial genome which encompass the origins of heavy (H) and light (L) strand replication. The first segment, which consists of 2398 nucleotides, contains the displacement loop (D-loop), the tRNA genes for threonine, proline and phenylalanine, the origin of H-strand replication, and the promoters of H- and L-strand transcription. The second segment, which consists of 447 nucleotides, contains the L-strand replication origin flanked by the tRNA genes for tryptophan, alanine, asparagine, cysteine, and tyrosine. A comparison of the sequences of the Xenopus laevis mitochondrial L-strand replication origin region and the eight tRNA genes with their counterparts from the mammalian mitochondrial genomes reveals that these regions are quite homologous, while its D-loop region shows only slight homology with those of the mammalian mitochondrial genomes. PMID:6308566

  3. The Complete Sequence of the Mitochondrial Genome of the Chamberednautilus (Mollusca: Cephalopoda)

    SciTech Connect

    Boore, Jeffrey L.

    2005-12-01

    Background: Mitochondria contain small genomes that arephysically separate from those of nuclei. Their comparison serves as amodel system for understanding the processes of genome evolution.Although complete mitochondrial genome sequences have been reported formore than 600 animals, the taxonomic sampling is highly biased towardvertebrates and arthropods, leaving much of the diversity yetuncharacterized. Results: The mitochondrial genome of a cephalopodmollusk, the Chambered Nautilus, is 16,258 nts in length and 59.5 percentA+T, both values that are typical of animal mitochondrial genomes. Itcontains the 37 genes that are typical for animal mtDNAs, with 15 on oneDNA strand and 22 on the other. The arrangement of these genes can bederived from that of the distantly related Katharina tunicata (Mollusca:Polyplacophora) by a switch in position of two large blocks of genes andtranspositions of four tRNA genes. There is strong skew in thedistribution of nucleotides between the two strands. There are an unusualnumber of non-coding regions and their function, if any, is not known;however, several of these demark abrupt shifts in nucleotide skew,suggesting that they may play roles in transcription and/or replication.One of the non-coding regions contains multiple repeats of a tRNA-likesequence. Some of the tRNA genes appear to overlap on the same strand,but this could be resolved if the polycistron were cleaved at thebeginning of the downstream gene, followed by polyadenylation of theproduct of the upstream gene to form a fully paired structure.Conclusions: Nautilus sp. mtDNA contains an expected gene content thathas experienced few rearrangements since the evolutionary split betweencephalopods and polyplacophorans. It contains an unusual number ofnon-coding regions, especially considering that these otherwise often aregenerated by the same processes that produce gene rearrangements. Thisappears to be yet another case where polyadenylation of mitochondrialtRNAs restores

  4. On the value of nuclear and mitochondrial gene sequences for reconstructing the phylogeny of vanilloid orchids (Vanilloideae, Orchidaceae)

    PubMed Central

    Cameron, Kenneth M.

    2009-01-01

    Background and Aims Most molecular phylogenetic studies of Orchidaceae have relied heavily on DNA sequences from the plastid genome. Nuclear and mitochondrial loci have only been superficially examined for their systematic value. Since 40% of the genera within Vanilloideae are achlorophyllous mycoheterotrophs, this is an ideal group of orchids in which to evaluate non-plastid gene sequences. Methods Phylogenetic reconstructions for Vanilloideae were produced using independent and combined data from the nuclear 18S, 5·8S and 26S rDNA genes and the mitochondrial atpA gene and nad1b-c intron. Key Results These new data indicate placements for genera such as Lecanorchis and Galeola, for which plastid gene sequences have been mostly unavailable. Nuclear and mitochondrial parsimony jackknife trees are congruent with each other and previously published trees based solely on plastid data. Because of high rates of sequence divergence among vanilloid orchids, even the short 5·8S rDNA gene provides impressive levels of resolution and support. Conclusions Orchid systematists are encouraged to sequence nuclear and mitochondrial gene regions along with the growing number of plastid loci available. PMID:19251715

  5. Characterization of the complete mitochondrial genome of Spirocerca lupi: sequence, gene organization and phylogenetic implications

    PubMed Central

    2013-01-01

    Background Spirocerca lupi is a life-threating parasitic nematode of dogs that has a cosmopolitan distribution but is most prevalent in tropical and subtropical countries. Despite its veterinary importance in canids, the epidemiology, molecular ecology and population genetics of this parasite still remain unexplored. Methods The complete mitochondrial (mt) genome of S. lupi was amplified in four overlapping long fragments using primers designed based on partial cox1, rrnS, cox2 and nad2 sequences. Phylogenetic re-construction of 13 spirurid species (including S. lupi) was carried out using Bayesian inference (BI) based on concatenated amino acid sequence datasets. Results The complete mt genome sequence of S. lupi is 13,780 bp in length, including 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lacks the atp8 gene. The gene arrangement is identical to that of Thelazia callipaeda (Thelaziidae) and Setaria digitata (Onchocercidae), but distinct from that of Dracunculus medinensis (Dracunculidae) and Heliconema longissimum (Physalopteridae). All genes are transcribed in the same direction and have a nucleotide composition high in A and T. The content of A + T is 73.73% for S. lupi, in accordance with mt genomes of other spirurid nematodes sequenced to date. Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes by BI showed that the S. lupi (Thelaziidae) is closely related to the families Setariidae and Onchocercidae. Conclusions The present study determined the complete mt genome sequence of S. lupi. These new mt genome dataset should provide novel mtDNA markers for studying the molecular epidemiology and population genetics of this parasite, and should have implications for the molecular diagnosis, prevention and control of spirocercosis in dogs and other canids. PMID:23433345

  6. Sequences homologous to yeast mitochondrial and bacteriophage T3 and T7 RNA polymerases are widespread throughout the eukaryotic lineage.

    PubMed Central

    Cermakian, N; Ikeda, T M; Cedergren, R; Gray, M W

    1996-01-01

    Although mitochondria and chloroplasts are considered to be descendants of eubacteria-like endo- symbionts, the mitochondrial RNA polymerase of yeast is a nucleus-encoded, single-subunit enzyme homologous to bacteriophage T3 and T7 RNA polymerases, rather than a multi-component, eubacterial-type alpha 2 beta beta' enzyme, as encoded in chloroplast DNA. To broaden our knowledge of the mitochondrial transcriptional apparatus, we have used a polymerase chain reaction (PCR) approach designed to amplify an internal portion of phage T3/T7-like RNA polymerase genes. Using this strategy, we have recovered sequences homologous to yeast mitochondrial and phage T3/T7 RNA polymerases from a phylogenetically broad range of multicellular and unicellular eukaryotes. These organisms display diverse patterns of mitochondrial genome organization and expression, and include species that separated from the main eukaryotic line early in the evolution of this lineage. In certain cases, we can deduce that PCR-amplified sequences, some of which contain small introns, are localized in nuclear DNA. We infer that the T3/T7-like RNA polymerase sequences reported here are likely derived from genes encoding the mitochondrial RNA polymerase in the organisms in which they occur, suggesting a phage T3/T7-like RNA polymerase was recruited to act in transcription in the mitochondrion at an early stage in the evolution of this organelle. PMID:8604305

  7. Complete mitochondrial genome of Cynopterus sphinx (Pteropodidae: Cynopterus).

    PubMed

    Li, Linmiao; Li, Min; Wu, Zhengjun; Chen, Jinping

    2015-01-01

    We have characterized the complete mitochondrial genome of Cynopterus sphinx (Pteropodidae: Cynopterus) and described its organization in this study. The total length of C. sphinx complete mitochondrial genome was 16,895 bp with the base composition of 32.54% A, 14.05% G, 25.82% T and 27.59% C. The complete mitochondrial genome included 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA) and 1 control region (D-loop). The control region was 1435 bp long with the sequence CATACG repeat 64 times. Three protein-coding genes (ND1, COI and ND4) were ended with incomplete stop codon TA or T. PMID:24409875

  8. The N-terminus of survivin is a mitochondrial-targeting sequence and Src regulator

    PubMed Central

    Dunajová, Lucia; Cash, Emily; Markus, Robert; Rochette, Sophie; Townley, Amelia R.

    2016-01-01

    ABSTRACT Survivin (also known as BIRC5) is a cancer-associated protein that exists in several locations in the cell. Its cytoplasmic residence in interphase cells is governed by CRM1 (also known as XPO1)-mediated nuclear exportation, and its localisation during mitosis to the centromeres and midzone microtubules is that of a canonical chromosomal passenger protein. In addition to these well-established locations, survivin is also a mitochondrial protein, but how it gets there and its function therein is presently unclear. Here, we show that the first ten amino acids at the N-terminus of survivin are sufficient to target GFP to the mitochondria in vivo, and ectopic expression of this decapeptide decreases cell adhesion and accelerates proliferation. The data support a signalling mechanism in which this decapeptide regulates the tyrosine kinase Src, leading to reduced focal adhesion plaques and disruption of F-actin organisation. This strongly suggests that the N-terminus of survivin is a mitochondrial-targeting sequence that regulates Src, and that survivin acts in concert with Src to promote tumorigenesis. PMID:27246243

  9. Sequence and organization of the complete mitochondrial genome of Hebius vibakari ruthveni from China.

    PubMed

    Xu, Chunzhu; Zhao, Shuai; Han, Xiaomin

    2016-07-01

    The mitochondrial genome sequence of Hebius vibakari ruthveni is analyzed and presented for the public for the first time. The genome was 17,259 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 control regions. The overall base composition is A (33.9%), C (26.5%), T (26.5%), and G (13.1%). Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 24 Colubridae species. It shows that two major phyletic lineages were present in Colubridae: Hebius and Thamnophis. Hebius comprised 16 species and was supported by bootstrap values of 99%. A clade (H. craspedogaster, H. metusium, H. johannis, H. bitaeniatum and H. octolineatum) as the sister taxon to another clade (H. parallelum, H. khasiense, H. Boulengeri and H. popei) was supported by bootstrap values of 66%. This clade with the H. Atemporale is the sister taxon to H. optatum, H. sauteri, and H. v. ruthveni. PMID:26029875

  10. The N-terminus of survivin is a mitochondrial-targeting sequence and Src regulator.

    PubMed

    Dunajová, Lucia; Cash, Emily; Markus, Robert; Rochette, Sophie; Townley, Amelia R; Wheatley, Sally P

    2016-07-15

    Survivin (also known as BIRC5) is a cancer-associated protein that exists in several locations in the cell. Its cytoplasmic residence in interphase cells is governed by CRM1 (also known as XPO1)-mediated nuclear exportation, and its localisation during mitosis to the centromeres and midzone microtubules is that of a canonical chromosomal passenger protein. In addition to these well-established locations, survivin is also a mitochondrial protein, but how it gets there and its function therein is presently unclear. Here, we show that the first ten amino acids at the N-terminus of survivin are sufficient to target GFP to the mitochondria in vivo, and ectopic expression of this decapeptide decreases cell adhesion and accelerates proliferation. The data support a signalling mechanism in which this decapeptide regulates the tyrosine kinase Src, leading to reduced focal adhesion plaques and disruption of F-actin organisation. This strongly suggests that the N-terminus of survivin is a mitochondrial-targeting sequence that regulates Src, and that survivin acts in concert with Src to promote tumorigenesis. PMID:27246243

  11. Phylogenetic relationships of land plants using mitochondrial small-subunit rDNA sequences.

    PubMed

    Duff, R J; Nickrent, D L

    1999-03-01

    Phylogenetic relationships among embryophytes (tracheophytes, mosses, liverworts, and hornworts) were examined using 21 newly generated mitochondrial small-subunit (19S) rDNA sequences. The "core" 19S rDNA contained more phylogenetically informative sites and lower homoplasy than either nuclear 18S or plastid 16S rDNA. Results of phylogenetic analyses using parsimony (MP) and likelihood (ML) were generally congruent. Using MP, two trees were obtained that resolved either liverworts or hornworts as the basal land plant clade. The optimal ML tree showed hornworts as basal. That topology was not statistically different from the two MP trees, thus both appear to be equally viable evolutionary hypotheses. High bootstrap support was obtained for the majority of higher level embryophyte clades named in a recent morphologically based classification, e.g., Tracheophyta, Euphyllophytina, Lycophytina, and Spermatophytata. Strong support was also obtained for the following monophyletic groups: hornworts, liverworts, mosses, lycopsids, leptosporangiate and eusporangiate ferns, gymnosperms and angiosperms. This molecular analysis supported a sister relationship between Equisetum and leptosporangiate ferns and a monophyletic gymnosperms sister to angiosperms. The topologies of deeper clades were affected by taxon inclusion (particularly hornworts) as demonstrated by jackknife analyses. This study represents the first use of mitochondrial 19S rDNA for phylogenetic purposes and it appears well-suited for examining intermediate to deep evolutionary relationships among embryophytes. PMID:10077500

  12. Origins of the Moken Sea Gypsies inferred from mitochondrial hypervariable region and whole genome sequences.

    PubMed

    Dancause, Kelsey Needham; Chan, Chim W; Arunotai, Narumon Hinshiranan; Lum, J Koji

    2009-02-01

    The origins of the Moken 'Sea Gypsies,' a group of traditionally boat-dwelling nomadic foragers, remain speculative despite previous examinations from linguistic, sociocultural and genetic perspectives. We explored Moken origin(s) and affinities by comparing whole mitochondrial genome and hypervariable segment I sequences from 12 Moken individuals, sampled from four islands of the Mergui Archipelago, to other mainland Asian, Island Southeast Asian (ISEA) and Oceanic populations. These analyses revealed a major (11/12) and a minor (1/12) haplotype in the population, indicating low mitochondrial diversity likely resulting from historically low population sizes, isolation and consequent genetic drift. Phylogenetic analyses revealed close relationships between the major lineage (MKN1) and ISEA, mainland Asian and aboriginal Malay populations, and of the minor lineage (MKN2) to populations from ISEA. MKN1 belongs to a recently defined subclade of the ancient yet localized M21 haplogroup. MKN2 is not closely related to any previously sampled lineages, but has been tentatively assigned to the basal M46 haplogroup that possibly originated among the original inhabitants of ISEA. Our analyses suggest that MKN1 originated within coastal mainland SEA and dispersed into ISEA and rapidly into the Mergui Archipelago within the past few thousand years as a result of climate change induced population pressure. PMID:19158811

  13. Sequencing and analysis of the complete mitochondrial genome of Elaphe davidi (Squamata: Colubridae).

    PubMed

    Xu, Chunzhu; Mu, Yanshuang; Kong, Qingran; Xie, Guilin; Guo, Zirong; Zhao, Shuai

    2016-07-01

    The mitochondrial genome sequence of Elaphe davidi is analyzed and presented for the first time in this work. The genome was 17,117 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 control region. The overall base composition is A (35.4%), C (25.2%), T (27.0%), and G (12.4%). The base compositions present clearly the A-T skew, which was most obviously in the control region and protein-coding genes. Mitochondrial genomes analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 12 Colubridae species. Two major phyletic lineages were present in Colubridae. A clade included the six species (Dinodon semicarinatus, E. poryphyracea, Oocatochus rufodorsatus, Orthriophis taeniurus, E. bimaculata and E. davidi) of subfamily Colubrinae except for Oligodon ningshaanensis. Another clade (Hypsiglena chlorophaea, H. unaocularus, H. torquata and Imantodes cenchoa) included Thermophis zhaoermii and O. ningshaanensis as the sister taxon to Colubrinae. The genus Elaphe, Dinodon, Oocatochus and Orthriophis formed a monophyletic group with the high bootstrap value (100 %) in all examinations. PMID:25806578

  14. Sequence and organization of the complete mitochondrial genome of the Ussuri mamushi (Gloydius ussuriensis).

    PubMed

    Han, Xiaomin; Zhao, Shuai; Xu, Chunzhu

    2016-07-01

    The mitochondrial genome sequence of Ussuri mamushi is analyzed and presented publically for the first time. The genome is 17,208 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 control regions. The overall base composition is A (32.4%), C (28.4%), T (26.3%) and G (12.9%). The base compositions clearly presented the A-C skew, which is the most obvious in the protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 13 Crotalinae species. It appeared that no less than two major phyletic lineages were present in Crotalinae. The main clades within the Crotalinae include Protobothrops. A clade (G. brevicaudus, G. ussuriensis, G. intermedius, and G. sahatilis) with the Ovophis as the sister taxon to Protobothrops was supported by bootstrap values of 88%. The four Gloydius species formed a paraphyletic group with the high bootstrap value (100%) in all examinations. PMID:26024132

  15. Arthropod Phylogenetics in Light of Three Novel Millipede (Myriapoda: Diplopoda) Mitochondrial Genomes with Comments on the Appropriateness of Mitochondrial Genome Sequence Data for Inferring Deep Level Relationships

    PubMed Central

    Brewer, Michael S.; Swafford, Lynn; Spruill, Chad L.; Bond, Jason E.

    2013-01-01

    Background Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. Results The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly). As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. Conclusions The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic signal renders the

  16. Mitochondrial genomes of two Sinochlora species (Orthoptera): novel genome rearrangements and recognition sequence of replication origin

    PubMed Central

    2013-01-01

    Background Orthoptera, the largest polyneopteran insect order, contains 2 suborders and 235 subfamilies. Orthoptera mitochondrial genomes (mitogenomes) follow the ancestral insect gene order, with the exception of a trnD-trnK rearrangement in Acridomorphs and rare tRNA inversions. A question still remains regarding whether a long thymine-nucleotide stretch (T-stretch) involved in the recognition of the replication origin exists in the control region (CR) of Orthoptera mitochondrial DNA (mtDNA). Herein, we completed the sequencing of whole mitogenomes of two congeners (Sinochlora longifissa and S. retrolateralis), which possess overlapping distribution areas. Additionally, we performed comparative mitogenomic analysis to depict evolutionary trends of Orthoptera mitogenomes. Results Both Sinochlora mitogenomes possess 37 genes and one CR, a common gene orientation, normal structures of transfer RNA and ribosomal RNA genes, rather low A+T bias, and significant C skew in the majority strand (J-strand), resembling all the other sequenced ensiferans. Both mitogenomes are characterized by (1) a large size resulting from multiple copies of an approximately 175 bp GC-rich tandem repeat within CR; (2) a novel gene order (rrnS-trnI-trnM-nad2-CR-trnQ-trnW), compared to the ancestral order (rrnS-CR-trnI-trnQ-trnM-nad2-trnW); and (3) redundant trnS(UCN) pseudogenes located between trnS(UCN) and nad1. Multiple independent duplication events followed by random and/or non-random loss occurred during Sinochlora mtDNA evolution. The Orthoptera mtDNA recognition sequence of the replication origin may be one of two kinds: a long T-stretch situated in or adjacent to a possible stem-loop structure or a variant of a long T-stretch located within a potential stem-loop structure. Conclusions The unique Sinochlora mitogenomes reveal that the mtDNA architecture within Orthoptera is more variable than previously thought, enriching our knowledge on mitogenomic genetic diversities. The novel

  17. Enabling dynamic interoperability with multiple community of interest (COI) systems

    NASA Astrophysics Data System (ADS)

    Armbruster, Austin; Martens, Eric J.; Corman, David E.

    2007-04-01

    A range of Community of Interest (COI) Infospheres and systems is being independently developed and deployed by separate elements of U. S. forces and potential coalition partners. Because future operations will increasingly rely on seamless exchange of information between coalition partners, it is critical that all tactical and command elements be able to dynamically interact with these diverse systems. Solving this issue requires that each network element (platform, commander, war-fighter, etc.) be able to span, dynamically join and leave different COI systems as operational requirements dictate. The COI Interoperability Agent (CIA) is the centerpiece of our solution. It will enable each battle space entity to join, interact with, and leave multiple COIs. Each CIA consists of a common core containing the Information Router, COI Initiator (COIN) factory, Platform Initiator (PIN) factory, and Security Manager Components along with one or more platform modules and COI modules. Bi-directional information flow is directed by the Information Router. The COIN enables dynamic connection to a COI. A COIN consists of two parts: 1) a Java Jar file containing the COI Module code establishing a COI connection and 2) a data component that configures the COI Module. The CIA uses the COIN factory to load and configure new COI Modules. The PIN factory fills a similar role for Platform Modules. The Platform Module contains code to link to a specific tactical entity. The CIA concept provides a path for the war-fighter to dynamically connect to multiple COIs without a priori knowledge of COIs that will be needed.

  18. Mitochondrial DNA population data of HV1 and HV2 sequences from Japanese individuals.

    PubMed

    Sekiguchi, Kazumasa; Imaizumi, Kazuhiko; Fujii, Koji; Mizuno, Natsuko; Ogawa, Yoshinori; Akutsu, Tomoko; Nakahara, Hiroaki; Kitayama, Tetsushi; Kasai, Kentaro

    2008-09-01

    Mitochondrial DNA sequences of the hypervariable regions HV1 and HV2 were determined for 1204 unrelated Japanese individuals. A total of 741 different mtDNA haplotypes were found, 157 of which were seen in multiple individuals. Twenty-seven of these individuals showed point heteroplasmy. The most frequent haplotype (16223T-16362C-73G-263G-315.1C) was found in 31 individuals and the second most frequent haplotypes (16129A-16223T- 16362C-73G-152C-263G-309.1C-315.1C) was found in 24 individuals. The haplotypes diversity and random match probability were calculated to be 0.9969 and 0.0040, respectively. PMID:18442943

  19. Sequencing and analysis of the complete mitochondrial genome of Elaphe anomala (Squamata Colubridae).

    PubMed

    Liu, Peng; Zhao, Wen-Ge

    2016-07-01

    In this study, the complete mitogenome sequence of Elaphe anomala (Squamata: Colubridae) is first determined using long PCR. It is a circular molecule of 17,164 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 2 control regions (CRI and CRII). The gene order and nucleotide composition of E. anomala are very similar with E. schrenckii. Mitochondrial genomes analyses based on the NJ method yield phylogenetic tree of 17 species snakes of Colubridae. Species E. anomala, E. schrenckii, E. bimaculata and E. davidi seemed to have formed a monophyletic group with the high bootstrap value (100%) except E. poryphyracea. Oligodon ningshaanensis and Thermophis zhaoermii are special species. The molecular data presented here provide a useful tool for setting the stage for further studies. PMID:26057014

  20. The complete sequence of mitochondrial genome of Siberian accentor (Prunella montanella).

    PubMed

    Yao, Jiyuan; Zhao, Xin; Li, Yumei; Li, Lingyu; Yan, Shouqing

    2016-09-01

    The Siberian accentor, Prunella montanella (Passeriformes, Prunellidae), is a small passerine bird. In this study, the complete mitochondrial genome sequence of Siberian accentor was determined. It has a total length of 16 832 bp, and contains 13 protein coding genes, 22 tRNA genes, two ribosome RNA genes, and one control region. The nucleotide composition is 30.1% for A, 31.0% for C, 15.0% for G and 23.9% for T, respectively. The overall GC content is lower than AT. The phylogenetic tree of Siberian accentor and 10 other species belonging to order Passeriformes was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of Siberian accentors. PMID:26226593

  1. Does behavior reflect phylogeny in swiftlets (Aves: Apodidae)? A test using cytochrome b mitochondrial DNA sequences.

    PubMed Central

    Lee, P L; Clayton, D H; Griffiths, R; Page, R D

    1996-01-01

    Swiftlets are small insectivorous birds, many of which nest in caves and are known to echolocate. Due to a lack of distinguishing morphological characters, the taxonomy of swiftlets is primarily based on the presence or absence of echolocating ability, together with nest characters. To test the reliability of these behavioral characters, we constructed an independent phylogeny using cytochrome b mitochondrial DNA sequences from swiftlets and their relatives. This phylogeny is broadly consistent with the higher classification of swifts but does not support the monophyly of swiftlets. Echolocating swiftlets (Aerodramus) and the nonecholocating "giant swiftlet" (Hydrochous gigas) group together, but the remaining nonecholocating swiftlets belonging to Collocalia are not sister taxa to these swiftlets. While echolocation may be a synapomorphy of Aerodramus (perhaps secondarily lost in Hydrochous), no character of Aerodramus nests showed a statistically significant fit to the molecular phylogeny, indicating that nest characters are not phylogenetically reliable in this group. Images Fig. 1 PMID:8692950

  2. Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

    USGS Publications Warehouse

    Dumbacher, J.P.; Pratt, T.K.; Fleischer, R.C.

    2003-01-01

    The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper. ?? 2003 Elsevier Science (USA). All rights reserved.

  3. Molecular phylogeny of the lemur family cheirogaleidae (primates) based on mitochondrial DNA sequences.

    PubMed

    Pastorini, J; Martin, R D; Ehresmann, P; Zimmermann, E; Forstner, M R

    2001-04-01

    Cheirogaleidae currently comprises five genera whose relationships remain contentious. The taxonomic status and phylogenetic position of both Mirza coquereli and Allocebus trichotis are still unclear. The taxonomic status of the recently discovered Microcebus ravelobensis (a sympatric sibling species of Microcebus murinus) and its phylogenetic position also require further examination. A approximately 2.4-kb mitochondrial DNA sequence including part of the COIII gene, complete ND3, ND4L, and ND4 genes, and 5 tRNAs was used to clarify relationships among cheirogaleids. Mirza and Microcebus form a clade representing the sister group of Allocebus, with a clade containing Cheirogaleus major and Cheirogaleus medius diverging first. M. ravelobensis and Microcebus rufus form a subclade within Microcebus, with M. murinus as its sister group. The molecular data support the generic status of Mirza coquereli and species-level divergence of M. ravelobensis. Furthermore, "M. rufus" may well represent more than one species. PMID:11286490

  4. A phylogeny of cockroaches and related insects based on DNA sequence of mitochondrial ribosomal RNA genes.

    PubMed Central

    Kambhampati, S

    1995-01-01

    Cockroaches are among the most ancient winged insects, the earliest fossils dating back to about 400 million years. Several conflicting phylogenies for cockroach families, subfamilies, and genera have been proposed in the past. In addition, the relationship of Cryptocercidae to other cockroach families and the relationship between the cockroach, Cryptocercus punctulatus, and the termite, Mastotermes darwiniensis, have generated debate. In this paper, a phylogeny for cockroaches, mantids, and termites based on DNA sequence of the mitochondrial ribosomal RNA genes is presented. The results indicated that cockroaches are a monophyletic group, whose sister group is Mantoidea. The inferred relationship among cockroach families was in agreement with the presently accepted phylogeny. However, there was only partial congruence at the subfamily and the generic levels. The phylogeny inferred here does not support a close relationship between C. punctulatus and M. darwiniensis. The apparent synapomorphies of these two species are likely a manifestation of convergent evolution because there are similarities in biology and habitat. PMID:7534409

  5. The complete mitochondrial genome sequence of Diptychus maculatus Steindachner (Cypriniformes: Cyprinidae).

    PubMed

    He, Dekui; Liang, Yangyang; Li, Chunhua; Wei, Chaojun; Chen, Yifeng

    2016-09-01

    Diptychus maculatus (Cypriniformes: Cyprinidae), the sole species of genus Diptychus, is an economically important freshwater fish widely distributed in Asia. In this study, we first sequenced the complete mitochondrial genome of D. maculatus. The genome is 16,835 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes as well as 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The gene composition and order are identical with most bony fishes. The overall nucleotide composition of the heavy strand is 27.7% A, 26.7% T, 26.5% C and 19.1% G. The mitogenome data would be useful for further genetics studies, phylogenetic analysis, and resource protection of D. maculatus and phylogenetic analysis of Schizothoracine fishes. PMID:25774947

  6. Complete mitochondrial genome sequence of Chestnut-flanked white-eye (Zosterops erythropleurus).

    PubMed

    Li, Yumei; Yao, Jiyuan; Zhao, Xin; Li, Lingyu; Yan, Shouqing

    2016-09-01

    The Chestnut-flanked white-eye (Zosterops erythropleurus) is a species of family Zosteropidae, which is distributed widely in the world. In the present study, the complete mitochondrial genome sequence of Chestnut-flanked white-eye was determined. It has a total length of 17 811 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions. The total base composition was 30.2% for A, 31.0% for C, 14.2% for G and 24.6% for T. The phylogenetic tree of Chestnut-flanked white-eye and 13 other species belonging to the order Passeriformes was built. The molecular data presented here will be useful to study the evolutionary relationships and genetic diversity of Chestnut-flanked white-eye. PMID:26260179

  7. Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores.

    PubMed

    Hoelzel, A R; Lopez, J V; Dover, G A; O'Brien, S J

    1994-08-01

    We describe a repetitive DNA region at the 3' end of the mitochondrial DNA (mtDNA) control region and compare it in 21 carnivore species representing eight carnivore families. The sequence and organization of the repetitive motifs can differ extensively between arrays; however, all motifs appear to be derived from the core motif "ACGT." Sequence data and Southern blot analysis demonstrate extensive heteroplasmy. The general form of the array is similar between heteroplasmic variants within an individual and between individuals within a species (varying primarily in the length of the array, though two clones from the northern elephant seal are exceptional). Within certain families, notably ursids, the array structure is also similar between species. Similarity between species was not apparent in other carnivore families, such as the mustelids, suggesting rapid changes in the organization and sequence of some arrays. The pattern of change seen within and between species suggests that a dominant mechanism involved in the evolution of these arrays is DNA slippage. A comparative analysis shows that the motifs that are being reiterated or deleted vary within and between arrays, suggesting a varying rate of DNA turnover. We discuss the evolutionary implications of the observed patterns of variation and extreme levels of heteroplasmy. PMID:7932782

  8. Application of mitochondrial genes sequences for measuring the genetic diversity of Arabian oryx.

    PubMed

    Khan, Haseeb A; Arif, Ibrahim A; Shobrak, Mohammad; Homaidan, Ali A Al; Farhan, Ahmad H Al; Sadoon, Mohammad Al

    2011-01-01

    Arabian oryx (Oryx leucoryx) had faced extinction in the wild more than three decades ago and was saved by the prudent efforts of captive breeding programs. A clear understanding of the molecular diversity of contemporary Arabian oryx population is important for the long term success of captive breeding and reintroduction of this potentially endangered species. We have sequenced the segments of mitochondrial DNA including12S rRNA, 16S rRNA, cytochrome b (Cyt-b) and control region (CR) genes of 24 captive-bred and reintroduced animals. Although the sequences of 12S rRNA, 16S rRNA and Cyt-b were found to be identical for all the samples, typical sequence variations in the CR gene were observed in the form of 7 haplotypes. One of these haplotypes has been reported earlier while the remaining 6 haplotypes are novel and represent different lineages from the founders. The haplotype and nucleotide diversities were found to be 0.789 and 0.009 respectively. The genetic distances among the 7 mtDNA haplotypes varied from 0.001 to 0.017. These findings are of potential relevance to the management of captive breeding programs for the conservation of Arabian oryx. PMID:21498924

  9. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing

    PubMed Central

    Weissensteiner, Hansi; Pacher, Dominic; Kloss-Brandstätter, Anita; Forer, Lukas; Specht, Günther; Bandelt, Hans-Jürgen; Kronenberg, Florian; Salas, Antonio; Schönherr, Sebastian

    2016-01-01

    Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth of the underlying phylogenetic tree summarizing the published mtDNA sequences, the manual process of haplogroup classification would be too time-consuming. The previously published classification tool HaploGrep provided an automatic way to address this issue. Here, we present the completely updated version HaploGrep 2 offering several advanced features, including a generic rule-based system for immediate quality control (QC). This allows detecting artificial recombinants and missing variants as well as annotating rare and phantom mutations. Furthermore, the handling of high-throughput data in form of VCF files is now directly supported. For data output, several graphical reports are generated in real time, such as a multiple sequence alignment format, a VCF format and extended haplogroup QC reports, all viewable directly within the application. In addition, HaploGrep 2 generates a publication-ready phylogenetic tree of all input samples encoded relative to the revised Cambridge Reference Sequence. Finally, new distance measures and optimizations of the algorithm increase accuracy and speed-up the application. HaploGrep 2 can be accessed freely and without any registration at http://haplogrep.uibk.ac.at. PMID:27084951

  10. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.

    PubMed

    Weissensteiner, Hansi; Pacher, Dominic; Kloss-Brandstätter, Anita; Forer, Lukas; Specht, Günther; Bandelt, Hans-Jürgen; Kronenberg, Florian; Salas, Antonio; Schönherr, Sebastian

    2016-07-01

    Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth of the underlying phylogenetic tree summarizing the published mtDNA sequences, the manual process of haplogroup classification would be too time-consuming. The previously published classification tool HaploGrep provided an automatic way to address this issue. Here, we present the completely updated version HaploGrep 2 offering several advanced features, including a generic rule-based system for immediate quality control (QC). This allows detecting artificial recombinants and missing variants as well as annotating rare and phantom mutations. Furthermore, the handling of high-throughput data in form of VCF files is now directly supported. For data output, several graphical reports are generated in real time, such as a multiple sequence alignment format, a VCF format and extended haplogroup QC reports, all viewable directly within the application. In addition, HaploGrep 2 generates a publication-ready phylogenetic tree of all input samples encoded relative to the revised Cambridge Reference Sequence. Finally, new distance measures and optimizations of the algorithm increase accuracy and speed-up the application. HaploGrep 2 can be accessed freely and without any registration at http://haplogrep.uibk.ac.at. PMID:27084951

  11. Mitochondrial DNA D-loop sequence variation in maternal lineages of Iranian native horses.

    PubMed

    Moridi, M; Masoudi, A A; Vaez Torshizi, R; Hill, E W

    2013-04-01

    To understand the origin and genetic diversity of Iranian native horses, mitochondrial DNA (mtDNA) D-loop sequences were generated for 95 horses from five breeds sampled in eight geographical locations in Iran. Sequence analysis of a 247-bp segment revealed a total of 27 haplotypes with 38 polymorphic sites. Twelve of 19 mtDNA haplogroups were identified in the samples. The most common haplotypes were found within haplogroup X2. Within-population haplotype and nucleotide diversities of the five breeds ranged from 0.838 ± 0.056 to 0.974 ± 0.022 and 0.011 ± 0.002 to 0.021 ± 0.001 respectively, indicating a relatively high genetic diversity in Iranian horses. The identification of several ancient sequences common between the breeds suggests that the lineage of the majority of Iranian horse breeds is old and obviously originated from a vast number of mares. We found in all native Iranian horse breeds lineages of the haplogroups D and K, which is concordant with the previous findings of Asian origins of these haplogroups. The presence of haplotypes E and K in our study also is consistent with a geographical west-east direction of increasing frequency of these haplotypes and a genetic fusion in Iranian horse breeds. PMID:22732008

  12. The complete mitochondrial genome sequence of the black-capped capuchin (Cebus apella).

    PubMed

    Bi, Xiao-Xin; Huang, Ling; Jing, Mei-Dong; Zhang, Li; Feng, Pei-Yong; Wang, Ai-Yun

    2012-04-01

    The phylogenetic relationships of primates have been extensively investigated, but key issues remain unresolved. Complete mitochondrial genome (mitogenome) data have many advantages in phylogenetic analyses, but such data are available for only 46 primate species. In this work, we determined the complete mitogenome sequence of the black-capped capuchin (Cebus apella). The genome was 16,538 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other primates. The control region contained several distinct repeat motifs, including a putative termination-associated sequence (TAS) and several conserved sequence blocks (CSB-F, E, D, C, B and 1). Among the protein-coding genes, the COII gene had lower nonsynonymous and synonymous substitutions rates while the ATP8 and ND4 genes had higher rates. A phylogenetic analysis using Maximum likelihood and Bayesian methods and the complete mitogenome data for platyrrhine species confirmed the basal position of the Callicebinae and the sister relationship between Atelinae and Cebidae, as well as the sister relationship between Aotinae (Aotus) and Cebinae (Cebus/Saimiri) in Cebidae. These conclusions agreed with the most recent molecular phylogenetic investigations on primates. This work provides a framework for the use of complete mitogenome information in phylogenetic analyses of the Platyrrhini and primates in general. PMID:22888306

  13. Selective neutrality of mitochondrial ND2 sequences, phylogeography and species limits in Sitta europaea.

    PubMed

    Zink, Robert M; Drovetski, Sergei V; Rohwer, Sievert

    2006-09-01

    Variation and geographic differentiation in mitochondrial DNA (mtDNA) was studied in the widespread and phenotypically variable Eurasian nuthatch (Sitta europaea). To assess whether sequences were evolving in a selectively neutral fashion, we used McDonald-Kreitman [Nature 351 (1991) 652] tests and a tree-based method, which suggested that although ND2 sequences are affected by natural selection against slightly deleterious alleles, the effects do not compromise phylogeographic inferences. Three phylogenetic species-level clades of nuthatches were discovered, corresponding to the Caucasus, southern Europe, and northern Europe plus Asia. Unimodal mismatch distributions within each clade suggest that populations have undergone recent growth. A westward range expansion was inferred from the geographic pattern in nucleotide diversity. Although samples were insufficient, it is possible that nuthatches in England and Japan are recently differentiated. Two specimens of the subspecies S. e. arctica formed a sister group to all other S. europaea, differing by ca. 10% uncorrected sequence divergence, pointing the need for additional study of this phenotypically distinct taxon. As with other species, mtDNA data support major phenotypic distinctions, but not subspecies. PMID:16716603

  14. Mitochondrial Cytochrome Oxidase I Gene Sequence Analysis of Aedes Albopictus in Malaysia.

    PubMed

    Ismail, Nurul-Ain; Dom, Nazri Che; Ismail, Rodziah; Ahmad, Abu Hassan; Zaki, Afiq; Camalxaman, Siti Nazrina

    2015-12-01

    A study was conducted to establish polymorphic variation of the mitochondrial DNA encoding the cytochrome oxidase subunit 1 (CO1) gene in Aedes albopictus isolated from 2 hot spot dengue-infested areas in the Subang Jaya District, Malaysia. A phylogenetic analysis was performed with the use of sequences obtained from USJ6 and Taman Subang Mas (TSM). Comparison of the local CO1 sequences with a laboratory strain (USM), alongside reference strains derived from the GenBank database revealed low genetic variation in terms of nucleotide differences and haplotype diversity. Four methods were used to construct a phylogenetic tree and illustrate the genetic relationship of the 37 Ae. albopictus populations based on the CO1 sequences, namely neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML), and Bayesian method, which revealed a distinct relationship between isolates from USJ6 and TSM. Our findings provide new information regarding the genetic diversity among morphologically similar Ae. albopictus, which has not been reported to date. PMID:26675451

  15. Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences.

    PubMed

    Lanave, C; Attimonelli, M; De Robertis, M; Licciulli, F; Liuni, S; Sbisá, E; Saccone, C

    1999-01-01

    The present paper describes AMmtDB, a database collecting the multi-aligned sequences of vertebrate mitochondrial genes coding for proteins and tRNAs, as well as the multiple alignment of the mammalian mtDNA main regulatory region (D-loop) sequences. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. As far as the genes coding for tRNAs are concerned, the multi-alignments based on the primary and the secondary structures are both provided; for the mammalian D-loop multi-alignments we report the conserved regions of the entire D-loop (CSB1, CSB2, CSB3, the central region, ETAS1 and ETAS2) as defined by Sbisà et al. [ Gene (1997), 205, 125-140). A flatfile format for AMmtDB has been designed allowing its implementation in SRS (http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB ). Data selected through SRS can be managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALV and PILEUP programs and then carefully optimized manually. PMID:9847158

  16. Mitochondrial DNA sequence analysis of four Alzheimer`s and Parkinson`s disease patients

    SciTech Connect

    Brown, M.D.; Shoffner, J.M.; Wallace, D.C.

    1996-01-22

    The mitochondrial DNA (mtDNA) sequence was determined on 3 patients with Alzheimer`s disease (AD) exhibiting AD plus Parkinson`s disease (PD) neuropathologic changes and one patient with PD. Patient mtDNA sequences were compared to the standard Cambridge sequence to identify base changes. In the first AD + PD patient, 2 of the 15 nucleotide substitutions may contribute to the neuropathology, a nucleotide pair (np) 4336 transition in the tRNA{sup Gln} gene found 7.4 times more frequently in patients than in controls, and a unique np 721 transition in the 12S rRNA gene which was not found in 70 other patients or 905 controls. In the second AD + PD patient, 27 nucleotide substitutions were detected, including an np 3397 transition in the ND1 gene which converts a conserved methionine to a valine. In the third AD + PD patient, 2 polymorphic base substitutions frequently found at increased frequency in Leber`s hereditary optic neuropathy patients were observed, an np 4216 transition in ND1 and an np 13708 transition in the ND5 gene. For the PD patient, 2 novel variants were observed among 25 base substitutions, an np 1709 substitution in the 16S rRNA gene and an np 15851 missense mutation in the cytb gene. Further studies will be required to demonstrate a casual role for these base substitutions in neurodegenerative disease. 68 refs., 2 tabs.

  17. Lack of geographic structure in mitochondrial DNA sequences of Bering Sea walleye pollock, Theragra chalcogramma.

    PubMed

    Shields, G F; Gust, J R

    1995-03-01

    We compared 511 nucleotides of mitochondrial DNA from 162 walleye pollock from 32 locations in the Bering Sea, the Shelikof Strait, and the Gulf of Alaska to learn about population structuring in this economically important species. Specifically, we tested for evidence of genetic heterogeneity among three sequence data sets: a 76-bp spacer, the control region, and spacers and control regions combined among six geographic regions: southwest Bering Sea, northern Bering Sea, western Aleutians, eastern Aleutians, the Donut Hole, and the Gulf of Alaska. No significant genetic heterogeneity was detected among spacer sequences or control regions, or spacers and control regions combined among areas of the Bering Sea. Slight genetic heterogeneity was detected when a "Western Bering" sample (southwest Bering and northern Bering) and an "Eastern Bering" sample (western Aleutians and eastern Aleutians) were compared. Presence of an abundant and widespread haplotype suggests recent establishment of the walleye pollock population in the Bering Sea. However, the ratio of nucleotide transitions to transversions in these pollock is extremely low, suggesting that the population may be old. Presence of a widespread and abundant haplotype, together with numerous rare ones, suggests a high variance in reproductive success for relatively few females, which may be disproportionately contributing to the survival of individual haplotypes. Sequencing of control regions in pollock may be less informative than conventional analysis of restriction fragment length polymorphisms or RFLP analysis of amplified variable sites. PMID:7749468

  18. Phylogenetic relationships of Indian caecilians (Amphibia: Gymnophiona) inferred from mitochondrial rRNA gene sequences.

    PubMed

    Wilkinson, Mark; A Sheps, Jonathan; Oommen, Oommen V; Cohen, Bernard L

    2002-06-01

    India has a diverse caecilian fauna, including representatives of three of the six currently recognized families, the Caeciliidae, Ichthyophiidae, the endemic Uraeotyphlidae, but previous molecular phylogenetic studies of caecilians have not included sequences for any Indian caecilians. Partial 12S and 16S mitochondrial gene sequences were obtained for a single representative of each of the caecilian families found in India and aligned against previously reported sequences for 13 caecilian species. The resulting alignment (16 taxa, 1200 sites, of which 288 cannot be aligned unambiguously) was analyzed using parsimony, maximum-likelihood, and distance methods. As judged by bootstrap proportions, decay indices, and leaf stabilities, well-supported relationships of the Indian caecilians are recovered from the alignment. The data (1) corroborate the hypothesis, based on morphology, that the Uraeotyphlidae and Ichthyophiidae are sister taxa, (2) recover a monophyletic Ichthyophiidae, including Indian and South East Asian representatives, and (3) place the Indian caeciliid Gegeneophis ramaswamii as the sister group of the caeciliid caecilians of the Seychelles. Rough estimates of divergence times suggest an origin of the Uraeotyphlidae and Ichthyophiidae while India was isolated from Laurasia and Africa and are most consistent with an Indian origin of these families and subsequent dispersal of ichthyophiids into South East Asia. PMID:12099794

  19. Heteroplasmy in the Mitochondrial Genomes of Human Lice and Ticks Revealed by High Throughput Sequencing

    PubMed Central

    Xiong, Haoyu; Barker, Stephen C.; Burger, Thomas D.; Raoult, Didier; Shao, Renfu

    2013-01-01

    The typical mitochondrial (mt) genomes of bilateral animals consist of 37 genes on a single circular chromosome. The mt genomes of the human body louse, Pediculus humanus, and the human head louse, Pediculus capitis, however, are extensively fragmented and contain 20 minichromosomes, with one to three genes on each minichromosome. Heteroplasmy, i.e. nucleotide polymorphisms in the mt genome within individuals, has been shown to be significantly higher in the mt cox1 gene of human lice than in humans and other animals that have the typical mt genomes. To understand whether the extent of heteroplasmy in human lice is associated with mt genome fragmentation, we sequenced the entire coding regions of all of the mt minichromosomes of six human body lice and six human head lice from Ethiopia, China and France with an Illumina HiSeq platform. For comparison, we also sequenced the entire coding regions of the mt genomes of seven species of ticks, which have the typical mitochondrial genome organization of bilateral animals. We found that the level of heteroplasmy varies significantly both among the human lice and among the ticks. The human lice from Ethiopia have significantly higher level of heteroplasmy than those from China and France (Pt<0.05). The tick, Amblyomma cajennense, has significantly higher level of heteroplasmy than other ticks (Pt<0.05). Our results indicate that heteroplasmy level can be substantially variable within a species and among closely related species, and does not appear to be determined by single factors such as genome fragmentation. PMID:24058467

  20. Heteroplasmy in the mitochondrial genomes of human lice and ticks revealed by high throughput sequencing.

    PubMed

    Xiong, Haoyu; Barker, Stephen C; Burger, Thomas D; Raoult, Didier; Shao, Renfu

    2013-01-01

    The typical mitochondrial (mt) genomes of bilateral animals consist of 37 genes on a single circular chromosome. The mt genomes of the human body louse, Pediculus humanus, and the human head louse, Pediculus capitis, however, are extensively fragmented and contain 20 minichromosomes, with one to three genes on each minichromosome. Heteroplasmy, i.e. nucleotide polymorphisms in the mt genome within individuals, has been shown to be significantly higher in the mt cox1 gene of human lice than in humans and other animals that have the typical mt genomes. To understand whether the extent of heteroplasmy in human lice is associated with mt genome fragmentation, we sequenced the entire coding regions of all of the mt minichromosomes of six human body lice and six human head lice from Ethiopia, China and France with an Illumina HiSeq platform. For comparison, we also sequenced the entire coding regions of the mt genomes of seven species of ticks, which have the typical mitochondrial genome organization of bilateral animals. We found that the level of heteroplasmy varies significantly both among the human lice and among the ticks. The human lice from Ethiopia have significantly higher level of heteroplasmy than those from China and France (Pt<0.05). The tick, Amblyomma cajennense, has significantly higher level of heteroplasmy than other ticks (Pt<0.05). Our results indicate that heteroplasmy level can be substantially variable within a species and among closely related species, and does not appear to be determined by single factors such as genome fragmentation. PMID:24058467

  1. The Complete Sequence of the Mitochondrial Genome of Butomus umbellatus – A Member of an Early Branching Lineage of Monocotyledons

    PubMed Central

    Cuenca, Argelia; Petersen, Gitte; Seberg, Ole

    2013-01-01

    In order to study the evolution of mitochondrial genomes in the early branching lineages of the monocotyledons, i.e., the Acorales and Alismatales, we are sequencing complete genomes from a suite of key taxa. As a starting point the present paper describes the mitochondrial genome of Butomus umbellatus (Butomaceae) based on next-generation sequencing data. The genome was assembled into a circular molecule, 450,826 bp in length. Coding sequences cover only 8.2% of the genome and include 28 protein coding genes, four rRNA genes, and 12 tRNA genes. Some of the tRNA genes and a 16S rRNA gene are transferred from the plastid genome. However, the total amount of recognized plastid sequences in the mitochondrial genome is only 1.5% and the amount of DNA transferred from the nucleus is also low. RNA editing is abundant and a total of 557 edited sites are predicted in the protein coding genes. Compared to the 40 angiosperm mitochondrial genomes sequenced to date, the GC content of the Butomus genome is uniquely high (49.1%). The overall similarity between the mitochondrial genomes of Butomus and Spirodela (Araceae), the closest relative yet sequenced, is low (less than 20%), and the two genomes differ in size by a factor 2. Gene order is also largely unconserved. However, based on its phylogenetic position within the core alismatids Butomus will serve as a good reference point for subsequent studies in the early branching lineages of the monocotyledons. PMID:23637852

  2. Mitochondrial DNA hypervariable region-1 sequence variation and phylogeny of the concolor gibbons, Nomascus.

    PubMed

    Monda, Keri; Simmons, Rachel E; Kressirer, Philipp; Su, Bing; Woodruff, David S

    2007-11-01

    The still little known concolor gibbons are represented by 14 taxa (five species, nine subspecies) distributed parapatrically in China, Myanmar, Vietnam, Laos and Cambodia. To set the stage for a phylogeographic study of the genus we examined DNA sequences from the highly variable mitochondrial hypervariable region-1 (HVR-1 or control region) in 51 animals, mostly of unknown geographic provenance. We developed gibbon-specific primers to amplify mtDNA noninvasively and obtained >477 bp sequences from 38 gibbons in North American and European zoos and >159 bp sequences from ten Chinese museum skins. In hindsight, we believe these animals represent eight of the nine nominal subspecies and four of the five nominal species. Bayesian, maximum likelihood and maximum parsimony haplotype network analyses gave concordant results and show Nomascus to be monophyletic. Significant intraspecific variation within N. leucogenys (17 haplotypes) is comparable with that reported earlier in Hylobates lar and less than half the known interspecific pairwise distances in gibbons. Sequence data support the recognition of five species (concolor, leucogenys, nasutus, gabriellae and probably hainanus) and suggest that nasutus is the oldest and leucogenys, the youngest taxon. In contrast, the subspecies N. c. furvogaster, N. c. jingdongensis, and N. leucogenys siki, are not recognizable at this otherwise informative genetic locus. These results show that HVR-1 sequence is variable enough to define evolutionarily significant units in Nomascus and, if coupled with multilocus microsatellite or SNP genotyping, more than adequate to characterize their phylogeographic history. There is an urgent need to obtain DNA from gibbons of known geographic provenance before they are extirpated to facilitate the conservation genetic management of the surviving animals. PMID:17455231

  3. The Complete Mitochondrial Genome Sequence of Bactericera cockerelli and Comparison with Three Other Psylloidea Species

    PubMed Central

    Wu, Fengnian; Cen, Yijing; Wallis, Christopher M.; Trumble, John T.; Prager, Sean; Yokomi, Ray; Zheng, Zheng; Deng, Xiaoling; Chen, Jianchi; Liang, Guangwen

    2016-01-01

    Potato psyllid (Bactericera cockerelli) is an important pest of potato, tomato and pepper. Not only could a toxin secreted by nymphs results in serious phytotoxemia in some host plants, but also over the past few years B. cockerelli was shown to transmit “Candidatus Liberibacter solanacearum”, the putative bacterial pathogen of potato zebra chip (ZC) disease, to potato and tomato. ZC has caused devastating losses to potato production in the western U.S., Mexico, and elsewhere. New knowledge of the genetic diversity of the B. cockerelli is needed to develop improved strategies to manage pest populations. Mitochondrial genome (mitogenome) sequencing provides important knowledge about insect evolution and diversity in and among populations. This report provides the first complete B. cockerelli mitogenome sequence as determined by next generation sequencing technology (Illumina MiSeq). The circular B. cockerelli mitogenome had a size of 15,220 bp with 13 protein-coding gene (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a non-coding region of 975 bp. The overall gene order of the B. cockerelli mitogenome is identical to three other published Psylloidea mitogenomes: one species from the Triozidae, Paratrioza sinica; and two species from the Psyllidae, Cacopsylla coccinea and Pachypsylla venusta. This suggests all of these species share a common ancestral mitogenome. However, sequence analyses revealed differences between and among the insect families, in particular a unique region that can be folded into three stem-loop secondary structures present only within the B. cockerelli mitogenome. A phylogenetic tree based on the 13 PCGs matched an existing taxonomy scheme that was based on morphological characteristics. The available complete mitogenome sequence makes it accessible to all genes for future population diversity evaluation of B. cockerelli. PMID:27227976

  4. The Complete Mitochondrial Genome Sequence of Bactericera cockerelli and Comparison with Three Other Psylloidea Species.

    PubMed

    Wu, Fengnian; Cen, Yijing; Wallis, Christopher M; Trumble, John T; Prager, Sean; Yokomi, Ray; Zheng, Zheng; Deng, Xiaoling; Chen, Jianchi; Liang, Guangwen

    2016-01-01

    Potato psyllid (Bactericera cockerelli) is an important pest of potato, tomato and pepper. Not only could a toxin secreted by nymphs results in serious phytotoxemia in some host plants, but also over the past few years B. cockerelli was shown to transmit "Candidatus Liberibacter solanacearum", the putative bacterial pathogen of potato zebra chip (ZC) disease, to potato and tomato. ZC has caused devastating losses to potato production in the western U.S., Mexico, and elsewhere. New knowledge of the genetic diversity of the B. cockerelli is needed to develop improved strategies to manage pest populations. Mitochondrial genome (mitogenome) sequencing provides important knowledge about insect evolution and diversity in and among populations. This report provides the first complete B. cockerelli mitogenome sequence as determined by next generation sequencing technology (Illumina MiSeq). The circular B. cockerelli mitogenome had a size of 15,220 bp with 13 protein-coding gene (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a non-coding region of 975 bp. The overall gene order of the B. cockerelli mitogenome is identical to three other published Psylloidea mitogenomes: one species from the Triozidae, Paratrioza sinica; and two species from the Psyllidae, Cacopsylla coccinea and Pachypsylla venusta. This suggests all of these species share a common ancestral mitogenome. However, sequence analyses revealed differences between and among the insect families, in particular a unique region that can be folded into three stem-loop secondary structures present only within the B. cockerelli mitogenome. A phylogenetic tree based on the 13 PCGs matched an existing taxonomy scheme that was based on morphological characteristics. The available complete mitogenome sequence makes it accessible to all genes for future population diversity evaluation of B. cockerelli. PMID:27227976

  5. Complete Mitochondrial DNA Sequence of the Mucoralean Fungus Absidia glauca, a Model for Studying Host-Parasite Interactions

    PubMed Central

    Ellenberger, Sabrina; Burmester, Anke

    2016-01-01

    The mitochondrial DNA (mtDNA) of Absidia glauca has been completely sequenced. It is 63,080 bp long, has a G+C content of 28%, and contains the standard fungal gene set. A. glauca is the recipient in a laboratory model for horizontal gene transfer with Parasitella parasitica as a donor of nuclei and mitochondria. PMID:27013042

  6. Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The mitochondrial (mt) genomes of two soybean rust pathogens, Phakopsora pachyrhizi and P. meibomiae, have been sequenced. The mt genome of P. pachyrhizi is a circular 31,825-bp molecule with a mean GC content of 34.6 percent, while P. meibomiae possesses a 32,520-bp circular molecule with a mean G...

  7. Full Mitochondrial Genome Sequence of the Sugar Beet Wireworm Limonius californicus (Coleoptera: Elateridae), a Common Agricultural Pest

    PubMed Central

    New, Daniel D.; Robison, Barrie D.; Rashed, Arash; Hohenlohe, Paul; Forney, Larry; Rashidi, Mahnaz; Wilson, Cathy M.; Settles, Matthew L.

    2016-01-01

    We report here the full mitochondrial genome sequence of Limonius californicus, a species of click beetle that is an agricultural pest in its larval form. The circular genome is 16.5 kb and contains 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. PMID:26798113

  8. Partial mitochondrial DNA sequences suggest the existence of a cryptic species within the Leucosphyrus group of the genus Anopheles (Diptera: Culicidae), forest malaria vectors, in northern Vietnam

    PubMed Central

    2010-01-01

    Background During the last decade, Southeast Asian countries have been very successful in reducing the burden of malaria. However, malaria remains endemic in these countries, especially in remote and forested areas. The Leucosphyrus group of the genus Anopheles harbors the most important malaria vectors in forested areas of Southeast Asia. In Vietnam, previous molecular studies have resulted in the identification of only Anopheles dirus sensu stricto (previously known as An. dirus species A) among the Leucosphyrus group members. However, Vietnamese entomologists have recognized that mosquitoes belonging to the Leucosphyrus group in northern Vietnam exhibit morphological characteristics similar to those of Anopheles takasagoensis, which has been reported only from Taiwan. Here, we aimed to confirm the genetic and morphological identities of the members of the Leucosphyrus group in Vietnam. Results In the molecular phylogenetic trees reconstructed using partial COI and ND6 mitochondrial gene sequences, samples collected from southern and central Vietnam clustered together with GenBank sequences of An. dirus that were obtained from Thailand. However, samples from northern Vietnam formed a distinct clade separated from both An. dirus and An. takasagoensis by other valid species. Conclusions The results suggest the existence of a cryptic species in northern Vietnam that is morphologically similar to, but phylogenetically distant from both An. dirus and An. takasagoensis. We have tentatively designated this possible cryptic species as Anopheles aff. takasagoensis for convenience, until a valid name is assigned. However, it is difficult to distinguish the species solely on the basis of morphological characteristics. Further studies on such as karyotypes and polytene chromosome banding patterns are necessary to confirm whether An. aff. takasagoensis is a valid species. Moreover, studies on (1) the geographic distribution, which is potentially spreading along the Vietnam

  9. Complete mitochondrial genome sequences for Crown-of-thorns starfish Acanthaster planci and Acanthaster brevispinus

    PubMed Central

    Yasuda, Nina; Hamaguchi, Masami; Sasaki, Miho; Nagai, Satoshi; Saba, Masaki; Nadaoka, Kazuo

    2006-01-01

    Background The crown-of-thorns starfish, Acanthaster planci (L.), has been blamed for coral mortality in a large number of coral reef systems situated in the Indo-Pacific region. Because of its high fecundity and the long duration of the pelagic larval stage, the mechanism of outbreaks may be related to its meta-population dynamics, which should be examined by larval sampling and population genetic analysis. However, A. planci larvae have undistinguished morphological features compared with other asteroid larvae, hence it has been difficult to discriminate A. planci larvae in plankton samples without species-specific markers. Also, no tools are available to reveal the dispersal pathway of A. planci larvae. Therefore the development of highly polymorphic genetic markers has the potential to overcome these difficulties. To obtain genomic information for these purposes, the complete nucleotide sequences of the mitochondrial genome of A. planci and its putative sibling species, A. brevispinus were determined and their characteristics discussed. Results The complete mtDNA of A. planci and A. brevispinus are 16,234 bp and 16,254 bp in size, respectively. These values fall within the length variation range reported for other metazoan mitochondrial genomes. They contain 13 proteins, 2 rRNA, and 22 tRNA genes and the putative control region in the same order as the asteroid, Asterina pectinifera. The A + T contents of A. planci and A. brevispinus on their L strands that encode the majority of protein-coding genes are 56.3% and 56.4% respectively and are lower than that of A. pectinifera (61.2%). The percent similarity of nucleotide sequences between A. planci and A. brevispinus is found to be highest in the CO2 and CO3 regions (both 90.6%) and lowest in ND2 gene (84.2%) among the 13 protein-coding genes. In the deduced putative amino acid sequences, CO1 is highly conserved (99.2%), and ATP8 apparently evolves faster any of the other protein-coding gene (85.2%). Conclusion

  10. Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach.

    PubMed

    Kocher, Arthur; Guilbert, Éric; Lhuillier, Émeline; Murienne, Jerôme

    2015-03-01

    Lace bugs (Tingidae) are a family of phytophagous heteropterans, some of which are important agricultural and forestry pests. They currently comprise around 2500 species distributed worldwide, for which only one mitochondrial genome has been described so far. We sequenced the complete mitochondrial genome and the nuclear ribosomal gene segment of the avocado lace bug Pseudacysta perseae using a genome skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including the one of the sycamore lace bug Corythucha ciliata, were retrieved to allow for comparisons and phylogenetic analyses. P. perseae mitochondrial genome was determined to be 15,850 bp long, and presented the typical organisation of insect mitogenomes. The phylogenetic analysis placed P. perseae as a sister to C. ciliata but did not confirm the monophyly of Miroidae including Tingidae. Our results contradicted widely accepted phylogenetic hypothesis, which highlights the limits of analyses based on mitochondrial data only. Shotgun sequencing approaches should provide substantial improvements in harmonizing mitochondrial and nuclear databases. PMID:25636225

  11. High-altitude adaptation of Tibetan chicken from MT-COI and ATP-6 perspective.

    PubMed

    Zhao, Xiaoling; Wu, Nan; Zhu, Qing; Gaur, Uma; Gu, Ting; Li, Diyan

    2016-09-01

    The problem of hypoxia adaptation in high altitudes is an unsolved brainteaser in the field of life sciences. As one of the best chicken breeds with adaptability to highland environment, the Tibetan chicken, is genetically different from lowland chicken breeds. In order to gain a better understanding of the mechanism of hypoxic adaptability in high altitude, in the present study, we focused on the MT-COI together with ATP-6 gene to explore the regulatory mechanisms for hypoxia adaptability in Tibet chicken. Here, we sequenced MT-COI of 29 Tibetan chickens and 30 Chinese domestic chickens and ATP-6 gene of 28 Tibetan chickens and 29 Chinese domestic chickens. In MT-COI gene, 9 single nucleotide polymorphisms (SNPs) were detected though none of these was a missense mutation, confirming the fact that MT-COI gene is a largely conservative sequence. In ATP-6 gene, 6 single nucleotide polymorphisms (SNPs) were detected and we found a missense mutation (m.9441G > A) in the ATP-6 gene of Tibetan chicken resulting in an amino acid substitution. Due to the critical role of ATP-6 gene in the proton translocation and energy metabolism, we speculated the possibility of this mutation playing an important role in easier energy conversion and metabolism in Tibetan chickens than Chinese domestic chickens so as to better adapt to the harsh environment of the high-altitude areas. The Median-joining profile also suggested that haplotype Ha2 has the ancestral position to the other haplotypes and has significant relationship with high-altitude adaptation in ATP-6 gene. Therefore, we considered that the polymorphism (m.9441G > A) in the ATP-6 gene may affect the specific functions of ATP-6 enzyme relating to high-altitude adaptation of Tibetan chicken and MT-COI gene is a largely conservative sequence. PMID:25693693

  12. Complete Mitochondrial DNA Sequences of the Threadfin Cichlid (Petrochromis trewavasae) and the Blunthead Cichlid (Tropheus moorii) and Patterns of Mitochondrial Genome Evolution in Cichlid Fishes

    PubMed Central

    Fischer, Christoph; Koblmüller, Stephan; Gülly, Christian; Schlötterer, Christian; Sturmbauer, Christian; Thallinger, Gerhard G.

    2013-01-01

    The cichlid fishes of the East African Great Lakes represent a model especially suited to study adaptive radiation and speciation. With several African cichlid genome projects being in progress, a promising set of closely related genomes is emerging, which is expected to serve as a valuable data base to solve questions on genotype-phenotype relations. The mitochondrial (mt) genomes presented here are the first results of the assembly and annotation process for two closely related but eco-morphologically highly distinct Lake Tanganyika cichlids, Petrochromis trewavasae and Tropheus moorii. The genomic sequences comprise 16,588 bp (P. trewavasae) and 16,590 bp (T. moorii), and exhibit the typical mitochondrial structure, with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region. Analyses confirmed that the two species are very closely related with an overall sequence similarity of 96%. We analyzed the newly generated sequences in the phylogenetic context of 21 published labroid fish mitochondrial genomes. Consistent with other vertebrates, the D-loop region was found to evolve faster than protein-coding genes, which in turn are followed by the rRNAs; the tRNAs vary greatly in the rate of sequence evolution, but on average evolve the slowest. Within the group of coding genes, ND6 evolves most rapidly. Codon usage is similar among examined cichlid tribes and labroid families; although a slight shift in usage patterns down the gene tree could be observed. Despite having a clearly different nucleotide composition, ND6 showed a similar codon usage. C-terminal ends of Cox1 exhibit variations, where the varying number of amino acids is related to the structure of the obtained phylogenetic tree. This variation may be of functional relevance for Cox1 synthesis. PMID:23826193

  13. Mitochondrial gene sequences and the molecular systematics of the artiodactyl subfamily bovinae.

    PubMed

    Janecek, L L; Honeycutt, R L; Adkins, R M; Davis, S K

    1996-08-01

    Nucleotide sequence evolution of the mitochondrial cytochrome c oxidase subunit II (COII) gene was used to examine the molecular phylogenetics and evolution of the Bovinae, a subfamily within the mammalian order Artiodactyla. The COII gene was sequenced in representatives of three bovine tribes (Bovini, Boselaphini, and Tragelaphini) and the outgroup taxon Capra (subfamily Caprinae). Although the phylogenetic analyses grouped Bison as sister to Bos, the genus Bison was paraphyletic, with the American bison being most closely related to species of Bos rather than to the European bison. COII data also supported a close relationship between African (Syncerus) and Asian (bubalus) buffaloes, the monophyly of the tribe Bovini, and a sister-group relationship between the tribes Bovini and Boselaphini. Analysis of nucleotide substitutions in the COII gene prompted a system of differential weighting of nucleotide substitutions for inferring phylogenetic relationships across the range of divergence times examined here (2-20 million years). Rates of evolution in the COII gene are examined and compared to evolutionary rates in mtDNA tRNA/rRNA genes and the D-loop among other artiodactyl taxa. PMID:8812311

  14. Mitochondrial sequence variation in ancient horses from the Carpathian Basin and possible modern relatives.

    PubMed

    Priskin, K; Szabó, K; Tömöry, G; Bogácsi-Szabó, E; Csányi, B; Eördögh, R; Downes, C S; Raskó, I

    2010-02-01

    Movements of human populations leave their traces in the genetic makeup of the areas affected; the same applies to the horses that move with their owners This study is concerned with the mitochondrial control region genotypes of 31 archaeological horse remains, excavated from pre-conquest Avar and post-conquest Hungarian burial sites in the Carpathian Basin dating from the sixth to the tenth century. To investigate relationships to other ancient and recent breeds, modern Hucul and Akhal Teke samples were also collected, and mtDNA control region (CR) sequences from 76 breeds representing 921 individual specimens were combined with our sequence data. Phylogenetic relationships among horse mtDNA CR haplotypes were estimated using both genetic distance and the non-dichotomous network method. Both methods indicated a separation between horses of the Avars and the Hungarians. Our results show that the ethnic changes induced by the Hungarian Conquest were accompanied by a corresponding change in the stables of the Carpathian Basin. PMID:19789983

  15. Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins

    PubMed Central

    Adcock, Gregory J.; Dennis, Elizabeth S.; Easteal, Simon; Huttley, Gavin A.; Jermiin, Lars S.; Peacock, W. James; Thorne, Alan

    2001-01-01

    DNA from ancient human remains provides perspectives on the origin of our species and the relationship between molecular and morphological variation. We report analysis of mtDNA from the remains of 10 ancient Australians. These include the morphologically gracile Lake Mungo 3 [≈60 thousand years (ka) before present] and three other gracile individuals from Holocene deposits at Willandra Lakes (<10 ka), all within the skeletal range of living Australians, and six Pleistocene/early Holocene individuals (15 to <8 ka) from Kow Swamp with robust morphologies outside the skeletal range of contemporary indigenous Australians. Lake Mungo 3 is the oldest (Pleistocene) “anatomically modern” human from whom DNA has been recovered. His mtDNA belonged to a lineage that only survives as a segment inserted into chromosome 11 of the nuclear genome, which is now widespread among human populations. This lineage probably diverged before the most recent common ancestor of contemporary human mitochondrial genomes. This timing of divergence implies that the deepest known mtDNA lineage from an anatomically modern human occurred in Australia; analysis restricted to living humans places the deepest branches in East Africa. The other ancient Australian individuals we examined have mtDNA sequences descended from the most recent common ancestor of living humans. Our results indicate that anatomically modern humans were present in Australia before the complete fixation of the mtDNA lineage now found in all living people. Sequences from additional ancient humans may further challenge current concepts of modern human origins. PMID:11209053

  16. Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs.

    PubMed Central

    Horai, S; Hayasaka, K; Kondo, R; Tsugane, K; Takahata, N

    1995-01-01

    We analyzed the complete mitochondrial DNA (mtDNA) sequences of three humans (African, European, and Japanese), three African apes (common and pygmy chimpanzees, and gorilla), and one orangutan in an attempt to estimate most accurately the substitution rates and divergence times of hominoid mtDNAs. Nonsynonymous substitutions and substitutions in RNA genes have accumulated with an approximately clock-like regularity. From these substitutions and under the assumption that the orangutan and African apes diverged 13 million years ago, we obtained a divergence time for humans and chimpanzees of 4.9 million years. This divergence time permitted calibration of the synonymous substitution rate (3.89 x 10(-8)/site per year). To obtain the substitution rate in the displacement (D)-loop region, we compared the three human mtDNAs and measured the relative abundance of substitutions in the D-loop region and at synonymous sites. The estimated substitution rate in the D-loop region was 7.00 x 10(-8)/site per year. Using both synonymous and D-loop substitutions, we inferred the age of the last common ancestor of the human mtDNAs as 143,000 +/- 18,000 years. The shallow ancestry of human mtDNAs, together with the observation that the African sequence is the most diverged among humans, strongly supports the recent African origin of modern humans, Homo sapiens sapiens. PMID:7530363

  17. Sequencing and characterization of the complete mitochondrial genome from the pancreatic fluke Eurytrema pancreaticum (Trematoda: Dicrocoeliidae).

    PubMed

    Chang, Qiao-Cheng; Liu, Guo-Hua; Gao, Jun-Feng; Zheng, Xu; Zhang, Yan; Duan, Hong; Yue, Dong-Mei; Fu, Xue; Su, Xin; Gao, Yuan; Wang, Chun-Ren

    2016-01-15

    The trematode Eurytrema pancreaticum is a parasite of ruminant pancreatic and bile ducts, and also occasionally infects humans, causing eurytremiasis. In spite of it being a common fluke of cattle and sheep in endemic regions, little is known about the genomic resources of the parasite. We sequenced the complete mitochondrial (mt) genome of E. pancreaticum. It is 15,031 bp in size, and encodes 36 genes: 12 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The E. pancreaticum mt gene order is the same as that of Dicrocoelium chinensis and Dicrocoelium dendriticum, and all genes are transcribed in the same direction. Phylogenetic analysis based on the concatenated amino acid sequences of 12 protein-coding genes by Bayesian inference shows that E. pancreaticum is closely related to D. chinensis and other members of the family Dicrocoeliidae with strong posterior probability support. The E. pancreaticum mt genome should prove to be a useful resource for comparative mt genomic studies of digenetic trematodes, and will provide a rich source of DNA markers for studies into the systematics, epidemiology, and population genetics of this parasite and other digenean trematodes. PMID:26434796

  18. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences

    PubMed Central

    Li, Hu; Shao, Renfu; Song, Nan; Song, Fan; Jiang, Pei; Li, Zhihong; Cai, Wanzhi

    2015-01-01

    Mitochondrial (mt) genome data have been proven to be informative for animal phylogenetic studies but may also suffer from systematic errors, due to the effects of accelerated substitution rate and compositional heterogeneity. We analyzed the mt genomes of 25 insect species from the four paraneopteran orders, aiming to better understand how accelerated substitution rate and compositional heterogeneity affect the inferences of the higher-level phylogeny of this diverse group of hemimetabolous insects. We found substantial heterogeneity in base composition and contrasting rates in nucleotide substitution among these paraneopteran insects, which complicate the inference of higher-level phylogeny. The phylogenies inferred with concatenated sequences of mt genes using maximum likelihood and Bayesian methods and homogeneous models failed to recover Psocodea and Hemiptera as monophyletic groups but grouped, instead, the taxa that had accelerated substitution rates together, including Sternorrhyncha (a suborder of Hemiptera), Thysanoptera, Phthiraptera and Liposcelididae (a family of Psocoptera). Bayesian inference with nucleotide sequences and heterogeneous models (CAT and CAT + GTR), however, recovered Psocodea, Thysanoptera and Hemiptera each as a monophyletic group. Within Psocodea, Liposcelididae is more closely related to Phthiraptera than to other species of Psocoptera. Furthermore, Thysanoptera was recovered as the sister group to Hemiptera. PMID:25704094

  19. Variability of the human mitochondrial DNA control region sequences in the Lithuanian population.

    PubMed

    Kasperaviciūte, Dalia; Kucinskas, Vaidutis

    2002-01-01

    The Lithuanians and Latvians are the only two Baltic cultures that survived until today. Since the Neolithic period the native inhabitants of the present-day Lithuanian territory have not been replaced by any other ethnic group. Therefore the genetic characterization of the present-day Lithuanians may shed some light on the early history of the Balts. We have analysed 120 DNA samples from two Lithuanian ethnolinguistic groups (Aukstaiciai and Zemaiciai) by direct sequencing of the first hypervariable segment (HVI) of the control region of mitochondrial DNA (mtDNA) and restriction enzyme digestion for polymorphic site 00073. On the basis of specific nucleotide substitutions the obtained sequences were classified to mtDNA haplogroups. This revealed the presence of almost all European haplogroups (except X) in the Lithuanian sample, including those that expanded through Europe in the Palaeolithic and those whose expansion occurred during the Neolithic. Molecular diversity indices (gene diversity 0.97, nucleotide diversity 0.012 and mean number of pairwise differences 4.5) were within the range usually reported in European populations. No significant differences between Aukstaiciai and Zemaiciai subgroups were found, but some slight differences need further investigation. PMID:12080181

  20. Evolutionary Relations of Hexanchiformes Deep-Sea Sharks Elucidated by Whole Mitochondrial Genome Sequences

    PubMed Central

    Tanaka, Keiko; Tomita, Taketeru; Suzuki, Shingo; Hosomichi, Kazuyoshi; Sano, Kazumi; Doi, Hiroyuki; Kono, Azumi; Inoko, Hidetoshi; Kulski, Jerzy K.; Tanaka, Sho

    2013-01-01

    Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA) sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes) species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi, Chlamydoselachus anguineus (frilled shark) is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved as Chlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus, H. nakamurai))). Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks. PMID:24089661

  1. Complete DNA sequence of the mitochondrial genome of the treehopper Leptobelus gazella (Membracoidea: Hemiptera).

    PubMed

    Zhao, Xing; Liang, Ai-Ping

    2016-09-01

    The first complete DNA sequence of the mitochondrial genome (mitogenome) of Leptobelus gazelle (Membracoidea: Hemiptera) is determined in this study. The circular molecule is 16,007 bp in its full length, which encodes a set of 37 genes, including 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs, and contains an A + T-rich region (CR). The gene numbers, content, and organization of L. gazelle are similar to other typical metazoan mitogenomes. Twelve of the 13 PCGs are initiated with ATR methionine or ATT isoleucine codons, except the atp8 gene that uses the ATC isoleucine as start signal. Ten of the 13 PCGs have complete termination codons, either TAA (nine genes) or TAG (cytb). The remaining 3 PCGs (cox1, cox2 and nad5) have incomplete termination codons T (AA). All of the 22 tRNAs can be folded in the form of a typical clover-leaf structure. The complete mitogenome sequence data of L. gazelle is useful for the phylogenetic and biogeographic studies of the Membracoidea and Hemiptera. PMID:25714149

  2. Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins.

    PubMed

    Adcock, G J; Dennis, E S; Easteal, S; Huttley, G A; Jermiin, L S; Peacock, W J; Thorne, A

    2001-01-16

    DNA from ancient human remains provides perspectives on the origin of our species and the relationship between molecular and morphological variation. We report analysis of mtDNA from the remains of 10 ancient Australians. These include the morphologically gracile Lake Mungo 3 [ approximately 60 thousand years (ka) before present] and three other gracile individuals from Holocene deposits at Willandra Lakes (<10 ka), all within the skeletal range of living Australians, and six Pleistocene/early Holocene individuals (15 to <8 ka) from Kow Swamp with robust morphologies outside the skeletal range of contemporary indigenous Australians. Lake Mungo 3 is the oldest (Pleistocene) "anatomically modern" human from whom DNA has been recovered. His mtDNA belonged to a lineage that only survives as a segment inserted into chromosome 11 of the nuclear genome, which is now widespread among human populations. This lineage probably diverged before the most recent common ancestor of contemporary human mitochondrial genomes. This timing of divergence implies that the deepest known mtDNA lineage from an anatomically modern human occurred in Australia; analysis restricted to living humans places the deepest branches in East Africa. The other ancient Australian individuals we examined have mtDNA sequences descended from the most recent common ancestor of living humans. Our results indicate that anatomically modern humans were present in Australia before the complete fixation of the mtDNA lineage now found in all living people. Sequences from additional ancient humans may further challenge current concepts of modern human origins. PMID:11209053

  3. The complete sequence of mitochondrial genome of polled yak (Bos grunniens).

    PubMed

    Chu, Min; Wu, Xiaoyun; Liang, Chunnian; Pei, Jie; Ding, Xuezhi; Guo, Xian; Bao, Pengjia; Yan, Ping

    2016-05-01

    Generally speaking, the hornless trait is also known as polled. Although the POLL locus could be assigned to a 1.36-Mb interval in the centromeric region of BTA1 (Georges et al., 1993; Drögemüller et al., 2005)), and (Liu et al., 2014) reported a 147-kb segment that included three protein-coding genes was the most likely location of the POLL mutation in domestic yaks, the underlying genetic basis for the polled trait is still unknown. In this work, the complete mitochondrial genome sequence of polled yak was determined for the first time. The total length of the mitogenome is 16,324 bp long, with the base composition of 33.72% A, 27.25% T, 25.83% C, and 13.20% G. It contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 non-coding region (D-loop region). The gene order of polled yak mitogenome is identical to that observed in most other vertebrates. The complete mitogenome sequence information of polled yak will provide useful data for further studies on protection of genetic resources and phylogenetic relationships within Bos grunniens. PMID:25347693

  4. The complete mitochondrial genome sequence of Trichopodus leerii (Perciformes: Osphronemidae) and phylogenetic studies of Osphronemidae.

    PubMed

    Wang, Guang-Peng; Liu, Wen-Jie; Si, Gui-Cai; Hu, Guo-Wen

    2016-07-01

    Trichopodus leerii has been given many popular names in the ornament market, such as pearl gourami, lace gourami and mosaic gourami, which causes confusion in species identification. This species belongs in the family Osphronemidae of Perciformes. This species and its congeners are characterized by a brownish-silver body, covered in a pearl-like pattern. In this study, we first determined and described the complete mitogenome sequence of T. leerii, which is 16,472 bp in length. The overall base composition is 29.2%, 27.3%, 28.0% and 15.5% for A, C, T and G, respectively, with a slight bias in the AT content (57.2%). All protein-coding genes share the start codon ATG and most of them have TAA or TAG as the stop codon, except ND4 and ND6 use an incomplete stop codon T. Maximum likelihood tree and Bayesian analyses based on partitioned nucleotide sequences of 12 mitochondrial protein-coding genes were constructed, and both yielded identical topologies. These results are expected to provide useful molecular data for species identification and further phylogenetic studies of Osphronemidae and Perciformes. PMID:26024133

  5. Mitochondrial sequence divergence among Antarctic killer whale ecotypes is consistent with multiple species.

    PubMed

    LeDuc, Richard G; Robertson, Kelly M; Pitman, Robert L

    2008-08-23

    Recently, three visually distinct forms of killer whales (Orcinus orca) were described from Antarctic waters and designated as types A, B and C. Based on consistent differences in prey selection and habitat preferences, morphological divergence and apparent lack of interbreeding among these broadly sympatric forms, it was suggested that they may represent separate species. To evaluate this hypothesis, we compared complete sequences of the mitochondrial control region from 81 Antarctic killer whale samples, including 9 type A, 18 type B, 47 type C and 7 type-undetermined individuals. We found three fixed differences that separated type A from B and C, and a single fixed difference that separated type C from A and B. These results are consistent with reproductive isolation among the different forms, although caution is needed in drawing further conclusions. Despite dramatic differences in morphology and ecology, the relatively low levels of sequence divergence in Antarctic killer whales indicate that these evolutionary changes occurred relatively rapidly and recently. PMID:18524738

  6. Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (Squamata: Eublepharidae).

    PubMed

    Jonniaux, Pierre; Kumazawa, Yoshinori

    2008-01-15

    Mitochondrial DNA sequences of approximately 2.3 kbp including the complete NADH dehydrogenase subunit 2 gene and its flanking genes, as well as parts of 12S and 16S rRNA genes were determined from major species of the eyelid gecko family Eublepharidae sensu [Kluge, A.G. 1987. Cladistic relationships in the Gekkonoidea (Squamata, Sauria). Misc. Publ. Mus. Zool. Univ. Michigan 173, 1-54.]. In contrast to previous morphological studies, phylogenetic analyses based on these sequences supported that Eublepharidae and Gekkonidae form a sister group with Pygopodidae, raising the possibility of homoplasious character change in some key features of geckos, such as reduction of movable eyelids and innovation of climbing toe pads. The phylogenetic analyses also provided a well-resolved tree for relationships between the eublepharid species. The Bayesian estimation of divergence times without assuming the molecular clock suggested the Jurassic divergence of Eublepharidae from Gekkonidae and radiations of most eublepharid genera around the Cretaceous. These dating results appeared to be robust against some conditional changes for time estimation, such as gene regions used, taxon representation, and data partitioning. Taken together with geological evidence, these results support the vicariant divergence of Eublepharidae and Gekkonidae by the breakup of Pangea into Laurasia and Gondwanaland, and recent dispersal of two African eublepharid genera from Eurasia to Africa after these landmasses were connected in the Early Miocene. PMID:18029117

  7. TOWARD A MOLECULAR PHYLOGENY FOR PEROMYSCUS: EVIDENCE FROM MITOCHONDRIAL CYTOCHROME-b SEQUENCES

    PubMed Central

    Bradley, Robert D.; Durish, Nevin D.; Rogers, Duke S.; Miller, Jacqueline R.; Engstrom, Mark D.; Kilpatrick, C. William

    2009-01-01

    One hundred DNA sequences from the mitochondrial cytochrome-b gene of 44 species of deer mice (Peromyscus (sensu stricto), 1 of Habromys, 1 of Isthmomys, 2 of Megadontomys, and the monotypic genera Neotomodon, Osgoodomys, and Podomys were used to develop a molecular phylogeny for Peromyscus. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were conducted to evaluate alternative hypotheses concerning taxonomic arrangements (sensu stricto versus sensu lato) of the genus. In all analyses, monophyletic clades were obtained that corresponded to species groups proposed by previous authors; however, relationships among species groups generally were poorly resolved. The concept of the genus Peromyscus based on molecular data differed significantly from the most current taxonomic arrangement. Maximum-likelihood and Bayesian trees depicted strong support for a clade placing Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys within Peromyscus. If Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are regarded as genera, then several species groups within Peromyscus (sensu stricto) should be elevated to generic rank. Isthmomys was associated with the genus Reithrodontomys; in turn this clade was sister to Baiomys, indicating a distant relationship of Isthmomys to Peromyscus. A formal taxonomic revision awaits synthesis of additional sequence data from nuclear markers together with inclusion of available allozymic and karyotypic data. PMID:19924266

  8. Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences

    USGS Publications Warehouse

    Shamblin, Brian M.; Bagley, Dean A.; Ehrhart, Llewellyn M.; Desjardin, Nicole A.; Martin, R. Erik; Hart, Kristen M.; Naro-Maciel, Eugenia; Rusenko, Kirt; Stiner, John C.; Sobel, Debra; Johnson, Chris; Wilmers, Thomas; Wright, Laura J.; Nairn, Campbell J.

    2014-01-01

    Green turtle (Chelonia mydas) nesting has increased dramatically in Florida over the past two decades, ranking the Florida nesting aggregation among the largest in the Greater Caribbean region. Individual beaches that comprise several hundred kilometers of Florida’s east coast and Keys support tens to thousands of nests annually. These beaches encompass natural to highly developed habitats, and the degree of demographic partitioning among rookeries was previously unresolved. We characterized the genetic structure of ten Florida rookeries from Cape Canaveral to the Dry Tortugas through analysis of 817 base pair mitochondrial DNA (mtDNA) control region sequences from 485 nesting turtles. Two common haplotypes, CM-A1.1 and CM-A3.1, accounted for 87 % of samples, and the haplotype frequencies were strongly partitioned by latitude along Florida’s Atlantic coast. Most genetic structure occurred between rookeries on either side of an apparent genetic break in the vicinity of the St. Lucie Inlet that separates Hutchinson Island and Jupiter Island, representing the finest scale at which mtDNA structure has been documented in marine turtle rookeries. Florida and Caribbean scale analyses of population structure support recognition of at least two management units: central eastern Florida and southern Florida. More thorough sampling and deeper sequencing are necessary to better characterize connectivity among Florida green turtle rookeries as well as between the Florida nesting aggregation and others in the Greater Caribbean region.

  9. DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification

    PubMed Central

    2013-01-01

    Background Mitochondrial DNA (mtDNA) typing can be a useful aid for identifying people from compromised samples when nuclear DNA is too damaged, degraded or below detection thresholds for routine short tandem repeat (STR)-based analysis. Standard mtDNA typing, focused on PCR amplicon sequencing of the control region (HVS I and HVS II), is limited by the resolving power of this short sequence, which misses up to 70% of the variation present in the mtDNA genome. Methods We used in-solution hybridisation-based DNA capture (using DNA capture probes prepared from modern human mtDNA) to recover mtDNA from post-mortem human remains in which the majority of DNA is both highly fragmented (<100 base pairs in length) and chemically damaged. The method ‘immortalises’ the finite quantities of DNA in valuable extracts as DNA libraries, which is followed by the targeted enrichment of endogenous mtDNA sequences and characterisation by next-generation sequencing (NGS). Results We sequenced whole mitochondrial genomes for human identification from samples where standard nuclear STR typing produced only partial profiles or demonstrably failed and/or where standard mtDNA hypervariable region sequences lacked resolving power. Multiple rounds of enrichment can substantially improve coverage and sequencing depth of mtDNA genomes from highly degraded samples. The application of this method has led to the reliable mitochondrial sequencing of human skeletal remains from unidentified World War Two (WWII) casualties approximately 70 years old and from archaeological remains (up to 2,500 years old). Conclusions This approach has potential applications in forensic science, historical human identification cases, archived medical samples, kinship analysis and population studies. In particular the methodology can be applied to any case, involving human or non-human species, where whole mitochondrial genome sequences are required to provide the highest level of maternal lineage discrimination

  10. Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences.

    PubMed

    Yu, N; Zheng, C; Zhang, Y P; Li, W H

    2000-07-01

    The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e. , represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau. On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister taxa of one steppe dweller and one shrub dweller is very low. These findings support the hypothesis that pikas have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution. PMID:10877942

  11. Long-PCR based next generation sequencing of the whole mitochondrial genome of the peacock skate Pavoraja nitida (Elasmobranchii: Arhynchobatidae).

    PubMed

    Yang, Lei; Naylor, Gavin J P

    2016-01-01

    We determined the complete mitochondrial genome sequence (16,760 bp) of the peacock skate Pavoraja nitida using a long-PCR based next generation sequencing method. It has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region in the typical vertebrate arrangement. Primers, protocols, and procedures used to obtain this mitogenome are provided. We anticipate that this approach will facilitate rapid collection of mitogenome sequences for studies on phylogenetic relationships, population genetics, and conservation of cartilaginous fishes. PMID:24938110

  12. Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia)

    NASA Astrophysics Data System (ADS)

    Fukami, Hironobu; Knowlton, Nancy

    2005-11-01

    Complete mitochondrial nucleotide sequences of two individuals each of Montastraea annularis, Montastraea faveolata, and Montastraea franksi were determined. Gene composition and order differed substantially from the sea anemone Metridium senile, but were identical to that of the phylogenetically distant coral genus Acropora. However, characteristics of the non-coding regions differed between the two scleractinian genera. Among members of the M. annularis complex, only 25 of 16,134 base pair positions were variable. Sixteen of these occurred in one colony of M. franksi, which (together with additional data) indicates the existence of multiple divergent mitochondrial lineages in this species. Overall, rates of evolution for these mitochondrial genomes were extremely slow (0.03 0.04% per million years based on the fossil record of the M. annularis complex). At higher taxonomic levels, patterns of genetic divergence and synonymous/nonsynonymous substitutions suggest non-neutral and unequal rates of evolution between the two lineages to which Montastraea and Acropora belong.

  13. Presence of two mitochondrial genomes in the mytilid Perumytilus purpuratus: Phylogenetic evidence for doubly uniparental inheritance

    PubMed Central

    Vargas, Jaime; Pérez, Montse; Toro, Jorge; Astorga, Marcela P.

    2015-01-01

    This study presents evidence, using sequences of ribosomal 16S and COI mtDNA, for the presence of two mitochondrial genomes in Perumytilus purpuratus. This may be considered evidence of doubly uniparental mtDNA inheritance. The presence of the two types of mitochondrial genomes differentiates females from males. The F genome was found in the somatic and gonadal tissues of females and in the somatic tissues of males; the M genome was found in the gonads and mantle of males only. For the mitochondrial 16S region, ten haplotypes were found for the F genome (nucleotide diversity 0.004), and 7 haplotypes for the M genome (nucleotide diversity 0.001), with a distance Dxy of 0.125 and divergence Kxy of 60.33%. For the COI gene 17 haplotypes were found for the F genome (nucleotide diversity 0.009), and 10 haplotypes for the M genome (nucleotide diversity 0.010), with a genetic distance Dxy of 0.184 and divergence Kxy of 99.97%. Our results report the presence of two well-differentiated, sex-specific types of mitochondrial genome (one present in the male gonad, the other in the female gonad), implying the presence of DUI in P. purpuratus. These results indicate that care must be taken in phylogenetic comparisons using mtDNA sequences of P. purpuratus without considering the sex of the individuals. PMID:26273220

  14. Presence of two mitochondrial genomes in the mytilid Perumytilus purpuratus: Phylogenetic evidence for doubly uniparental inheritance.

    PubMed

    Vargas, Jaime; Pérez, Montse; Toro, Jorge; Astorga, Marcela P

    2015-05-01

    This study presents evidence, using sequences of ribosomal 16S and COI mtDNA, for the presence of two mitochondrial genomes in Perumytilus purpuratus. This may be considered evidence of doubly uniparental mtDNA inheritance. The presence of the two types of mitochondrial genomes differentiates females from males. The F genome was found in the somatic and gonadal tissues of females and in the somatic tissues of males; the M genome was found in the gonads and mantle of males only. For the mitochondrial 16S region, ten haplotypes were found for the F genome (nucleotide diversity 0.004), and 7 haplotypes for the M genome (nucleotide diversity 0.001), with a distance Dxy of 0.125 and divergence Kxy of 60.33%. For the COI gene 17 haplotypes were found for the F genome (nucleotide diversity 0.009), and 10 haplotypes for the M genome (nucleotide diversity 0.010), with a genetic distance Dxy of 0.184 and divergence Kxy of 99.97%. Our results report the presence of two well-differentiated, sex-specific types of mitochondrial genome (one present in the male gonad, the other in the female gonad), implying the presence of DUI in P. purpuratus. These results indicate that care must be taken in phylogenetic comparisons using mtDNA sequences of P. purpuratus without considering the sex of the individuals. PMID:26273220

  15. Simultaneous detection of human mitochondrial DNA and nuclear-inserted mitochondrial-origin sequences (NumtS) using forensic mtDNA amplification strategies and pyrosequencing technology.

    PubMed

    Bintz, Brittania J; Dixon, Groves B; Wilson, Mark R

    2014-07-01

    Next-generation sequencing technologies enable the identification of minor mitochondrial DNA variants with higher sensitivity than Sanger methods, allowing for enhanced identification of minor variants. In this study, mixtures of human mtDNA control region amplicons were subjected to pyrosequencing to determine the detection threshold of the Roche GS Junior(®) instrument (Roche Applied Science, Indianapolis, IN). In addition to expected variants, a set of reproducible variants was consistently found in reads from one particular amplicon. A BLASTn search of the variant sequence revealed identity to a segment of a 611-bp nuclear insertion of the mitochondrial control region (NumtS) spanning the primer-binding sites of this amplicon (Nature 1995;378:489). Primers (Hum Genet 2012;131:757; Hum Biol 1996;68:847) flanking the insertion were used to confirm the presence or absence of the NumtS in buccal DNA extracts from twenty donors. These results further our understanding of human mtDNA variation and are expected to have a positive impact on the interpretation of mtDNA profiles using deep-sequencing methods in casework. PMID:24738853

  16. Analyses of the population structure in a global collection of Phytophthora nicotianae isolates inferred from mitochondrial and nuclear DNA sequences.

    PubMed

    Mammella, Marco A; Martin, Frank N; Cacciola, Santa O; Coffey, Michael D; Faedda, Roberto; Schena, Leonardo

    2013-06-01

    Genetic variation within the heterothallic cosmopolitan plant pathogen Phytophthora nicotianae was determined in 96 isolates from a wide range of hosts and geographic locations by characterizing four mitochondrial (10% of the genome) and three nuclear loci. In all, 52 single-nucleotide polymorphisms (SNPs) (an average of 1 every 58 bp) and 313 sites with gaps representing 5,450 bases enabled the identification of 50 different multilocus mitochondrial haplotypes. Similarly, 24 SNPs (an average of 1 every 69 bp), with heterozygosity observed at each locus, were observed in three nuclear regions (hyp, scp, and β-tub) differentiating 40 multilocus nuclear genotypes. Both mitochondrial and nuclear markers revealed a high level of dispersal of isolates and an inconsistent geographic structuring of populations. However, a specific association was observed for host of origin and genetic grouping with both nuclear and mitochondrial sequences. In particular, the majority of citrus isolates from Italy, California, Florida, Syria, Albania, and the Philippines clustered in the same mitochondrial group and shared at least one nuclear allele. A similar association was also observed for isolates recovered from Nicotiana and Solanum spp. The present study suggests an important role of nursery populations in increasing genetic recombination within the species and the existence of extensive phenomena of migration of isolates that have been likely spread worldwide with infected plant material. PMID:23384862

  17. A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta

    PubMed Central

    Shen, Xin; Ma, Xiaoyin; Ren, Jianfeng; Zhao, Fangqing

    2009-01-01

    Background There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum. Results The mitochondrial genome of P.esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups. Conclusion This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including

  18. The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes.

    PubMed

    Li, Libo; Wang, Bin; Liu, Yang; Qiu, Yin-Long

    2009-06-01

    Land plants possess some of the most unusual mitochondrial genomes among eukaryotes. However, in early land plants these genomes resemble those of green and red algae or early eukaryotes. The question of when during land plant evolution the dramatic change in mtDNAs occurred remains unanswered. Here we report the first completely sequenced mitochondrial genome of the hornwort, Megaceros aenigmaticus, a member of the sister group of vascular plants. It is a circular molecule of 184,908 base pairs, with 32 protein genes, 3 rRNA genes, 17 tRNA genes, and 30 group II introns. The genome contains many genes arranged in the same order as in those of a liverwort, a moss, several green and red algae, and Reclinomonas americana, an early-branching eukaryote with the most ancestral form of mtDNA. In particular, the gene order between mtDNAs of the hornwort and Physcomitrella patens (moss) differs by only 8 inversions and translocations. However, the hornwort mtDNA possesses 4 derived features relative to green alga mtDNAs--increased genome size, RNA editing, intron gains, and gene losses--which were all likely acquired during the origin and early evolution of land plants. Overall, this genome and those of other 2 bryophytes show that mitochondrial genomes in early land plants, unlike their seed plant counterparts, exhibit a mixed mode of conservative yet dynamic evolution. PMID:19475442

  19. Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis.

    PubMed

    Engdahl, Cecilia; Larsson, Pär; Näslund, Jonas; Bravo, Mayra; Evander, Magnus; Lundström, Jan O; Ahlm, Clas; Bucht, Göran

    2014-05-01

    Mosquito-borne infectious diseases are emerging in many regions of the world. Consequently, surveillance of mosquitoes and concomitant infectious agents is of great importance for prediction and prevention of mosquito-borne infectious diseases. Currently, morphological identification of mosquitoes is the traditional procedure. However, sequencing of specified genes or standard genomic regions, DNA barcoding, has recently been suggested as a global standard for identification and classification of many different species. Our aim was to develop a genetic method to identify mosquitoes and to study their relationship. Mosquitoes were captured at collection sites in northern Sweden and identified morphologically before the cytochrome c oxidase subunit I (COI) gene sequences of 14 of the most common mosquito species were determined. The sequences obtained were then used for phylogenetic placement, for validation and benchmarking of phenetic classifications and finally to develop a hierarchical PCR-based typing scheme based on single nucleotide polymorphism sites (SNPs) to enable rapid genetic identification, circumventing the need for morphological characterization. The results showed that exact phylogenetic relationships between mosquito taxa were preserved at shorter evolutionary distances, but at deeper levels, they could not be inferred with confidence using COI gene sequence data alone. Fourteen of the most common mosquito species in Sweden were identified by the SNP/PCR-based typing scheme, demonstrating that genetic typing using SNPs of the COI gene is a useful method for identification of mosquitoes with potential for worldwide application. PMID:24215491

  20. The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary patterns within green algae.

    PubMed Central

    Turmel, M; Lemieux, C; Burger, G; Lang, B F; Otis, C; Plante, I; Gray, M W

    1999-01-01

    Green plants appear to comprise two sister lineages, Chlorophyta (classes Chlorophyceae, Ulvophyceae, Trebouxiophyceae, and Prasinophyceae) and Streptophyta (Charophyceae and Embryophyta, or land plants). To gain insight into the nature of the ancestral green plant mitochondrial genome, we have sequenced the mitochondrial DNAs (mtDNAs) of Nephroselmis olivacea and Pedinomonas minor. These two green algae are presumptive members of the Prasinophyceae. This class is thought to include descendants of the earliest diverging green algae. We find that Nephroselmis and Pedinomonas mtDNAs differ markedly in size, gene content, and gene organization. Of the green algal mtDNAs sequenced so far, that of Nephroselmis (45,223 bp) is the most ancestral (minimally diverged) and occupies the phylogenetically most basal position within the Chlorophyta. Its repertoire of 69 genes closely resembles that in the mtDNA of Prototheca wickerhamii, a later diverging trebouxiophycean green alga. Three of the Nephroselmis genes (nad10, rpl14, and rnpB) have not been identified in previously sequenced mtDNAs of green algae and land plants. In contrast, the 25,137-bp Pedinomonas mtDNA contains only 22 genes and retains few recognizably ancestral features. In several respects, including gene content and rate of sequence divergence, Pedinomonas mtDNA resembles the reduced mtDNAs of chlamydomonad algae, with which it is robustly affiliated in phylogenetic analyses. Our results confirm the existence of two radically different patterns of mitochondrial genome evolution within the green algae. PMID:10488238

  1. A Phylogenetic Analysis of Greek Isolates of Aspergillus Species Based on Morphology and Nuclear and Mitochondrial Gene Sequences

    PubMed Central

    Krimitzas, Antonios; Kouvelis, Vassili N.; Kapsanaki-Gotsi, Evangelia; Typas, Milton A.

    2013-01-01

    Aspergillus species originating from Greece were examined by morphological and molecular criteria to explore the diversity of this genus. The phylogenetic relationships of these species were determined using sequences from the ITS and IGS region of the nuclear rRNA gene complex, two nuclear genes (β-tubulin (benA) and RNA polymerase II second largest subunit (rpb2)) and two mitochondrial genes (small rRNA subunit (rns) and cytochrome oxidase subunit I (cox1)) and, where available, related sequences from databases. The morphological characters of the anamorphs and teleomorphs, and the single gene phylogenetic trees, differentiated and placed the species examined in the well-supported sections of Aenei, Aspergillus, Bispori, Candidi, Circumdati, Clavati, Cremei, Flavi, Flavipedes, Fumigati, Nidulantes, Nigri, Restricti, Terrei, Usti, and Zonati, with few uncertainties. The combined use of the three commonly employed nuclear genes (benA, rpb2, and ITS), the IGS region, and two less often used mitochondrial gene sequences (rns and cox1) as a single unit resolved several taxonomic ambiguities. A phylogenetic tree was inferred using Neighbour-Joining, Maximum Parsimony, and Bayesian methods. The strains examined formed seven well-supported clades within the genus Aspergillus. Altogether, the concatenated nuclear and mitochondrial sequences offer additional tools for an improved understanding of phylogenetic relationships within this genus. PMID:23762830

  2. Molecular phylogeny of commercially important lobster species from Indian coast inferred from mitochondrial and nuclear DNA sequences.

    PubMed

    Jeena, N S; Gopalakrishnan, A; Radhakrishnan, E V; Kizhakudan, Joe K; Basheer, V S; Asokan, P K; Jena, J K

    2016-07-01

    Lobsters constitute low-volume high-value crustacean fishery resource along Indian coast. For the conservation and management of this declining resource, accurate identification of species and larvae is essential. The objectives of this work were to generate species-specific molecular signatures of 11 commercially important species of lobsters of families Palinuridae and Scyllaridae and to reconstruct a phylogeny to clarify the evolutionary relationships among genera and species included in this study. Partial sequences were generated for all the candidate species from sampling sites along the Indian coast using markers like Cytochrome oxidase I (COI), 16SrRNA, 12SrRNA, and 18SrRNA genes, and analyzed. The genetic identities of widely distributed Thenus species along the Indian coast to be Thenus unimaculatus and the sub-species of Panulirus homarus to be P. homarus homarus were confirmed. Phylogeny reconstruction using the individual gene and concatenated mtDNA data set were carried out. The overall results suggested independent monophyly of Scyllaridae and Stridentes of Palinuridae. The interspecific divergence was found to be highest for the 12SrRNA compared with other genes. Significant incongruence between mtDNA and nuclear 18SrRNA gene tree topologies was observed. The results hinted an earlier origin for Palinuridae compared with Scyllaridae. The DNA sequence data generated from this study will aid in the correct identification of lobster larvae and will find application in research related to larval transport and distribution. PMID:26065848

  3. Nucleotide sequence analysis of the hypervariable region III of mitochondrial DNA in Thais.

    PubMed

    Thongngam, Punlop; Leewattanapasuk, Worraanong; Bhoopat, Tanin; Sangthong, Padchanee

    2016-07-01

    This study analyzed the nucleotide sequences of the hypervariable region III (HVRIII) of mitochondrial DNA in Thai individuals. Buccal swab samples were randomly obtained from 100 healthy, unrelated, adult (18-60 years old), volunteer donors living in Thailand. Eighteen different haplotypes were found, of which 11 haplotypes were unique. The most frequent haplotypes observed were 522D-523D. Nucleotide transition from Thymine (T) to Cytosine (C) at position 489 (43%) was the most frequent substitution. Nucleotide transversions were also observed at position 433 (Adenine (A) to C, 1%) and position 499 (Guanine (G) to C, 1%). Fifty-three samples presented nucleotide insertion and deletion of C and A (CA) at position 514-523. Insertion of 1AC (3%) and 2AC (2%) were observed. Deletion of 1CA (53%) and 2CA (2%) at position 514-523 were revealed. The deletion of T at position 459 was observed. The haplotype diversity, random match probability, and discrimination power were calculated to be 0.7770, 0.2308, and 0.7692, respectively. PMID:27107562

  4. The Mitochondrial Genome of Conus textile, coxI-coxII Intergenic Sequences and Conoidean Evolution

    PubMed Central

    Bandyopadhyay, Pradip K; Stevenson, Bradford J.; Ownby, John-Paul; Cady, Matthew T.; Watkins, Maren; Olivera, Baldomero M.

    2009-01-01

    The cone snails belong to the superfamily Conoidea, comprising ∼10,000 venomous marine gastropods. We determined the complete mitochondrial DNA sequence of Conus textile. The gene order is identical in Conus textile, Lophiotoma cerithiformis (another Conoidean gastropod), and the neogastropod Ilyanassa obsoleta, (not in the superfamily Conoidea). However, the intergenic interval between the coxI/coxII genes, was much longer in C. textile (165 bp) than in any other previously analyzed gastropod. We used the intergenic region to evaluate evolutionary patterns. In most neogastropods and three conidean families the intergenic interval is small (<30 nucleotides). Within Conus, the variation is from 130-170 bp, and each different clade within Conus has a narrower size distribution. In Conasprella, a subgenus traditionally assigned to Conus, the intergenic regions vary between 200-500 bp, suggesting that the species in Conasprella are not congeneric with Conus. The intergenic region was used for phylogenetic analysis of a group of fish-hunting Conus, despite the short length resolution was better than using standard markers. Thus, the coxI/coxII intergenic region can be used both to define evolutionary relationships between species in a clade, and to understand broad evolutionary patterns across the large superfamily Conoidea. PMID:17936021

  5. Genomic mitochondrial DNA-like sequences in normal and tumor tissue of mouse and rat

    SciTech Connect

    Hadler, H.I.; Devadas, K.; Mahalingam, R. )

    1990-02-26

    The restriction enzyme Kpn I, which does not cut mouse mitochondrial DNA (mtDNA) generated families of nuclear DNA with mtDNA-like sequences from both the normal liver of DBA/2 mice and a lymphoid leukemic ascites cell line, L1210, started by methylcholanthrene in DBA/2 mice. The family of the new Kpn l mtDNA-like element is most evident in tumor. The Southern blot banding patterns of the families were so altered by additional digestion with Pst I, which does cut mouse mtDNA, that the Kpn I mtDNA-like elements were implicated have different arrangement in tumor. KPn I which also does not cut rat mtDNA generated families of Kpn I mtDNA-like elements from normal rat liver and from a rat hepatoma (freshly induced by diethylnitrosoamine) in a mode analogous so that described for the mouse. These experiments stem from our unitary hypothesis for carcinogenesis presented 18 years ago.

  6. Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences.

    PubMed

    Kochzius, Marc; Söller, Rainer; Khalaf, Maroof A; Blohm, Dietmar

    2003-09-01

    This study investigates the molecular phylogeny of seven lionfishes of the genera Dendrochirus and Pterois. MP, ML, and NJ phylogenetic analysis based on 964 bp of partial mitochondrial DNA sequences (cytochrome b and 16S rDNA) revealed two main clades: (1) "Pterois" clade (Pterois miles and Pterois volitans), and (2) "Pteropterus-Dendrochirus" clade (remainder of the sampled species). The position of Dendrochirus brachypterus either basal to the main clades or in the "Pteropterus-Dendrochirus" clade cannot be resolved. However, the molecular phylogeny did not support the current separation of the genera Pterois and Dendrochirus. The siblings P. miles and P. volitans are clearly separated and our results support the proposed allopatric or parapatric distribution in the Indian and Pacific Ocean. However, the present analysis cannot reveal if P. miles and P. volitans are separate species or two populations of a single species, because the observed separation in different clades can be either explained by speciation or lineage sorting. Molecular clock estimates for the siblings P. miles and P. volitans suggest a divergence time of 2.4-8.3 mya, which coincide with geological events that created vicariance between populations of the Indian and Pacific Ocean. PMID:12927126

  7. Relationships among brown lemurs (Eulemur fulvus) based on mitochondrial DNA sequences.

    PubMed

    Pastorini, J; Forstner, M R; Martin, R D

    2000-09-01

    The brown lemurs (Eulemur fulvus) include seven subspecies, whose evolutionary relationships remain contentious. In particular, it is unclear whether the Malagasy and Comorian E. f. fulvus populations are differentiated at the subspecific level (E. f. mayottensis). Furthermore, it has been suggested that E. f. collaris and E. f. albocollaris are separate species. Analyses of approximately 2400 bp of mitochondrial DNA sequence data from part of the COIII gene, together with complete genes for ND3, ND4L, and ND4 and 5 tRNAs, resolved 34 E. fulvus specimens into six clades: ((albocollaris, collaris) (rufus (rufus (fulvus/mayottensis (albifrons/fulvus/sanfordi))))). Based on the information available and our analyses we conclude that E. f. albocollaris and E. f. collaris do not represent species distinct from E. fulvus and that Comorian brown lemurs do not deserve subspecific rank. No genetic differentiation was detected between E. f. albifrons and E. f. sanfordi; on the other hand, there are obviously two separate lineages of E. f. rufus. PMID:10991794

  8. A new hypothesis of squamate evolutionary relationships from nuclear and mitochondrial DNA sequence data

    SciTech Connect

    Townsend, Ted M.; Larson, Allan; Louis, Edward; Macey, J. Robert

    2004-05-19

    Squamate reptiles serve as model systems for evolutionary studies of a variety of morphological and behavioral traits, and phylogeny is crucial to many generalizations derived from such studies. Specifically, the traditional dichotomy between Iguania and Scleroglossa has been correlated with major evolutionary shifts within Squamata. We present a molecular phylogenetic study of squamates using DNA sequence data from the nuclear genes RAG-1 and c-mos and the mitochondrial ND2 region, sampling all major clades and most major subclades. Monophyly of Iguania, Anguimorpha, and almost all currently recognized squamate families is strongly supported. However, monophyly is rejected for Scleroglossa, Varanoidea, and several other higher taxa, and Iguania is highly nested within Squamata. Limblessness evolved independently in snakes, dibamids, and amphisbaenians, suggesting widespread morphological convergence or parallelism in limbless, burrowing forms. Amphisbaenians are the sister group of lacertids, and snakes are grouped with iguanians and anguimorphs. Dibamids diverged early in squamate evolutionary history. Xantusiidae is the sister taxon of Cordylidae. Studies of functional tongue morphology and feeding mode have found significant differences between Scleroglossa and Iguania, and our finding of a nonmonophyletic Scleroglossa and a highly nested Iguania suggest that similar states evolved separately in Sphenodon and Iguania, and that jaw prehension is the ancestral feeding mode in squamates.

  9. Strategies for complete mitochondrial genome sequencing on Ion Torrent PGM™ platform in forensic sciences.

    PubMed

    Zhou, Yishu; Guo, Fei; Yu, Jiao; Liu, Feng; Zhao, Jinling; Shen, Hongying; Zhao, Bin; Jia, Fei; Sun, Zhu; Song, He; Jiang, Xianhua

    2016-05-01

    Next generation sequencing (NGS) is a time saving and cost-efficient method to detect the complete mitochondrial genome (mtGenome) compared to Sanger sequencing. In this study we focused on developing strategies for mtGenome sequencing on the Ion Torrent PGM™ platform and NGS data analysis. With our experience, 4, 15 and 30 samples could be loaded onto Ion 314™, Ion 316™ and Ion 318™ chips respectively at a pooling concentration of 26pM, achieving to sufficient average coverage of ≥1500 × and well strand balance of 1.05. Data processing software is essential to NGS mega data analysis. The in-house Perl scripts were developed for primary data analysis to screen out uncertain positions and samples from variant call format (VCF) reports and for pedigree study to perform pairwise comparisons. The Integrative Genomic Viewer (IGV) and the NextGENe software were introduced to secondary data analysis. The mthap and EMMA were employed for haplogroup assignment. The dataset was reviewed and approved by the EMPOP as the final version, which showed 2.66% error rate generated from the Torrent Variant Caller (TVC). Across the mtGenome, 4022 variants were found at 725 nucleotide positions, where ratio of transitions to transversions was estimated at 20.89:1 and 22.18% of variants was concentrated at hypervariable segments I and II (HVS-I and HVS-II). Totally, 107 complete mtGenome haplotypes were observed from 107 Northern Chinese Han and assigned to 88 haplogroups. The random match probability (RMP) of complete mtGenome was calculated as 0.009345794, decreasing 26.19% by comparison to that of HVS-I only, and the haplotype diversity (HD) was evaluated as 1, increasing 0.33% by comparison to that of HVS-I only. Principal component analysis (PCA) showed that our population was clustered to East and Southeast Asians. The strategies in this study are suitable for complete mtGenome sequencing on Ion Torrent PGM™ platform and Northern Chinese Han (EMP00670) is the first

  10. The Complete Nucleotide Sequence of the Mitochondrial Genome of Bactrocera minax (Diptera: Tephritidae)

    PubMed Central

    Zhang, Bin; Nardi, Francesco; Hull-Sanders, Helen; Wan, Xuanwu; Liu, Yinghong

    2014-01-01

    The complete 16,043 bp mitochondrial genome (mitogenome) of Bactrocera minax (Diptera: Tephritidae) has been sequenced. The genome encodes 37 genes usually found in insect mitogenomes. The mitogenome information for B. minax was compared to the homologous sequences of Bactrocera oleae, Bactrocera tryoni, Bactrocera philippinensis, Bactrocera carambolae, Bactrocera papayae, Bactrocera dorsalis, Bactrocera correcta, Bactrocera cucurbitae and Ceratitis capitata. The analysis indicated the structure and organization are typical of, and similar to, the nine closely related species mentioned above, although it contains the lowest genome-wide A+T content (67.3%). Four short intergenic spacers with a high degree of conservation among the nine tephritid species mentioned above and B. minax were observed, which also have clear counterparts in the control regions (CRs). Correlation analysis among these ten tephritid species revealed close positive correlation between the A+T content of zero-fold degenerate sites (P0FD), the ratio of nucleotide substitution frequency at P0FD sites to all degenerate sites (zero-fold degenerate sites, two-fold degenerate sites and four-fold degenerate sites) and amino acid sequence distance (ASD) were found. Further, significant positive correlation was observed between the A+T content of four-fold degenerate sites (P4FD) and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites; however, we found significant negative correlation between ASD and the A+T content of P4FD, and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites. A higher nucleotide substitution frequency at non-synonymous sites compared to synonymous sites was observed in nad4, the first time that has been observed in an insect mitogenome. A poly(T) stretch at the 5′ end of the CR followed by a [TA(A)]n-like stretch was also found. In addition, a highly conserved G+A-rich sequence block was observed in front of the

  11. Phylogenetic relationships in European Ceriporiopsis species inferred from nuclear and mitochondrial ribosomal DNA sequences.

    PubMed

    Tomšovský, Michal; Menkis, Audrius; Vasaitis, Rimvydas

    2010-04-01

    The aim of this work was to clarify taxonomy and examine evolutionary relationships within European Ceriporiopsis species using a combined analysis of the large subunit (nLSU) nuclear rRNA and small subunit (mtSSU) mitochondrial rRNA gene sequences. Data from the ITS region were applied to enhance the view of the phylogenetic relationships among different species. The studied samples grouped into four complex clades, suggesting that the genus Ceriporiopsis is polyphyletic. The generic type Ceriporiopsis gilvescens formed a separate group together with Ceriporiopsis guidella and Phlebia spp. in the phlebioid clade. In this clade, the closely related species Ceriporiopsis resinascens and Ceriporiopsis pseudogilvescens grouped together with Ceriporiopsis aneirina. C. resinascens and C. pseudogilvescens have identical LSU and SSU sequences but differ in ITS. Ceriporiopsis pannocincta also fell in the phlebioid clade, but showed closer proximity to Gloeoporus dichrous than to C. gilvescens or C. aneirina-C. pseudogilvescens-C. resinascens group. Another clade was composed of a Ceriporiopsis balaenae-Ceriporiopsis consobrina group and was found to be closely related to Antrodiella and Frantisekia, with the overall clade highly reminiscent of the residual polyporoid clade. The monotypic genus Pouzaroporia, erected in the past for Ceriporiopsis subrufa due to its remarkable morphological differences, also fell within the residual polyporoid clade. Ceriporiopsis subvermispora held an isolated position from the other species of the genus. Therefore, the previously proposed name Gelatoporia subvermispora has been adopted for this species. Physisporinus rivulosus appeared unrelated to two other European Physisporinus species. Moreover, Ceriporiopsis (=Skeletocutis) jelicii grouped in a separate clade, distinct from Ceriporiopsis species. Finally, the ITS data demonstrated the proximity of some Ceriporiopsis species (Ceriporiopsis portcrosensis and Ceriporiopsis

  12. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.

    PubMed

    Miya, Masaki; Takeshima, Hirohiko; Endo, Hiromitsu; Ishiguro, Naoya B; Inoue, Jun G; Mukai, Takahiko; Satoh, Takashi P; Yamaguchi, Motoomi; Kawaguchi, Akira; Mabuchi, Kohji; Shirai, Shigeru M; Nishida, Mutsumi

    2003-01-01

    A recent preliminary study using complete mitochondrial DNA sequences from 48 species of teleosts has suggested that higher teleostean phylogenies should be reinvestigated on the basis of more intensive taxonomic sampling. As a second step towards the resolution of higher teleostean phylogenies, which have been described as the "(unresolved) bush at the top of the tree," we reanalyzed their relationships using mitogenomic data from 100 purposefully chosen species that fully represented all of the higher teleostean orders, except for the Batrachoidiformes. Unweighted and weighted maximum parsimony analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding 3rd codon positions) and 21 transfer RNA (tRNA) genes (stem regions only) from each species. The resultant trees were well resolved and largely congruent, with most internal branches being supported by high statistical values. All major, comprehensive groups above ordinal level as currently defined in higher teleosts (with the exception of the Neoteleostei and several monotypic groups), such as the Eurypterygii, Ctenosquamata, Acanthomorpha, Paracanthopterygii, Acanthopterygii, and Percomorpha, appeared to be nonmonophyletic in the present tree. Such incongruities largely resulted from differences in the placement and/or limits of the orders Ateleopodiformes, Lampridiformes, Polymixiiformes, Ophidiiformes, Lophiiformes, Beryciformes, Stephanoberyciformes, and Zeiformes, long-standing problematic taxa in systematic ichthyology. Of these, the resulting phylogenetic positions of the Ophidiiformes and Lophiiformes were totally unexpected, because, although they have consistently been considered relatively primitive groups within higher teleosts (Paracanthopterygii), they were confidently placed within a crown group of teleosts, herein called the Percomorpha. It should be noted that many unexpected, but highly supported relationships were found

  13. The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing

    PubMed Central

    Hung, Chih-Ming; Lin, Rong-Chien; Chu, Jui-Hua; Yeh, Chia-Fen; Yao, Chiou-Ju; Li, Shou-Hsien

    2013-01-01

    The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species. PMID:23437111

  14. Complete mitochondrial genome sequences of Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, Gulf sturgeon, A. o. desotoi and European sturgeon A. sturio (Acipenseriformes: Acipenseridae) obtained through next generation sequencing.

    PubMed

    Popović, Danijela; Baca, Mateusz; Panagiotopoulou, Hanna

    2016-07-01

    Complete mitochondrial genome sequences of European sturgeon and two subspecies of the North American, Atlantic and Gulf sturgeons were determined using MiSeq Illumina technology. All three genomes show typical vertebrate organization. They possess 22 tRNA genes, 13 protein-coding genes, 2 rRNA (ribosomal RNA) genes and a non-coding control region. Excluding ND6, all protein-coding genes are on the heavy strand. The whole mitogenome sequences have been deposited in GenBank under accession numbers KP997216-KP997218. PMID:26017050

  15. Eurotatorian paraphyly: Revisiting phylogenetic relationships based on the complete mitochondrial genome sequence of Rotaria rotatoria (Bdelloidea: Rotifera: Syndermata)

    PubMed Central

    2009-01-01

    Background The Syndermata (Rotifera+Acanthocephala) is one of the best model systems for studying the evolutionary origins and persistence of different life styles because it contains a series of lineage-specific life histories: Monogononta (cyclic parthenogenetic and free-living), Bdelloidea (entirely parthenogenetic and mostly benthic dweller), Seisonidea (exclusively bisexual and epizoic or ectoparasitic), and Acanthocephala (sexual and obligatory endoparasitic). Providing phylogenetic resolution to the question of Eurotatoria (Monogononta and Bdelloidea) monophyly versus paraphyly is a key factor for better understanding the evolution of different life styles, yet this matter is not clearly resolved. In this study, we revisited this issue based on comparative analysis of complete mitochondrial genome information for major groups of the Syndermata. Results We determined the first complete mitochondrial genome sequences (15,319 bp) of a bdelloid rotifer, Rotaria rotatoria. In order to examine the validity of Eurotatoria (Monogononta and Bdelloidea) monophyly/paraphyly, we performed phylogenetic analysis of amino acid sequences for eleven protein-coding genes sampled from a wide variety of bilaterian representatives. The resulting mitochondrial genome trees, inferred using different algorithms, consistently failed to recover Monogononta and Bdelloidea as monophyletic, but instead identified them as a paraphyletic assemblage. Bdelloidea (as represented by R. rotatoria) shares most common ancestry with Acanthocephala (as represented by L. thecatus) rather than with monogonont B. plicatilis, the other representative of Eurotatoria. Conclusion Comparisons of inferred amino acid sequence and gene arrangement patterns with those of other metazoan mtDNAs (including those of acanthocephalan L. thecatus and monogonont B. plicatilis) support the hypothesis that Bdelloidea shares most common ancestry with Acanthocephala rather than with Monogononta. From this finding, we

  16. Complete mitochondrial genome sequence and mutations of the insulin resistance model inbred C57BL/6 mice strain.

    PubMed

    Meng, Xiao-Mei; Tang, Yu-Xiao; Wang, Ji-Chang; Dong, Yao-Zhong

    2016-05-01

    In the present work we undertook the complete mitochondrial genome sequencing of an important insulin resistance model inbred rat strain for the first time. The total length of the mitogenome was 16,308 bp. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The mutation events were also reported. PMID:25350740

  17. Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae.

    PubMed

    Man, Zhang; Yishu, Wang; Peng, Yan; Xiaobing, Wu

    2011-07-01

    We report complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae, whose gene orders match those of other crocodilians. Phylogenetic analyses based on the sequences of 12 mitochondrial protein-coding genes support monophyly of two crocodilian taxonomic families, Alligatoridae (genera Alligator, Caiman, and Paleosuchus) and Crocodylidae (genera Crocodylus, Gavialis, Mecistops, Osteolaemus, and Tomistoma). Our results are consistent with monophyly of all crocodilian genera. Within Alligatoridae, genus Alligator is the sister taxon of a clade comprising Caiman and Paleosuchus. Within Crocodylidae, the basal phylogenetic split separates a clade comprising Gavialis and Tomistoma from a clade comprising Crocodylus, Mecistops, and Osteolaemus. Mecistops and Osteolaemus form the sister taxon to Crocodylus. Within Crocodylus, we sampled five Indopacific species, whose phylogenetic ordering is ((C. mindorensis, C. novaeguineae), (C. porosus, (C. siamensis, C. palustris))). The African species C. niloticus and New World species C. acutus form the sister taxon to the Indopacific species, although our sampling lacks three other New World species and an Australian species of Crocodylus. PMID:21463698

  18. Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes

    PubMed Central

    Rubinstein, Nimrod D.; Feldstein, Tamar; Shenkar, Noa; Botero-Castro, Fidel; Griggio, Francesca; Mastrototaro, Francesco; Delsuc, Frédéric; Douzery, Emmanuel J.P.; Gissi, Carmela; Huchon, Dorothée

    2013-01-01

    Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polym