Science.gov

Sample records for rhinovirus genome evolution

  1. Analysis of Complete Genome Sequences of Human Rhinovirus

    PubMed Central

    Palmenberg, Ann C.; Rathe, Jennifer A.; Liggett, Stephen B.

    2010-01-01

    Human Rhinovirus (HRV) infection is the cause of about one-half of asthma and COPD exacerbations. With >100 serotypes in the HRV reference set an effort was undertaken to sequence their complete genomes so as to understand diversity, structural variation, and evolution of the virus. Analysis revealed conserved motifs, hypervariable regions, a potential fourth HRV species, within-serotype variation in field isolates, a non-scanning internal ribosome entry site, and evidence for HRV recombination. Techniques have now been developed using next generation sequencing to generate complete genomes from patient isolates with high throughput, deep coverage, and low costs. Thus relationships can now be sought between obstructive lung phenotypes and variation in HRV genomes in infected patients, and, potential novel therapeutic strategies developed based on HRV sequence. PMID:20471068

  2. The genomic signature of human rhinoviruses A, B and C.

    PubMed

    Megremis, Spyridon; Demetriou, Philippos; Makrinioti, Heidi; Manoussaki, Alkistis E; Papadopoulos, Nikolaos G

    2012-01-01

    Human rhinoviruses are single stranded positive sense RNA viruses that are presented in more than 50% of acute upper respiratory tract infections. Despite extensive studies on the genetic diversity of the virus, little is known about the forces driving it. In order to explain this diversity, many research groups have focused on protein sequence requirements for viable, functional and transmissible virus but have missed out an important aspect of viral evolution such as the genomic ontology of the virus. This study presents for the first time the genomic signature of 111 fully sequenced HRV strains from all three groups HRV-A, HRV-B and HRV-C. We observed an HRV genome tendency to eliminate CpG and UpA dinucleotides, coupling with over-representation of UpG and CpA. We propose a specific mechanism which describes how rapid changes in the HRV genomic sequence can take place under the strict control of conservation of the polypeptide backbone. Moreover, the distribution of the observed under- and over-represented dinucleotides along the HRV genome is presented. Distance matrice tables based on CpG and UpA odds ratios were constructed and viewed as heatmaps and distance trees. None of the suppressions can be attributed to codon usage or in RNA secondary structure requirements. Since viral recognition is dependent on RNA motifs rich in CpG and UpA, it is possible that the overall described genome evolution mechanism acts in order to protect the virus from host recognition. PMID:23028561

  3. Rhinovirus Infections

    MedlinePLUS

    ... Issues Listen Text Size Email Print Share Rhinovirus Infections Page Content Article Body More than any other illness, rhinoviruses (rhin means “nose”) are associated with the common cold. Rhinoviruses may also ... throats, ear infections, sinus infections, and to a lesser degree, pneumonia ...

  4. Human Rhinoviruses

    PubMed Central

    Lamson, Daryl M.; St. George, Kirsten; Walsh, Thomas J.

    2013-01-01

    Human rhinoviruses (HRVs), first discovered in the 1950s, are responsible for more than one-half of cold-like illnesses and cost billions of dollars annually in medical visits and missed days of work. Advances in molecular methods have enhanced our understanding of the genomic structure of HRV and have led to the characterization of three genetically distinct HRV groups, designated groups A, B, and C, within the genus Enterovirus and the family Picornaviridae. HRVs are traditionally associated with upper respiratory tract infection, otitis media, and sinusitis. In recent years, the increasing implementation of PCR assays for respiratory virus detection in clinical laboratories has facilitated the recognition of HRV as a lower respiratory tract pathogen, particularly in patients with asthma, infants, elderly patients, and immunocompromised hosts. Cultured isolates of HRV remain important for studies of viral characteristics and disease pathogenesis. Indeed, whether the clinical manifestations of HRV are related directly to viral pathogenicity or secondary to the host immune response is the subject of ongoing research. There are currently no approved antiviral therapies for HRVs, and treatment remains primarily supportive. This review provides a comprehensive, up-to-date assessment of the basic virology, pathogenesis, clinical epidemiology, and laboratory features of and treatment and prevention strategies for HRVs. PMID:23297263

  5. Evolution of genome architecture.

    PubMed

    Koonin, Eugene V

    2009-02-01

    Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection. The empirical basis underlying Darwin's conclusions consisted of numerous observations made by him and other naturalists on the exquisite adaptations of animals and plants to their natural habitats and on the impressive results of artificial selection. Darwin fully appreciated the importance of heredity but was unaware of the nature and, in fact, the very existence of genomes. A century and a half after the publication of the "Origin", we have the opportunity to draw conclusions from the comparisons of hundreds of genome sequences from all walks of life. These comparisons suggest that the dominant mode of genome evolution is quite different from that of the phenotypic evolution. The genomes of vertebrates, those purported paragons of biological perfection, turned out to be veritable junkyards of selfish genetic elements where only a small fraction of the genetic material is dedicated to encoding biologically relevant information. In sharp contrast, genomes of microbes and viruses are incomparably more compact, with most of the genetic material assigned to distinct biological functions. However, even in these genomes, the specific genome organization (gene order) is poorly conserved. The results of comparative genomics lead to the conclusion that the genome architecture is not a straightforward result of continuous adaptation but rather is determined by the balance between the selection pressure, that is itself dependent on the effective population size and mutation rate, the level of recombination, and the activity of selfish elements. Although genes and, in many cases, multigene regions of genomes possess elaborate architectures that ensure regulation of expression, these arrangements are evolutionarily volatile and typically change substantially even on short evolutionary scales when gene sequences diverge minimally. Thus, the observed genome architectures are, mostly, products of neutral processes or epiphenomena of more general selective processes, such as selection for genome streamlining in successful lineages with large populations. Selection for specific gene arrangements (elements of genome architecture) seems only to modulate the results of these processes. PMID:18929678

  6. Nematode genome evolution.

    PubMed Central

    Coghlan, Avril

    2005-01-01

    Nematodes are the most abundant type of animal on earth, and live in hot springs, polar ice, soil, fresh and salt water, and as parasites of plants, vertebrates, insects, and other nematodes. This extraordinary ability to adapt, which hints at an underlying genetic plasticity, has long fascinated biologists. The fully sequenced genomes of Caenorhabditis elegans and Caenorhabditis briggsae, and ongoing sequencing projects for eight other nematodes, provide an exciting opportunity to investigate the genomic changes that have enabled nematodes to invade many different habitats. Analyses of the C. elegans and C. briggsae genomes suggest that these include major changes in gene content; as well as in chromosome number, structure and size. Here I discuss how the data set of ten genomes will be ideal for tackling questions about nematode evolution, as well as questions relevant to all eukaryotes. PMID:18050393

  7. The evolution of animal genomes.

    PubMed

    Dunn, Casey W; Ryan, Joseph F

    2015-12-01

    Genome sequences are now available for hundreds of species sampled across the animal phylogeny, bringing key features of animal genome evolution into sharper focus. The field of animal evolutionary genomics has focused on identifying and classifying the diversity genomic features, reconstructing the history of evolutionary changes in animal genomes, and testing hypotheses about the evolutionary relationships of animals. The grand challenges moving forward are to connect evolutionary changes in genomes with particular evolutionary changes in phenotypes, and to determine which changes are driven by selection. This will require far greater genome sampling both across and within species, extensive phenotype data, a well resolved animal phylogeny, and advances in comparative methods. PMID:26363125

  8. Rhinovirus infections in the upper airway.

    PubMed

    Winther, Birgit

    2011-03-01

    The majority of cold and flulike illnesses are caused by human rhinoviruses (HRVs). Improved detection of HRV has shown that HRVs are also associated with more serious illness, such as exacerbation of asthma, wheezing illnesses in children, chronic obstructive pulmonary disease, cardiopulmonary disease, and fatal pneumonia in immune-compromised patients. HRV is a major cause of acute viral respiratory tract infections in hospitalized children and is among the leading causes of childhood mortality worldwide. Detection of the HRV genome by reverse transcriptase-polymerase chain reaction and genomic sequencing has brought to light a new clade, HRV-C, to the already recognized HRV-A and HRV-B clades. The clinical complications related to all rhinovirus infections include acute otitis media, acute sinusitis, and acute bronchitis. The enormous public health implications from those diseases far overshadow those of the common cold. This article provides an overview of the pathogenesis of rhinovirus infection in the upper airways. Most research has been done in young healthy adults with self-limiting experimental and natural rhinovirus infections, and this may set the stage for understanding rhinovirus infections in the ear, sinus, and lower airways. PMID:21364225

  9. Hidden magicians of genome evolution.

    PubMed

    Kumar, C Sandeep; Qureshi, Sameera Fatima; Ali, Altaf; Satyanarayana, M L; Rangaraju, Advithi; Venkateshwari, A; Nallari, Pratibha

    2013-06-01

    Transposable elements (TEs) represent genome's dynamic component, causing mutations and genetic variations. Transposable elements can invade eukaryotic genomes in a short span; these are silenced by homology-dependent gene silencing and some functional parts of silenced elements are utilized to perform novel cellular functions. However, during the past two decades, major interest has been focused on the positive contribution of these elements in the evolution of genomes. The interaction between mobile DNAs and their host genomes are quite diverse, ranging from modifications of gene structure to alterations in general genome architecture and can be regarded as hidden magicians in shaping evolution of genomes. Some of the prominent examples that impressively demonstrate the beneficial impact of TEs on host biology over evolutionary time include their role in structure and functions of eukaryotic genomes. PMID:23852286

  10. Genome dynamics during experimental evolution.

    PubMed

    Barrick, Jeffrey E; Lenski, Richard E

    2013-12-01

    Evolutionary changes in organismal traits may occur either gradually or suddenly. However, until recently, there has been little direct information about how phenotypic changes are related to the rate and the nature of the underlying genotypic changes. Technological advances that facilitate whole-genome and whole-population sequencing, coupled with experiments that 'watch' evolution in action, have brought new precision to and insights into studies of mutation rates and genome evolution. In this Review, we discuss the evolutionary forces and ecological processes that govern genome dynamics in various laboratory systems in the context of relevant population genetic theory, and we relate these findings to evolution in natural populations. PMID:24166031

  11. Evolution of plant genome architecture.

    PubMed

    Wendel, Jonathan F; Jackson, Scott A; Meyers, Blake C; Wing, Rod A

    2016-01-01

    We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement. PMID:26926526

  12. Integrating sequence, evolution and functional genomics in regulatory genomics

    PubMed Central

    Vingron, Martin; Brazma, Alvis; Coulson, Richard; van Helden, Jacques; Manke, Thomas; Palin, Kimmo; Sand, Olivier; Ukkonen, Esko

    2009-01-01

    With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome. PMID:19226437

  13. Evolution of the cancer genome

    PubMed Central

    Yates, Lucy R.; Campbell, Peter J.

    2013-01-01

    The advent of massively parallel sequencing technologies has allowed the characterization of cancer genomes at an unprecedented resolution. Investigation of the mutational landscape of tumours is providing new insights into cancer genome evolution, laying bare the interplay of somatic mutation, adaptation of clones to their environment and natural selection. These studies have demonstrated the extent of the heterogeneity of cancer genomes, have allowed inferences to be made about the forces that act on nascent cancer clones as they evolve and have shown insight into the mutational processes that generate genetic variation. Here we review our emerging understanding of the dynamic evolution of the cancer genome and of the implications for basic cancer biology and the development of antitumour therapy. PMID:23044827

  14. Evolution of the cancer genome.

    PubMed

    Yates, Lucy R; Campbell, Peter J

    2012-11-01

    The advent of massively parallel sequencing technologies has allowed the characterization of cancer genomes at an unprecedented resolution. Investigation of the mutational landscape of tumours is providing new insights into cancer genome evolution, laying bare the interplay of somatic mutation, adaptation of clones to their environment and natural selection. These studies have demonstrated the extent of the heterogeneity of cancer genomes, have allowed inferences to be made about the forces that act on nascent cancer clones as they evolve and have shown insight into the mutational processes that generate genetic variation. Here we review our emerging understanding of the dynamic evolution of the cancer genome and of the implications for basic cancer biology and the development of antitumour therapy. PMID:23044827

  15. Widespread Recurrent Evolution of Genomic Features

    PubMed Central

    Maeso, Ignacio; Roy, Scott William; Irimia, Manuel

    2012-01-01

    The recent explosion of genome sequences from all major phylogenetic groups has unveiled an unexpected wealth of cases of recurrent evolution of strikingly similar genomic features in different lineages. Here, we review the diverse known types of recurrent evolution in eukaryotic genomes, with a special focus on metazoans, ranging from reductive genome evolution to origins of splice-leader trans-splicing, from tandem exon duplications to gene family expansions. We first propose a general classification scheme for evolutionary recurrence at the genomic level, based on the type of driving force—mutation or selection—and the environmental and genomic circumstances underlying these forces. We then discuss various cases of recurrent genomic evolution under this scheme. Finally, we provide a broader context for repeated genomic evolution, including the unique relationship of genomic recurrence with the genotype–phenotype map, and the ways in which the study of recurrent genomic evolution can be used to understand fundamental evolutionary processes. PMID:22417916

  16. Reverse genetic engineering of the human rhinovirus serotype 16 genome to introduce an antibody-detectable tag.

    PubMed

    Walker, Erin J; Jensen, Lora M; Ghildyal, Reena

    2015-01-01

    The ability to accurately detect viral proteins during infection is essential for virology research, and the lack of specific antibodies can make this detection difficult. Reverse genetic engineering of virus genomes to alter the wild-type genome is a powerful technique to introduce a detectable tag onto a viral protein. Here we outline a method to incorporate an influenza hemagglutinin epitope tag onto the 2A protease of HRV16. The method uses site-directed mutagenesis PCR to introduce the sequence for the HA antigen onto either the C or N termini of 2A protease while keeping the relevant internal cleavage sites intact. The new viral product is then cloned into a wild-type HRV16 plasmid and transfected into Ohio Hela cells to produce recombinant virus. PMID:25261314

  17. Critical analysis of rhinovirus RNA load quantification by real-time reverse transcription-PCR.

    PubMed

    Schibler, Manuel; Yerly, Sabine; Vieille, Gal; Docquier, Mylne; Turin, Lara; Kaiser, Laurent; Tapparel, Caroline

    2012-09-01

    Rhinoviruses are the most frequent cause of human respiratory infections, and quantitative rhinovirus diagnostic tools are needed for clinical investigations. Although results obtained by real-time reverse-transcription PCR (RT-PCR) assays are frequently converted to viral RNA loads, this presents several limitations regarding accurate virus RNA quantification, particularly given the need to reliably quantify all known rhinovirus genotypes with a single assay. Using an internal extraction control and serial dilutions of an in vitro-transcribed rhinovirus RNA reference standard, we validated a quantitative one-step real-time PCR assay. We then used chimeric rhinovirus genomes with 5'-untranslated regions (5'UTRs) originating from the three rhinovirus species and from one enterovirus to estimate the impact of the 5'UTR diversity. Respiratory specimens from infected patients were then also analyzed. The assay quantification ability ranged from 4.10 to 9.10 log RNA copies/ml, with an estimated error margin of 10%. This variation was mainly linked to target variability and interassay variability. Taken together, our results indicate that our assay can reliably estimate rhinovirus RNA load, provided that the appropriate error margin is used. In contrast, due to the lack of a universal rhinovirus RNA standard and the variability related to sample collection procedures, accurate absolute rhinovirus RNA quantification in respiratory specimens is currently hardly feasible. PMID:22718934

  18. Polyploidy and genome evolution in plants.

    PubMed

    Soltis, Pamela S; Marchant, D Blaine; Van de Peer, Yves; Soltis, Douglas E

    2015-12-01

    Plant genomes vary in size and complexity, fueled in part by processes of whole-genome duplication (WGD; polyploidy) and subsequent genome evolution. Despite repeated episodes of WGD throughout the evolutionary history of angiosperms in particular, the genomes are not uniformly large, and even plants with very small genomes carry the signatures of ancient duplication events. The processes governing the evolution of plant genomes following these ancient events are largely unknown. Here, we consider mechanisms of diploidization, evidence of genome reorganization in recently formed polyploid species, and macroevolutionary patterns of WGD in plant genomes and propose that the ongoing genomic changes observed in recent polyploids may illustrate the diploidization processes that result in ancient signatures of WGD over geological timescales. PMID:26656231

  19. Three tiers of genome evolution in reptiles

    PubMed Central

    Organ, Chris L.; Moreno, Ricardo Godnez; Edwards, Scott V.

    2008-01-01

    Characterization of reptilian genomes is essential for understanding the overall diversity and evolution of amniote genomes, because reptiles, which include birds, constitute a major fraction of the amniote evolutionary tree. To better understand the evolution and diversity of genomic characteristics in Reptilia, we conducted comparative analyses of online sequence data from Alligator mississippiensis (alligator) and Sphenodon punctatus (tuatara) as well as genome size and karyological data from a wide range of reptilian species. At the whole-genome and chromosomal tiers of organization, we find that reptilian genome size distribution is consistent with a model of continuous gradual evolution while genomic compartmentalization, as manifested in the number of microchromosomes and macrochromosomes, appears to have undergone early rapid change. At the sequence level, the third genomic tier, we find that exon size in Alligator is distributed in a pattern matching that of exons in Gallus (chicken), especially in the 101200 bp size class. A small spike in the fraction of exons in the 301 bp1 kb size class is also observed for Alligator, but more so for Sphenodon. For introns, we find that members of Reptilia have a larger fraction of introns within the 101 bp2 kb size class and a lower fraction of introns within the 530 kb size class than do mammals. These findings suggest that the mode of reptilian genome evolution varies across three hierarchical levels of the genome, a pattern consistent with a mosaic model of genomic evolution. PMID:21669810

  20. Cell Death in Genome Evolution

    PubMed Central

    Teng, Xinchen; Hardwick, J. Marie

    2015-01-01

    Inappropriate survival of abnormal cells underlies tumorigenesis. Most discoveries about programmed cell death have come from studying model organisms. Revisiting the experimental contexts that inspired these discoveries helps explain confounding biases that inevitably accompany such discoveries. Amending early biases has added a newcomer to the collection of cell death models. Analysis of gene-dependent death in yeast revealed the surprising influence of single gene mutations on subsequent eukaryotic genome evolution. Similar events may influence the selection for mutations during early tumorigenesis. The possibility that an early random mutation might drive the selection for a cancer driver mutation is conceivable but difficult to demonstrate. This was tested in yeast, revealing that mutation of almost any gene appears to specify the selection for a new second mutation. Some human tumors contain pairs of mutant genes homologous to co-occurring mutant genes in yeast. Here we consider how yeast again provide novel insights into tumorigenesis. PMID:25725369

  1. Clinical and molecular features of human rhinovirus C

    PubMed Central

    Bochkov, Yury A.; Gern, James E.

    2012-01-01

    A newly discovered group of human rhinoviruses (HRVs) has been classified as the HRV-C species based on distinct genomic features. HRV-Cs circulate worldwide, and are important causes of upper and lower respiratory illnesses. Methods to culture and produce these viruses have recently been developed, and should enable identification of unique features of HRV-C replication and biology. PMID:22285901

  2. Darwinian evolution in the light of genomics

    PubMed Central

    Koonin, Eugene V.

    2009-01-01

    Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future. PMID:19213802

  3. Darwinian evolution in the light of genomics.

    PubMed

    Koonin, Eugene V

    2009-03-01

    Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or 'forest' of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future. PMID:19213802

  4. Evolution of small prokaryotic genomes

    PubMed Central

    Martínez-Cano, David J.; Reyes-Prieto, Mariana; Martínez-Romero, Esperanza; Partida-Martínez, Laila P.; Latorre, Amparo; Moya, Andrés; Delaye, Luis

    2015-01-01

    As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria); metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature. PMID:25610432

  5. Genome architecture drives protein evolution in ciliates.

    PubMed

    Zufall, Rebecca A; McGrath, Casey L; Muse, Spencer V; Katz, Laura A

    2006-09-01

    Studies of microbial eukaryotes have been pivotal in the discovery of biological phenomena, including RNA editing, self-splicing RNA, and telomere addition. Here we extend this list by demonstrating that genome architecture, namely the extensive processing of somatic (macronuclear) genomes in some ciliate lineages, is associated with elevated rates of protein evolution. Using newly developed likelihood-based procedures for studying molecular evolution, we investigate 6 genes to compare 1) ciliate protein evolution to that of 3 other clades of eukaryotes (plants, animals, and fungi) and 2) protein evolution in ciliates with extensively processed macronuclear genomes to that of other ciliate lineages. In 5 of the 6 genes, ciliates are estimated to have a higher ratio of nonsynonymous/synonymous substitution rates, consistent with an increase in the rate of protein diversification in ciliates relative to other eukaryotes. Even more striking, there is a significant effect of genome architecture within ciliates as the most divergent proteins are consistently found in those lineages with the most highly processed macronuclear genomes. We propose a model whereby genome architecture-specifically chromosomal processing, amitosis within macronuclei, and epigenetics-allows ciliates to explore protein space in a novel manner. Further, we predict that examination of diverse eukaryotes will reveal additional evidence of the impact of genome architecture on molecular evolution. PMID:16760419

  6. Genomic tumor evolution of breast cancer.

    PubMed

    Sato, Fumiaki; Saji, Shigehira; Toi, Masakazu

    2016-01-01

    Owing to recent technical development of comprehensive genome-wide analysis such as next generation sequencing, deep biological insights of breast cancer have been revealed. Information of genomic mutations and rearrangements in patients' tumors is indispensable to understand the mechanism in carcinogenesis, progression, metastasis, and resistance to systemic treatment of breast cancer. To date, comprehensive genomic analyses illustrate not only base substitution patterns and lists of driver mutations and key rearrangements, but also a manner of tumor evolution. Breast cancer genome is dynamically changing and evolving during cancer development course from non-invasive disease via invasive primary tumor to metastatic tumor, and during treatment exposure. The accumulation pattern of base substitution and genomic rearrangement looks gradual and punctuated, respectively, in analogy with contrasting theories for evolution manner of species, Darwin's phyletic gradualism, and Eldredge and Gould's "punctuated equilibrium". Liquid biopsy is a non-invasive method to detect the genomic evolution of breast cancer. Genomic mutation patterns in circulating tumor cells and circulating cell-free tumor DNA represent those of tumors existing in patient body. Liquid biopsy methods are now under development for future application to clinical practice of cancer treatment. In this article, latest knowledge regarding breast cancer genome, especially in terms of 'tumorevolution', is summarized. PMID:25998191

  7. Evolutionary relationships within the human rhinovirus genus: comparison of serotypes 89, 2, and 14.

    PubMed Central

    Duechler, M; Skern, T; Sommergruber, W; Neubauer, C; Gruendler, P; Fogy, I; Blaas, D; Kuechler, E

    1987-01-01

    The complete nucleotide sequence of the genome of human rhinovirus type 89 was determined from the cDNA that had been cloned into Escherichia coli. The genome is 7152 nucleotides long and contains a single large open reading frame of 2164 codons. Translation commences at position 619 and ends 42 nucleotides before the poly(A) tract. The positions of three proteolytic cleavage sites in the polyprotein were determined by N-terminal amino acid sequencing of the capsid proteins; the remainder were predicted from comparisons with other picornaviruses. Extensive similarity between the derived amino acid sequences of human rhinovirus types 89 and 2 was found, whereas the similarity between human rhinovirus types 89 and 14 was considerably less. It is apparent that human rhinoviruses may be more closely related than has been previously thought. PMID:3033653

  8. Binding of a cellular factor to the 3' untranslated region of the RNA genomes of entero- and rhinoviruses plays a role in virus replication.

    PubMed

    Mellits, K H; Meredith, J M; Rohll, J B; Evans, D J; Almond, J W

    1998-07-01

    The presence of cellular factors that bind to the 3' untranslated region (UTR) of picornaviruses was investigated by electrophoretic mobility shift assays (EMSAs). A cellular factor(s) that binds specifically the 3' UTR of polio-, coxsackie- and rhinoviruses was detected. Furthermore, this factor(s) is distinct from those which bind to the 5' terminal 88 nt (the 'cloverleaf') of poliovirus. Mutations within the 3' UTR which decrease the affinity of the RNA for the cellular factor in EMSAs decrease RNA replication and virus viability. Revertants of these mutants display changes which are predicted to stabilize the RNA secondary structure of the 3' UTR. These results indicate that binding of a cellular factor to the UTR plays a role in virus replication and that RNA secondary structure is important for this function. PMID:9680135

  9. The Genomic Landscape of Compensatory Evolution

    PubMed Central

    Kalapis, Dorottya; Kovács, Károly; Fekete, Gergely; Farkas, Zoltán; Lázár, Viktória; Hrtyan, Mónika; Kemmeren, Patrick; Groot Koerkamp, Marian J. A.; Rutkai, Edit; Holstege, Frank C. P.; Papp, Balázs; Pál, Csaba

    2014-01-01

    Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations. However, as deleterious mutations are common in natural populations, they generate a strong selection pressure to mitigate their detrimental effects through compensatory genetic changes. This process can potentially influence directions of adaptive evolution by enabling evolutionary routes that are otherwise inaccessible. Therefore, the extent to which compensatory mutations shape genomic evolution is of central importance. Here, we studied the capacity of the baker's yeast genome to compensate the complete loss of genes during evolution, and explored the long-term consequences of this process. We initiated laboratory evolutionary experiments with over 180 haploid baker's yeast genotypes, all of which initially displayed slow growth owing to the deletion of a single gene. Compensatory evolution following gene loss was rapid and pervasive: 68% of the genotypes reached near wild-type fitness through accumulation of adaptive mutations elsewhere in the genome. As compensatory mutations have associated fitness costs, genotypes with especially low fitnesses were more likely to be subjects of compensatory evolution. Genomic analysis revealed that as compensatory mutations were generally specific to the functional defect incurred, convergent evolution at the molecular level was extremely rare. Moreover, the majority of the gene expression changes due to gene deletion remained unrestored. Accordingly, compensatory evolution promoted genomic divergence of parallel evolving populations. However, these different evolutionary outcomes are not phenotypically equivalent, as they generated diverse growth phenotypes across environments. Taken together, these results indicate that gene loss initiates adaptive genomic changes that rapidly restores fitness, but this process has substantial pleiotropic effects on cellular physiology and evolvability upon environmental change. Our work also implies that gene content variation across species could be partly due to the action of compensatory evolution rather than the passive loss of genes. PMID:25157590

  10. The evolution of the human genome.

    PubMed

    Simonti, Corinne N; Capra, John A

    2015-12-01

    Human genomes hold a record of the evolutionary forces that have shaped our species. Advances in DNA sequencing, functional genomics, and population genetic modeling have deepened our understanding of human demographic history, natural selection, and many other long-studied topics. These advances have also revealed many previously underappreciated factors that influence the evolution of the human genome, including functional modifications to DNA and histones, conserved 3D topological chromatin domains, structural variation, and heterogeneous mutation patterns along the genome. Using evolutionary theory as a lens to study these phenomena will lead to significant breakthroughs in understanding what makes us human and why we get sick. PMID:26338498

  11. Association of Rhinovirus Infections with Asthma

    PubMed Central

    Gern, James E.; Busse, William W.

    1999-01-01

    Rhinoviruses are the most common cause of the common cold, but they can cause more severe illnesses in people with underlying lung disorders such as asthma, chronic obstructive pulmonary disease, or cystic fibrosis. Epidemiologic studies with sensitive detection methods such as PCR have identified rhinovirus infection as a major source of asthma exacerbations in both children and adults, especially during the spring and fall. Since rhinoviruses cause little tissue destruction, it is presumed that the immune response to the infection may play an important role in the pathogenesis of rhinovirus-induced exacerbations of asthma. This review examines the epidemiologic association between rhinovirus infections and exacerbations of asthma and outlines current information on immune responses to rhinovirus infection and potential connections between antiviral responses and preexisting allergic inflammation. Finally, current and future strategies for treating rhinovirus infections and virus-induced exacerbations of asthma are discussed. PMID:9880472

  12. Genome plasticity and systems evolution in Streptomyces

    PubMed Central

    2012-01-01

    Background Streptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation. Results We present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication. Conclusions Our results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A better understanding of the LSE gene families will, on the other hand, bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes, such as the production of novel antibiotics, pathogenesis, and adaptive response to environmental challenges. PMID:22759432

  13. Punctuated Evolution of Prostate Cancer Genomes

    PubMed Central

    Baca, Sylvan C.; Prandi, Davide; Lawrence, Michael S.; Mosquera, Juan Miguel; Romanel, Alessandro; Drier, Yotam; Park, Kyung; Kitabayashi, Naoki; MacDonald, Theresa Y.; Ghandi, Mahmoud; Van Allen, Eliezer; Kryukov, Gregory V.; Sboner, Andrea; Theurillat, Jean-Philippe; Soong, T. David; Nickerson, Elizabeth; Auclair, Daniel; Tewari, Ashutosh; Beltran, Himisha; Onofrio, Robert C.; Boysen, Gunther; Guiducci, Candace; Barbieri, Christopher E.; Cibulskis, Kristian; Sivachenko, Andrey; Carter, Scott L.; Saksena, Gordon; Voet, Douglas; Ramos, Alex H; Winckler, Wendy; Cipicchio, Michelle; Ardlie, Kristin; Kantoff, Philip W.; Berger, Michael F.; Gabriel, Stacey B.; Golub, Todd R.; Meyerson, Matthew; Lander, Eric S.; Elemento, Olivier; Getz, Gad; Demichelis, Francesca; Rubin, Mark A.; Garraway, Levi A.

    2013-01-01

    SUMMARY The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term “chromoplexy”, frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis. PMID:23622249

  14. Evolution of gastropod mitochondrial genome arrangements

    PubMed Central

    2008-01-01

    Background Gastropod mitochondrial genomes exhibit an unusually great variety of gene orders compared to other metazoan mitochondrial genome such as e.g those of vertebrates. Hence, gastropod mitochondrial genomes constitute a good model system to study patterns, rates, and mechanisms of mitochondrial genome rearrangement. However, this kind of evolutionary comparative analysis requires a robust phylogenetic framework of the group under study, which has been elusive so far for gastropods in spite of the efforts carried out during the last two decades. Here, we report the complete nucleotide sequence of five mitochondrial genomes of gastropods (Pyramidella dolabrata, Ascobulla fragilis, Siphonaria pectinata, Onchidella celtica, and Myosotella myosotis), and we analyze them together with another ten complete mitochondrial genomes of gastropods currently available in molecular databases in order to reconstruct the phylogenetic relationships among the main lineages of gastropods. Results Comparative analyses with other mollusk mitochondrial genomes allowed us to describe molecular features and general trends in the evolution of mitochondrial genome organization in gastropods. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (ME, MP, ML, BI) arrived at a single topology, which was used to reconstruct the evolution of mitochondrial gene rearrangements in the group. Conclusion Four main lineages were identified within gastropods: Caenogastropoda, Vetigastropoda, Patellogastropoda, and Heterobranchia. Caenogastropoda and Vetigastropoda are sister taxa, as well as, Patellogastropoda and Heterobranchia. This result rejects the validity of the derived clade Apogastropoda (Caenogastropoda + Heterobranchia). The position of Patellogastropoda remains unclear likely due to long-branch attraction biases. Within Heterobranchia, the most heterogeneous group of gastropods, neither Euthyneura (because of the inclusion of P. dolabrata) nor Pulmonata (polyphyletic) nor Opisthobranchia (because of the inclusion S. pectinata) were recovered as monophyletic groups. The gene order of the Vetigastropoda might represent the ancestral mitochondrial gene order for Gastropoda and we propose that at least three major rearrangements have taken place in the evolution of gastropods: one in the ancestor of Caenogastropoda, another in the ancestor of Patellogastropoda, and one more in the ancestor of Heterobranchia. PMID:18302768

  15. Genomic and systems evolution in Vibrionaceae species

    PubMed Central

    Gu, Jianying; Neary, Jennifer; Cai, Hong; Moshfeghian, Audrey; Rodriguez, Stephen A; Lilburn, Timothy G; Wang, Yufeng

    2009-01-01

    Background The steadily increasing number of prokaryotic genomes has accelerated the study of genome evolution; in particular, the availability of sets of genomes from closely related bacteria has facilitated the exploration of the mechanisms underlying genome plasticity. The family Vibrionaceae is found in the Gammaproteobacteria and is abundant in aquatic environments. Taxa from the family Vibrionaceae are diversified in their life styles; some species are free living, others are symbiotic, and others are human pathogens. This diversity makes this family a useful set of model organisms for studying bacterial evolution. This evolution is driven by several forces, among them gene duplication and lateral gene transfer, which are believed to provide raw material for functional redundancy and novelty. The resultant gene copy increase in one genome is then detected as lineage-specific expansion (LSE). Results Here we present the results of a detailed comparison of the genomes of eleven Vibrionaceae strains that have distinct life styles and distinct phenotypes. The core genome shared by all eleven strains is composed of 1,882 genes, which make up about 31%50% of the genome repertoire. We further investigated the distribution and features of genes that have been specifically expanded in one unique lineage of the eleven strains. Abundant duplicate genes have been identified in the eleven Vibrionaceae strains, with 111% of the whole genomes composed lineage specific radiations. These LSEs occurred in two distinct patterns: the first type yields one or more copies of a single gene; we call this a single gene expansion. The second pattern has a high evolutionary impact, as the expansion involves two or more gene copies in a block, with the duplicated block located next to the original block (a contiguous block expansion) or at some distance from the original block (a discontiguous block expansion). We showed that LSEs involve genes that are tied to defense and pathogenesis mechanisms as well as in the fundamental life cycle of Vibrionaceae species. Conclusion Our results provide evidence of genome plasticity and rapid evolution within the family Vibrionaceae. The comparisons point to sources of genomic variation and candidates for lineage-specific adaptations of each Vibrionaceae pathogen or nonpathogen strain. Such lineage specific expansions could reveal components in bacterial systems that, by their enhanced genetic variability, can be tied to responses to environmental challenges, interesting phenotypes, or adaptive pathogenic responses to host challenges. PMID:19594870

  16. Comparative genomics reveals insights into avian genome evolution and adaptation

    PubMed Central

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

    2015-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  17. Comparative genomics reveals insights into avian genome evolution and adaptation.

    PubMed

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; Antunes, Agostinho; Greenwold, Matthew J; Meredith, Robert W; deen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R; Alfaro-Nez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V; Hara, Erina; Smith, Julia; Farr, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, Joo Paulo; Khan, Imran; Springer, Mark S; Gatesy, John; Hoffmann, Federico G; Opazo, Juan C; Hstad, Olle; Sawyer, Roger H; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A; Green, Richard E; O'Brien, Stephen J; Griffin, Darren; Johnson, Warren E; Haussler, David; Ryder, Oliver A; Willerslev, Eske; Graves, Gary R; Alstrm, Per; Fjelds, Jon; Mindell, David P; Edwards, Scott V; Braun, Edward L; Rahbek, Carsten; Burt, David W; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D; Gilbert, M Thomas P; Wang, Jun

    2014-12-12

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  18. Comparative genomics of brain size evolution

    PubMed Central

    Enard, Wolfgang

    2014-01-01

    Which genetic changes took place during mammalian, primate and human evolution to build a larger brain? To answer this question, one has to correlate genetic changes with brain size changes across a phylogeny. Such a comparative genomics approach provides unique information to better understand brain evolution and brain development. However, its statistical power is limited for example due to the limited number of species, the presumably complex genetics of brain size evolution and the large search space of mammalian genomes. Hence, it is crucial to add functional information, for example by limiting the search space to genes and regulatory elements known to play a role in the relevant cell types during brain development. Similarly, it is crucial to experimentally follow up on hypotheses generated by such a comparative approach. Recent progress in understanding the molecular and cellular mechanisms of mammalian brain development, in genome sequencing and in genome editing, promises to make a close integration of evolutionary and experimental methods a fruitful approach to better understand the genetics of mammalian brain size evolution. PMID:24904382

  19. Integrons: natural tools for bacterial genome evolution.

    PubMed

    Rowe-Magnus, D A; Mazel, D

    2001-10-01

    Integrons were first identified as the primary mechanism for antibiotic resistance gene capture and dissemination among Gram-negative bacteria. More recently, their role in genome evolution has been extended with the discovery of larger integron structures, the super-integrons, as genuine components of the genomes of many species throughout the gamma-proteobacterial radiation. The functional platforms of these integrons appear to be sedentary, whereas their gene cassette contents are highly variable. Nevertheless, the gene cassettes for which an activity has been experimentally demonstrated encode proteins related to simple adaptive functions and their recruitment is seen as providing the bacterial host with a selective advantage. The widespread occurrence of the integron system among Gram-negative bacteria is discussed, with special focus on the super-integrons. Some of the adaptive functions encoded by these genes are also reviewed, and implications of integron-mediated genome evolution in the emergence of novel bacterial species are highlighted. PMID:11587934

  20. Molecular and Phylogenetic Analyses of Bovine Rhinovirus Type 2 Shows it is Closely Related to Foot-and-Mouth Disease Virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine rhinovirus 2 (BRV2), a causative agent of respiratory disease in cattle, is currently an unclassified species tentatively assigned to the genus rhinovirus in the family Picornaviridae. A nearly full-length cDNA of the BRV2 genome was cloned and the nucleotide sequence from the poly(C) to the ...

  1. Survival of rhinoviruses on human fingers.

    PubMed

    L'Huillier, A G; Tapparel, C; Turin, L; Boquete-Suter, P; Thomas, Y; Kaiser, L

    2015-04-01

    Rhinovirus is the main cause of the common cold, which remains the most frequent infection worldwide among humans. Knowledge and understanding of the rhinovirus transmission route is important to reduce morbidity as only preventive measures are effective. In this study, we investigated the potential of rhinovirus to survive on fingers. Rhinovirus-B14 was deposited on fingers for 30, 60, 90 and 120 min. Survival was defined as the ability of the virus to grow after 7 days, confirmed by immunofluorescence. Rhinovirus survival was not dependent on incubation time on fingers. Droplet disruption had no influence on survival. Survival was frequent with high rhinovirus concentrations, but rare with low-concentration droplets, which corresponded to the usual rhinovirus concentrations in mucus observed in children and adults, respectively. Our study confirms that rhinovirus infectiousness is related to the viral concentration in droplets and suggests that children represent the main transmission source, which occurs only rarely via adults. It confirms also that rhinovirus hand-related transmission is possible and supports hand hygiene as a key prevention measure. PMID:25614158

  2. Microsatellites in Pursuit of Microbial Genome Evolution

    PubMed Central

    Saeed, Abdullah F.; Wang, Rongzhi; Wang, Shihua

    2016-01-01

    Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1–6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 –to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology. PMID:26779133

  3. Chimeric Rhinoviruses Obtained via Genetic Engineering or Artificially Induced Recombination Are Viable Only if the Polyprotein Coding Sequence Derives from the Same Species

    PubMed Central

    Schibler, Manuel; Piuz, Isabelle; Hao, Weidong

    2015-01-01

    ABSTRACT Recombination is a widespread phenomenon that ensures both the stability and variation of RNA viruses. This phenomenon occurs with different frequencies within species of the Enterovirus genus. Intraspecies recombination is described frequently among non-rhinovirus enteroviruses but appears to be sporadic in rhinoviruses. Interspecies recombination is even rarer for rhinoviruses and mostly is related to ancient events which contributed to the speciation of these viruses. We reported that artificially engineered 5? untranslated region (UTR) interspecies rhinovirus/rhinovirus or rhinovirus/non-rhinovirus enterovirus recombinants are fully viable. Using a similar approach, we demonstrated in this study that exchanges of the P1-2A polyprotein region between members of the same rhinovirus species, but not between members of different species, give rise to competent chimeras. To further assess the rhinovirus intra- and interspecies recombination potential, we used artificially induced recombination by cotransfection of 5?-end-deleted and 3?-end-deleted and replication-deficient genomes. In this system, intraspecies recombination also resulted in viable viruses with high frequency, whereas no interspecies rhinovirus recombinants could be recovered. Mapping intraspecies recombination sites within the polyprotein highlighted recombinant hotspots in nonstructural genes and at gene boundaries. Notably, all recombinants occurring at gene junctions presented in-frame sequence duplications, whereas most intragenic recombinants were homologous. Taken together, our results suggest that only intraspecies recombination gives rise to viable rhinovirus chimeras in the polyprotein coding region and that recombination hotspots map to nonstructural genes with in-frame duplications at gene boundaries. These data provide new insights regarding the mechanism and limitations of rhinovirus recombination. IMPORTANCE Recombination represents a means to ensure both the stability and the variation of RNA viruses. While intraspecies recombination is described frequently among non-rhinovirus enteroviruses, it seems to occur more rarely in rhinoviruses. Interspecies recombination is even rarer in this virus group and is mostly related to ancient events, which contributed to its speciation. We used engineered chimeric genomes and artificially induced RNA recombination to study experimentally the recombination potential of rhinoviruses and analyze recombination sites. Our results suggest that only intraspecies recombination gives rise to viable chimeras in the polyprotein coding region. Furthermore, characterization of intraspecies chimeras provides new insight into putative recombination hotspots within the polyprotein. In summary, we applied two powerful and complementary experimental approaches to improve current knowledge on rhinovirus recombination. PMID:25653446

  4. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution

    PubMed Central

    Rocha, Eduardo P. C.; Blanchard, Alain

    2002-01-01

    Mycoplasmas evolved by a drastic reduction in genome size, but their genomes contain numerous repeated sequences with important roles in their evolution. We have established a bioinformatic strategy to detect the major recombination hot-spots in the genomes of Mycoplasma pneumoniae, Mycoplasma genitalium, Ureaplasma urealyticum and Mycoplasma pulmonis. This allowed the identification of large numbers of potentially variable regions, as well as a comparison of the relative recombination potentials of different genomic regions. Different trends are perceptible among mycoplasmas, probably due to different functional and structural constraints. The largest potential for illegitimate recombination in M.pulmonis is found at the vsa locus and its comparison in two different strains reveals numerous changes since divergence. On the other hand, the main M.pneumoniae and M.genitalium adhesins rely on large distant repeats and, hence, homologous recombination for variation. However, the relation between the existence of repeats and antigenic variation is not necessarily straightforward, since repeats of P1 adhesin were found to be anti-correlated with epitopes recognized by patient antibodies. These different strategies have important consequences for the structures of genomes, since large distant repeats correlate well with the major chromosomal rearrangements. Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in comparison to co-oriented repeats. PMID:11972343

  5. Genomic Evolution of the Ascomycete Yeasts

    SciTech Connect

    Riley, Robert; Haridas, Sajeet; Salamov, Asaf; Boundy-Mills, Kyria; Goker, Markus; Hittinger, Chris; Klenk, Hans-Peter; Lopes, Mariana; Meir-Kolthoff, Jan P.; Rokas, Antonis; Rosa, Carlos; Scheuner, Carmen; Soares, Marco; Stielow, Benjamin; Wisecaver, Jennifer H.; Wolfe, Ken; Blackwell, Meredith; Kurtzman, Cletus; Grigoriev, Igor; Jeffries, Thomas

    2015-03-16

    Yeasts are important for industrial and biotechnological processes and show remarkable metabolic and phylogenetic diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. Phylogenetic analysis of these and previously published yeast genomes helped resolve the placement of species including Saitoella complicata, Babjeviella inositovora, Hyphopichia burtonii, and Metschnikowia bicuspidata. Moreover, we find that alternative nuclear codon usage, where CUG encodes serine instead of leucine, are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes, and a tendency towards more introns in early-diverging species. Analysis of enzyme phylogeny gives insights into the evolution of metabolic capabilities such as methanol utilization and assimilation of alternative carbon sources.

  6. Molecular evolution of genes in avian genomes

    PubMed Central

    2010-01-01

    Background Obtaining a draft genome sequence of the zebra finch (Taeniopygia guttata), the second bird genome to be sequenced, provides the necessary resource for whole-genome comparative analysis of gene sequence evolution in a non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and to contrast these with the situation in mammals, we aligned the protein-coding sequences of 8,384 1:1 orthologs of chicken, zebra finch, a lizard and three mammalian species. Results We found clear differences in the substitution rate at fourfold degenerate sites, being lowest in the ancestral bird lineage, intermediate in the chicken lineage and highest in the zebra finch lineage, possibly reflecting differences in generation time. We identified positively selected and/or rapidly evolving genes in avian lineages and found an over-representation of several functional classes, including anion transporter activity, calcium ion binding, cell adhesion and microtubule cytoskeleton. Conclusions Focusing specifically on genes of neurological interest and genes differentially expressed in the unique vocal control nuclei of the songbird brain, we find a number of positively selected genes, including synaptic receptors. We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between ω and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes. PMID:20573239

  7. The mode and tempo of genome size evolution in eukaryotes

    PubMed Central

    Oliver, Matthew J.; Petrov, Dmitri; Ackerly, David; Falkowski, Paul; Schofield, Oscar M.

    2007-01-01

    Eukaryotic genome size varies over five orders of magnitude; however, the distribution is strongly skewed toward small values. Genome size is highly correlated to a number of phenotypic traits, suggesting that the relative lack of large genomes in eukaryotes is due to selective removal. Using phylogenetic contrasts, we show that the rate of genome size evolution is proportional to genome size, with the fastest rates occurring in the largest genomes. This trend is evident across the 20 major eukaryotic clades analyzed, indicating that over long time scales, proportional change is the dominant and universal mode of genome-size evolution in eukaryotes. Our results reveal that the evolution of eukaryotic genome size can be described by a simple proportional model of evolution. This model explains the skewed distribution of eukaryotic genome sizes without invoking strong selection against large genomes. PMID:17420184

  8. Chromosome Evolution and Genome Miniaturization in Minifish

    PubMed Central

    Liu, Shaojun; Hui, Tan Heok; Tan, Sze Ley; Hong, Yunhan

    2012-01-01

    Background Paedocypris is a newly established genus of fish in Southeast Asia. Paedocypris is characterized by several unique features, including a tiny adult size (thus named miniature fish or minifish), fragmentary habitats of acidic peat blackwater swamps, an unusual reproduction mode and truncated development. These peculiarities lend themselves excellent for studying chromosome evolution and rapid speciation in vertebrates but also make them highly controversial for the phylogenetic position. Methodology and Principal Findings We have established an organ procedure to prepare chromosome spreads from tiny organs of minifish and performed a cytogenetic study on two species of the genus Paedocypris, namely P. carbunculus (Pc) and P. sp. Singkep (Ps). We found 30 and 34 chromosomes in diploid cells of Pc and Ps, respectively, which are unusual in teleost fishes. The diploid metaphase has 5 pairs of metacentrics and 7 pairs of subtelocentrics in Pc compared to 3 pairs of metacentrics and 11 pairs of subtelocentrics in Ps, whereas the haploid metaphase contains 5 metacentrics and 7 subtelocentrics in Pc compared to 3 metacentrics and 11 subtelocentrics Ps. Chromosome behavior in first meiosis revealed the presence of a chromosomal ring consisting of 2 metacentrics in Pc, suggesting that centric fusion rather than fission was responsible for the karyotypic evolution from Ps to Pc. Flow cytometry revealed that Pc had a 45% nuclear staining intensity relative to medaka whose genome is 700 Mb in size and contains 0.81 pg DNA. The Pc genome should have 315 Mb in length and 0.36 pg of DNA, which represent one of the smallest values in vertebrates, suggesting genome miniaturization in this organism. Conclusions Our data demonstrate that gross chromosome rearrangements and genome miniaturization have accompanied the evolution of Paedocypris fishes. Our data also place Paedocypris outside currently described taxa of the Cypriniformes. PMID:22615970

  9. Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

    SciTech Connect

    Lykidis, Athanasios

    2006-12-01

    Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.

  10. Using genomic tools to study regulatory evolution.

    PubMed

    Gilad, Yoav

    2012-01-01

    Differences in gene regulation are thought to play an important role in speciation and adaptation. Comparative genomic studies of gene expression levels have identified a large number of differentially expressed genes among species, and, in a number of cases, also pointed to connections between interspecies differences in gene regulation and differences in ultimate physiological or morphological phenotypes. The mechanisms underlying changes in gene regulation are also being actively studied using comparative genomic approaches. However, the relative importance of different regulatory mechanisms to interspecies differences in gene expression levels is not yet well understood. In particular, it is often difficult to infer causality between apparent differences in regulatory mechanisms and changes in gene expression levels, a challenge that is compounded by the fact that the link between sequence variation and gene regulation is not clear. Indeed, in certain cases, gene regulation can be conserved even when sequences at associated regulatory elements have changed. In this chapter, I examine different genomic approaches to the study of regulatory evolution and the underlying genetic and epigenetic regulatory mechanisms. I try to distinguish between hypothesis-driven and exploratory studies, and argue that the latter class of studies provides valuable information in its own right as well as necessary context for the former. I discuss issues related to study designs and statistical analyses of genomic studies, and review the evidence for natural selection on gene expression levels and associated regulatory mechanisms. Most of the issues that are discussed pertain to the general nature of multivariate genomic data, and thus are often relevant regardless of the technology that is used to collect high-throughput genomic data (for example, microarrays or massively parallel sequencing). PMID:22399466

  11. Productive entry pathways of human rhinoviruses.

    PubMed

    Fuchs, Renate; Blaas, Dieter

    2012-01-01

    Currently, complete or partial genome sequences of more than 150 human rhinovirus (HRV) isolates are known. Twelve species A use members of the low-density lipoprotein receptor family for cell entry, whereas the remaining HRV-A and all HRV-B bind ICAM-1. HRV-Cs exploit an unknown receptor. At least all A and B type viruses depend on receptor-mediated endocytosis for infection. In HeLa cells, they are internalized mainly by a clathrin- and dynamin-dependent mechanism. Upon uptake into acidic compartments, the icosahedral HRV capsid expands by ~4% and holes open at the 2-fold axes, close to the pseudo-3-fold axes and at the base of the star-shaped dome protruding at the vertices. RNA-protein interactions are broken and new ones are established, the small internal myristoylated capsid protein VP4 is expelled, and amphipathic N-terminal sequences of VP1 become exposed. The now hydrophobic subviral particle attaches to the inner surface of endosomes and transfers its genomic (+) ssRNA into the cytosol. The RNA leaves the virus starting with the poly(A) tail at its 3'-end and passes through a membrane pore contiguous with one of the holes in the capsid wall. Alternatively, the endosome is disrupted and the RNA freely diffuses into the cytoplasm. PMID:23227049

  12. Distinct cellular receptor interactions in poliovirus and rhinoviruses

    PubMed Central

    Xing, Li; Tjarnlund, Karin; Lindqvist, Birgitta; Kaplan, Gerardo G.; Feigelstock, Dino; Cheng, R.Holland; Casasnovas, Jos M.

    2000-01-01

    Receptor binding to human poliovirus type 1 (PV1/M) and the major group of human rhinoviruses (HRV) was studied comparatively to uncover the evolution of receptor recognition in picornaviruses. Surface plas mon resonance showed receptor binding to PV1/M with faster association and dissociation rates than to HRV3 and HRV16, two serotypes that have similar binding kinetics. The faster rate for receptor association to PV1/M suggested a relatively more accessible binding site. Thermodynamics for receptor binding to the viruses and assays for receptor-mediated virus uncoating showed a more disruptive receptor interaction with PV1/M than with HRV3 or HRV16. Cryo-electron microscopy and image reconstruction of receptorPV1/M complexes revealed receptor binding to the wall of surface protrusions surrounding the canyon, a depressive surface in the capsid where the rhinovirus receptor binds. These data reveal more exposed receptor-binding sites in poliovirus than rhinoviruses, which are less protected from immune surveillance but more suited for receptor-mediated virus uncoating and entry at the cell surface. PMID:10716921

  13. The genomic evolution of human prostate cancer.

    PubMed

    Mitchell, T; Neal, D E

    2015-07-14

    Prostate cancers are highly prevalent in the developed world, with inheritable risk contributing appreciably to tumour development. Genomic heterogeneity within individual prostate glands and between patients derives predominantly from structural variants and copy-number aberrations. Subtypes of prostate cancers are being delineated through the increasing use of next-generation sequencing, but these subtypes are yet to be used to guide the prognosis or therapeutic strategy. Herein, we review our current knowledge of the mutational landscape of human prostate cancer, describing what is known of the common mutations underpinning its development. We evaluate recurrent prostate-specific mutations prior to discussing the mutational events that are shared both in prostate cancer and across multiple cancer types. From these data, we construct a putative overview of the genomic evolution of human prostate cancer. PMID:26125442

  14. The genomic evolution of human prostate cancer

    PubMed Central

    Mitchell, T; Neal, D E

    2015-01-01

    Prostate cancers are highly prevalent in the developed world, with inheritable risk contributing appreciably to tumour development. Genomic heterogeneity within individual prostate glands and between patients derives predominantly from structural variants and copy-number aberrations. Subtypes of prostate cancers are being delineated through the increasing use of next-generation sequencing, but these subtypes are yet to be used to guide the prognosis or therapeutic strategy. Herein, we review our current knowledge of the mutational landscape of human prostate cancer, describing what is known of the common mutations underpinning its development. We evaluate recurrent prostate-specific mutations prior to discussing the mutational events that are shared both in prostate cancer and across multiple cancer types. From these data, we construct a putative overview of the genomic evolution of human prostate cancer. PMID:26125442

  15. Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Complete mitochondrial genome sequences have become important tools for the study of genome architecture, phylogeny, and molecular evolution. Despite the rapid increase in available mitogenomes, the taxonomic sampling often poorly reflects phylogenetic diversity and is often also biased ...

  16. Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction

    PubMed Central

    diCenzo, George C.; MacLean, Allyson M.; Milunovic, Branislava; Golding, G. Brian; Finan, Turlough M.

    2014-01-01

    Many bacteria carry two or more chromosome-like replicons. This occurs in pathogens such as Vibrio cholerea and Brucella abortis as well as in many N2-fixing plant symbionts including all isolates of the alfalfa root-nodule bacteria Sinorhizobium meliloti. Understanding the evolution and role of this multipartite genome organization will provide significant insight into these important organisms; yet this knowledge remains incomplete, in part, because technical challenges of large-scale genome manipulations have limited experimental analyses. The distinct evolutionary histories and characteristics of the three replicons that constitute the S. meliloti genome (the chromosome (3.65 Mb), pSymA megaplasmid (1.35 Mb), and pSymB chromid (1.68 Mb)) makes this a good model to examine this topic. We transferred essential genes from pSymB into the chromosome, and constructed strains that lack pSymB as well as both pSymA and pSymB. This is the largest reduction (45.4%, 3.04 megabases, 2866 genes) of a prokaryotic genome to date and the first removal of an essential chromid. Strikingly, strains lacking pSymA and pSymB (ΔpSymAB) lost the ability to utilize 55 of 74 carbon sources and various sources of nitrogen, phosphorous and sulfur, yet the ΔpSymAB strain grew well in minimal salts media and in sterile soil. This suggests that the core chromosome is sufficient for growth in a bulk soil environment and that the pSymA and pSymB replicons carry genes with more specialized functions such as growth in the rhizosphere and interaction with the plant. These experimental data support a generalized evolutionary model, in which non-chromosomal replicons primarily carry genes with more specialized functions. These large secondary replicons increase the organism's niche range, which offsets their metabolic burden on the cell (e.g. pSymA). Subsequent co-evolution with the chromosome then leads to the formation of a chromid through the acquisition of functions core to all niches (e.g. pSymB). PMID:25340565

  17. Reverse genetics system for studying human rhinovirus infections.

    PubMed

    Lee, Wai-Ming; Wang, Wensheng; Bochkov, Yury A; Lee, Iris

    2015-01-01

    Human rhinovirus (HRV) contains a 7.2 kb messenger-sense RNA genome which is the template for reproducing progeny viruses after it enters the cytoplasm of a host cell. Reverse genetics refers to the regeneration of progeny viruses from an artificial cDNA copy of the RNA genome of an RNA virus. It has been a powerful molecular genetic tool for studying HRV and other RNA viruses because the artificial DNA stage makes it practical to introduce specific mutations into the viral RNA genome. This chapter uses HRV-16 as the model virus to illustrate the strategy and methods for constructing and cloning the artificial cDNA copy of a full-length HRV genome, identifying the infectious cDNA clone isolates, and selecting the most vigorous cDNA clone isolate to serve as the standard parental clone for future molecular genetic study of the virus. PMID:25261313

  18. Constraints and plasticity in genome and molecular-phenome evolution

    PubMed Central

    Koonin, Eugene V.; Wolf, Yuri I.

    2012-01-01

    Multiple constraints variously affect different parts of the genomes of diverse life forms. The selective pressures that shape the evolution of viral, archaeal, bacterial and eukaryotic genomes differ markedly, even among relatively closely related animal and bacterial lineages; by contrast, constraints affecting protein evolution seem to be more universal. The constraints that shape the evolution of genomes and phenomes are complemented by the plasticity and robustness of genome architecture, expression and regulation. Taken together, these findings are starting to reveal complex networks of evolutionary processes that must be integrated to attain a new synthesis of evolutionary biology. PMID:20548290

  19. Apprehending multicellularity: regulatory networks, genomics and evolution

    PubMed Central

    Aravind, L.; Anantharaman, Vivek; Venancio, Thiago M.

    2009-01-01

    The genomic revolution has provided the first glimpses of the architecture of regulatory networks. Combined with evolutionary information, the “network view” of life processes leads to remarkable insights into how biological systems have been shaped by various forces. This understanding is critical because biological systems, including regulatory networks, are not products of engineering but of historical contingencies. In this light, we attempt a synthetic overview of the natural history of regulatory networks operating in the development and differentiation of multicellular organisms. We first introduce regulatory networks and their organizational principles as can be deduced using ideas from the graph theory. We then discuss findings from comparative genomics to illustrate the effects of lineage-specific expansions, gene-loss, and non-protein-coding DNA on the architecture of networks. We consider the interaction between expansions of transcription factors, and cis regulatory and more general chromatin state stabilizing elements in the emergence of morphological complexity. Finally, we consider a case study of the Notch sub-network, which is present throughout Metazoa, to examine how such a regulatory system has been pieced together in evolution from new innovations and pre-existing components that were originally functionally distinct. PMID:19530132

  20. Genome reduction as the dominant mode of evolution

    PubMed Central

    Wolf, Yuri I; Koonin, Eugene V

    2013-01-01

    A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron-rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification. PMID:23801028

  1. Genome size diversity in orchids: consequences and evolution

    PubMed Central

    Leitch, I. J.; Kahandawala, I.; Suda, J.; Hanson, L.; Ingrouille, M. J.; Chase, M. W.; Fay, M. F.

    2009-01-01

    Background The amount of DNA comprising the genome of an organism (its genome size) varies a remarkable 40 000-fold across eukaryotes, yet most groups are characterized by much narrower ranges (e.g. 14-fold in gymnosperms, 3- to 4-fold in mammals). Angiosperms stand out as one of the most variable groups with genome sizes varying nearly 2000-fold. Nevertheless within angiosperms the majority of families are characterized by genomes which are small and vary little. Species with large genomes are mostly restricted to a few monocots families including Orchidaceae. Scope A survey of the literature revealed that genome size data for Orchidaceae are comparatively rare representing just 327 species. Nevertheless they reveal that Orchidaceae are currently the most variable angiosperm family with genome sizes ranging 168-fold (1C = 0·33–55·4 pg). Analysing the data provided insights into the distribution, evolution and possible consequences to the plant of this genome size diversity. Conclusions Superimposing the data onto the increasingly robust phylogenetic tree of Orchidaceae revealed how different subfamilies were characterized by distinct genome size profiles. Epidendroideae possessed the greatest range of genome sizes, although the majority of species had small genomes. In contrast, the largest genomes were found in subfamilies Cypripedioideae and Vanilloideae. Genome size evolution within this subfamily was analysed as this is the only one with reasonable representation of data. This approach highlighted striking differences in genome size and karyotype evolution between the closely related Cypripedium, Paphiopedilum and Phragmipedium. As to the consequences of genome size diversity, various studies revealed that this has both practical (e.g. application of genetic fingerprinting techniques) and biological consequences (e.g. affecting where and when an orchid may grow) and emphasizes the importance of obtaining further genome size data given the considerable phylogenetic gaps which have been highlighted by the current study. PMID:19168860

  2. Evolution, language and analogy in functional genomics

    NASA Technical Reports Server (NTRS)

    Benner, S. A.; Gaucher, E. A.

    2001-01-01

    Almost a century ago, Wittgenstein pointed out that theory in science is intricately connected to language. This connection is not a frequent topic in the genomics literature. But a case can be made that functional genomics is today hindered by the paradoxes that Wittgenstein identified. If this is true, until these paradoxes are recognized and addressed, functional genomics will continue to be limited in its ability to extrapolate information from genomic sequences.

  3. Interpreting Mammalian Evolution using Fugu Genome Comparisons

    SciTech Connect

    Stubbs, L; Ovcharenko, I; Loots, G G

    2004-04-02

    Comparative sequence analysis of the human and the pufferfish Fugu rubripes (fugu) genomes has revealed several novel functional coding and noncoding regions in the human genome. In particular, the fugu genome has been extremely valuable for identifying transcriptional regulatory elements in human loci harboring unusually high levels of evolutionary conservation to rodent genomes. In such regions, the large evolutionary distance between human and fishes provides an additional filter through which functional noncoding elements can be detected with high efficiency.

  4. Evolution of genome size and complexity in the rhabdoviridae.

    PubMed

    Walker, Peter J; Firth, Cadhla; Widen, Steven G; Blasdell, Kim R; Guzman, Hilda; Wood, Thomas G; Paradkar, Prasad N; Holmes, Edward C; Tesh, Robert B; Vasilakis, Nikos

    2015-02-01

    RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3' to 5' direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae. PMID:25679389

  5. Evolution of Genome Size and Complexity in the Rhabdoviridae

    PubMed Central

    Walker, Peter J.; Firth, Cadhla; Widen, Steven G.; Blasdell, Kim R.; Guzman, Hilda; Wood, Thomas G.; Paradkar, Prasad N.; Holmes, Edward C.; Tesh, Robert B.; Vasilakis, Nikos

    2015-01-01

    RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3’ to 5’ direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae. PMID:25679389

  6. A taste of pineapple evolution through genome sequencing.

    PubMed

    Xu, Qing; Liu, Zhong-Jian

    2015-12-01

    The genome sequence assembly of the highly heterozygous Ananas comosus and its varieties is an impressive technical achievement. The sequence opens the door to a greater understanding of pineapple morphology and evolution. PMID:26620110

  7. The amphioxus genome and the evolution of the chordate karyotype

    SciTech Connect

    Putnam, Nicholas H.; Butts, Thomas; Ferrier, David E.K.; Furlong, Rebecca F.; Hellsten, Uffe; Kawashima, Takeshi; Robinson-Rechavi, Marc; Shoguchi, Eiichi; Terry, Astrid; Yu, Jr-Kai; Benito-Gutierrez, Elia; Dubchak, Inna; Garcia-Fernandez, Jordi; Gibson-Brown, Jeremy J.; Grigoriev, Igor V.; Horton, Amy C.; de Jong, Pieter J.; Jurka, Jerzy; Kapitonov, Vladimir; Kohara, Yuji; Kuroki, Yoko; Lindquist, Erika; Lucas, Susan; Osoegawa, Kazutoyo; Pennacchio, Len A.; Salamov, Asaf A.; Satou, Yutaka; Sauka-Spengler, Tatjana; Schmutz [, Jeremy; Shin-I, Tadasu; Toyoda, Atsushi; Bronner-Fraser, Marianne; Fujiyama, Asao; Holland, Linda Z.; Holland, Peter W. H.; Satoh, Nori; Rokhsar, Daniel S.

    2008-04-01

    Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage with a fossil record dating back to the Cambrian. We describe the structure and gene content of the highly polymorphic {approx}520 million base pair genome of the Florida lancelet Branchiostoma floridae, and analyze it in the context of chordate evolution. Whole genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets, and vertebrates), and allow reconstruction of not only the gene complement of the last common chordate ancestor, but also a partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

  8. The amphioxus genome and the evolution of the chordate karyotype.

    PubMed

    Putnam, Nicholas H; Butts, Thomas; Ferrier, David E K; Furlong, Rebecca F; Hellsten, Uffe; Kawashima, Takeshi; Robinson-Rechavi, Marc; Shoguchi, Eiichi; Terry, Astrid; Yu, Jr-Kai; Benito-Gutiérrez, E Lia; Dubchak, Inna; Garcia-Fernàndez, Jordi; Gibson-Brown, Jeremy J; Grigoriev, Igor V; Horton, Amy C; de Jong, Pieter J; Jurka, Jerzy; Kapitonov, Vladimir V; Kohara, Yuji; Kuroki, Yoko; Lindquist, Erika; Lucas, Susan; Osoegawa, Kazutoyo; Pennacchio, Len A; Salamov, Asaf A; Satou, Yutaka; Sauka-Spengler, Tatjana; Schmutz, Jeremy; Shin-I, Tadasu; Toyoda, Atsushi; Bronner-Fraser, Marianne; Fujiyama, Asao; Holland, Linda Z; Holland, Peter W H; Satoh, Nori; Rokhsar, Daniel S

    2008-06-19

    Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution. PMID:18563158

  9. Evolution of Genome Size and Complexity in Pinus

    PubMed Central

    Morse, Alison M.; Peterson, Daniel G.; Islam-Faridi, M. Nurul; Smith, Katherine E.; Magbanua, Zenaida; Garcia, Saul A.; Kubisiak, Thomas L.; Amerson, Henry V.; Carlson, John E.; Nelson, C. Dana; Davis, John M.

    2009-01-01

    Background Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood. Methodology/Principal Findings Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA. Conclusions/Significance Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes. PMID:19194510

  10. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

    PubMed Central

    Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A. P.; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J. Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

    2014-01-01

    Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

  11. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.

    PubMed

    Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A P; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

    2014-01-01

    Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

  12. Genome size shifts: karyotype evolution in Crepis section Neglectoides (Asteraceae).

    PubMed

    Enke, N; Kunze, R; Pustahija, F; Glckner, G; Zimmermann, J; Oberlnder, J; Kamari, G; Siljak-Yakovlev, S

    2015-07-01

    Plant genome size evolution is a very dynamic process: the ancestral genome of angiosperms was initially most likely small, which led to a tendency towards genome increase during evolution. However, findings in several angiosperm lineages demonstrate mechanisms that also led to genome size contraction. Recent molecular investigations on the Asteraceae genus Crepis suggest that several genomic reduction events have occurred during the evolution of the genus. This study focuses on the Mediterranean Crepis sect. Neglectoides, which includes three species with some of the smallest genomes within the whole genus. Crepis neglecta has the largest genome in sect. Neglectoides, approximately twice the size of the two species Crepis cretica and Crepis hellenica. Whereas C.cretica and C.hellencia are more closely related to each other than to C.neglecta the karyotypes of the latter species and C.cretica are similar, while that of C.hellenica differs considerably. Here, the karyotypic organisation of the three species is investigated with fluorescence in-situ hybridisation and studied in a molecular phylogenetic framework based on the nuclear markers Actin, CHR12, CPN60B, GPCR1 and XTH23. Our findings further corroborate the occurrence of genome size contraction in Crepis, and suggest that the difference in genome size between C.neglecta and C.cretica is mostly due to elimination of dispersed repetitive elements, whereas chromosomal reorganisation was involved in the karyotype formation of C.hellenica. PMID:25683604

  13. Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales.

    PubMed

    Dong, Wenpan; Xu, Chao; Cheng, Tao; Zhou, Shiliang

    2013-01-01

    Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles. PMID:24205047

  14. Ins and outs of plastid genome evolution.

    PubMed

    Wolfe, K H; Morden, C W; Palmer, J D

    1991-12-01

    Recent findings have established cracks in the straight-laced image of the plastid genome as a molecule whose sole function is photosynthesis and whose gene content is highly conserved. Genes for numerous non-photosynthetic functions have been identified. Algal plastid genomes contain many genes with no homologs in angiosperms, and the recent transfer of genes from the plastid to the nuclear genome has been described. Wholesale abandonment of genes encoding photosynthetic and gene-expression functions has occurred in the plastid genomes of a non-green plant and alga. The origins of plastid DNA, its use in phylogenetic studies, and the origins of plastid introns are also reviewed. PMID:1822284

  15. Ins and outs of plastid genome evolution.

    TOXLINE Toxicology Bibliographic Information

    Wolfe KH; Morden CW; Palmer JD

    1991-12-01

    Recent findings have established cracks in the straight-laced image of the plastid genome as a molecule whose sole function is photosynthesis and whose gene content is highly conserved. Genes for numerous non-photosynthetic functions have been identified. Algal plastid genomes contain many genes with no homologs in angiosperms, and the recent transfer of genes from the plastid to the nuclear genome has been described. Wholesale abandonment of genes encoding photosynthetic and gene-expression functions has occurred in the plastid genomes of a non-green plant and alga. The origins of plastid DNA, its use in phylogenetic studies, and the origins of plastid introns are also reviewed.

  16. Evolution Analysis of Simple Sequence Repeats in Plant Genome

    PubMed Central

    Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

    2015-01-01

    Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1–3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution. PMID:26630570

  17. Human rhinovirus 2: complete nucleotide sequence and proteolytic processing signals in the capsid protein region.

    PubMed Central

    Skern, T; Sommergruber, W; Blaas, D; Gruendler, P; Fraundorfer, F; Pieler, C; Fogy, I; Kuechler, E

    1985-01-01

    cDNA clones representing the entire genome of human rhinovirus 2 have been obtained and used to determine the complete nucleotide sequence. The genome consists of 7102 nucleotides and possesses a long open reading frame of 6450 nucleotides; this reading frame is initiated 611 nucleotides from the 5' end and stops 42 nucleotides from the polyA tract. The N-terminal sequences of three of the viral capsid proteins have been elucidated, thus defining the positions of three cleavage sites on the polyprotein. The extensive amino acid sequence homology with poliovirus and human rhinovirus 14 enabled the other cleavage sites to be predicted. Cleavages in the 3' half of the molecule appear to take place predominantly at Gln-Gly pairs, whereas those in the 5' half (including the capsid proteins) are more heterogeneous. PMID:2987843

  18. Rapid Genome Evolution Revealed by Comparative Sequence Analysis of Orthologous Regions from Four Triticeae Genomes

    PubMed Central

    Gu, Yong Qiang; Coleman-Derr, Devin; Kong, Xiuying; Anderson, Olin D.

    2004-01-01

    Bread wheat (Triticum aestivum) is an allohexaploid species, consisting of three subgenomes (A, B, and D). To study the molecular evolution of these closely related genomes, we compared the sequence of a 307-kb physical contig covering the high molecular weight (HMW)-glutenin locus from the A genome of durum wheat (Triticum turgidum, AABB) with the orthologous regions from the B genome of the same wheat and the D genome of the diploid wheat Aegilops tauschii (Anderson et al., 2003; Kong et al., 2004). Although gene colinearity appears to be retained, four out of six genes including the two paralogous HMW-glutenin genes are disrupted in the orthologous region of the A genome. Mechanisms involved in gene disruption in the A genome include retroelement insertions, sequence deletions, and mutations causing in-frame stop codons in the coding sequences. Comparative sequence analysis also revealed that sequences in the colinear intergenic regions of these different genomes were generally not conserved. The rapid genome evolution in these regions is attributable mainly to the large number of retrotransposon insertions that occurred after the divergence of the three wheat genomes. Our comparative studies indicate that the B genome diverged prior to the separation of the A and D genomes. Furthermore, sequence comparison of two distinct types of allelic variations at the HMW-glutenin loci in the A genomes of different hexaploid wheat cultivars with the A genome locus of durum wheat indicates that hexaploid wheat may have more than one tetraploid ancestor. PMID:15122014

  19. Insights into bilaterian evolution from three spiralian genomes

    PubMed Central

    Simakov, Oleg; Marletaz, Ferdinand; Cho, Sung-Jin; Edsinger-Gonzales, Eric; Havlak, Paul; Hellsten, Uffe; Kuo, Dian-Han; Larsson, Tomas; Lv, Jie; Arendt, Detlev; Savage, Robert; Osoegawa, Kazutoyo; de Jong, Pieter; Grimwood, Jane; Chapman, Jarrod A.; Shapiro, Harris; Aerts, Andrea; Otillar, Robert P.; Terry, Astrid Y.; Boore, Jeffrey L.; Grigoriev, Igor V.; Lindberg, David R.; Seaver, Elaine C.; Weisblat, David A.; Putnam, Nicholas H.; Rokhsar, Daniel S.

    2014-01-01

    Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology13. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome. PMID:23254933

  20. Insights into bilaterian evolution from three spiralian genomes

    SciTech Connect

    Simakov, Oleg; Marletaz, Ferdinand; Cho, Sung-Jin; Edsinger-Gonzales, Eric; Havlak, Paul; Hellsten, Uffe; Kuo, Dian-Han; Larsson, Tomas; Lv, Jie; Arendt, Detlev; Savage, Robert; Osoegawa, Kazutoyo; de Jong, Pieter; Grimwood, Jane; Chapman, Jarrod A.; Shapiro, Harris; Otillar, Robert P.; Terry, Astrid Y.; Boore, Jeffrey L.; Grigoriev, Igor V.; Lindberg, David R.; Seaver, Elaine C.; Weisblat, David A.; Putnam, Nicholas H.; Rokhsar, Daniel S.; Aerts, Andrea

    2012-01-07

    Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.

  1. Global Distribution of Novel Rhinovirus Genotype

    PubMed Central

    Renwick, Neil; Venter, Marietjie; Jarman, Richard G.; Ghosh, Dhrubaa; Kndgen, Sophie; Shrestha, Sanjaya K.; Hoegh, A. Mette; Casas, Inmaculada; Adjogoua, Edgard Valerie; Akoua-Koffi, Chantal; Myint, Khin Saw; Williams, David T.; Chidlow, Glenys; van den Berg, Ria; Calvo, Cristina; Koch, Orienka; Palacios, Gustavo; Kapoor, Vishal; Villari, Joseph; Dominguez, Samuel R.; Holmes, Kathryn V.; Harnett, Gerry; Smith, David; Mackenzie, John S.; Ellerbrok, Heinz; Schweiger, Brunhilde; Schnning, Kristian; Chadha, Mandeep S.; Leendertz, Fabian H.; Mishra, A.C.; Gibbons, Robert V.; Holmes, Edward C.; Lipkin, W. Ian

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years. PMID:18507910

  2. Chloroplast Genome Evolution in the Euglenaceae.

    PubMed

    Bennett, Matthew S; Triemer, Richard E

    2015-01-01

    Over the last few years multiple studies have been published outlining chloroplast genomes that represent many of the photosynthetic euglenid genera. However, these genomes were scattered throughout the euglenophyceaean phylogenetic tree, and focused on comparisons with Euglena gracilis. Here, we present a study exclusively on taxa within the Euglenaceae. Six new chloroplast genomes were characterized, those of Cryptoglena skujai, E. gracilis var. bacillaris, Euglena viridis, Euglenaria anabaena, Monomorphina parapyrum, and Trachelomonas volvocina, and added to six previously published chloroplast genomes to determine if trends existed within the family. With this study: at least one genome has now been characterized for each genus, the genomes of different strains from two taxa were characterized to explore intraspecific variability, and a second taxon has been characterized for the genus Monomorphina to examine intrageneric variability. Overall results showed a large amount of variability among the genomes, though a few trends could be identified both within Euglenaceae and within Euglenophyta. In addition, the intraspecific analysis indicated that the similarity of a genome sequence between strains was taxon dependent, and the intrageneric analysis indicated that the majority of the evolutionary changes within the Euglenaceae occurred intergenerically. PMID:25976746

  3. Reticulate Evolution of the Rye Genome[W][OPEN

    PubMed Central

    Martis, Mihaela M.; Zhou, Ruonan; Haseneyer, Grit; Schmutzer, Thomas; Vrna, Jan; Kubalkov, Marie; Knig, Susanne; Kugler, Karl G.; Scholz, Uwe; Hackauf, Bernd; Korzun, Viktor; Schn, Chris-Carolin; Doleel, Jaroslav; Bauer, Eva; Mayer, Klaus F.X.; Stein, Nils

    2013-01-01

    Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (?8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon, rice [Oryza sativa], and sorghum [Sorghum bicolor]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution. PMID:24104565

  4. Convergent evolution of the genomes of marine mammals

    PubMed Central

    Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret E.; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

    2015-01-01

    Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and are therefore a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and de novo assembled the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome, and that a subset were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that while convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare. PMID:25621460

  5. Convergent evolution of the genomes of marine mammals

    USGS Publications Warehouse

    Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

    2015-01-01

    Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

  6. Convergent evolution of the genomes of marine mammals.

    PubMed

    Foote, Andrew D; Liu, Yue; Thomas, Gregg W C; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E; Hunter, Margaret E; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J; Vijay, Nagarjun; Wolf, Jochen B W; Hahn, Matthew W; Muzny, Donna M; Worley, Kim C; Gilbert, M Thomas P; Gibbs, Richard A

    2015-03-01

    Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare. PMID:25621460

  7. [Molecular targeted therapy and genomic evolution of breast cancer].

    PubMed

    Sato, Fumiaki; Toi, Masakazu

    2015-08-01

    Owing to development of next generation sequencer (NGS), deep biological insights of breast cancer have been provided. Information of genomic mutations and rearrangements in patients' tumors is required to understand the mechanism in resistance of molecular targeted medicine. To date, NGS analyses illustrated not only base substitution patterns and lists of driver mutations and key rearrangements, but also a manner of tumor evolution. Breast cancer genome is dynamically changing and evolving during cancer development course and treatment procedures. Liquid biopsy is a non-invasive method to detect the genomic evolution of breast cancer, which is now under development for future application to clinical practice of cancer treatment. In this article, latest knowledge regarding breast cancer genome, especially in terms of 'evolution', is summarized. PMID:26281691

  8. An Inherited Efficiencies Model of Non-Genomic Evolution

    NASA Technical Reports Server (NTRS)

    New, Michael H.; Pohorille, Andrew

    1999-01-01

    A model for the evolution of biological systems in the absence of a nucleic acid-like genome is proposed and applied to model the earliest living organisms -- protocells composed of membrane encapsulated peptides. Assuming that the peptides can make and break bonds between amino acids, and bonds in non-functional peptides are more likely to be destroyed than in functional peptides, it is demonstrated that the catalytic capabilities of the system as a whole can increase. This increase is defined to be non-genomic evolution. The relationship between the proposed mechanism for evolution and recent experiments on self-replicating peptides is discussed.

  9. Marsupial Genome Sequences: Providing Insight into Evolution and Disease

    PubMed Central

    Deakin, Janine E.

    2012-01-01

    Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences. PMID:24278712

  10. Marsupial genome sequences: providing insight into evolution and disease.

    PubMed

    Deakin, Janine E

    2012-01-01

    Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences. PMID:24278712

  11. Structure, Function, and Evolution of the Thiomonas spp. Genome

    PubMed Central

    Arsne-Ploetze, Florence; Koechler, Sandrine; Marchal, Marie; Coppe, Jean-Yves; Chandler, Michael; Bonnefoy, Violaine; Brochier-Armanet, Cline; Barakat, Mohamed; Barbe, Valrie; Battaglia-Brunet, Fabienne; Bruneel, Odile; Bryan, Christopher G.; Cleiss-Arnold, Jessica; Cruveiller, Stphane; Erhardt, Mathieu; Heinrich-Salmeron, Audrey; Hommais, Florence; Joulian, Catherine; Krin, Evelyne; Lieutaud, Aurlie; Livremont, Didier; Michel, Caroline; Muller, Daniel; Ortet, Philippe; Proux, Caroline; Siguier, Patricia; Roche, David; Rouy, Zo; Salvignol, Grgory; Slyemi, Djamila; Talla, Emmanuel; Weiss, Stphanie; Weissenbach, Jean; Mdigue, Claudine; Bertin, Philippe N.

    2010-01-01

    Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live. PMID:20195515

  12. CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus

    PubMed Central

    Paez-Espino, David; Sharon, Itai; Morovic, Wesley; Stahl, Buffy; Thomas, Brian C.

    2015-01-01

    ABSTRACT Many bacteria rely on CRISPR-Cas systems to provide adaptive immunity against phages, predation by which can shape the ecology and functioning of microbial communities. To characterize the impact of CRISPR immunization on phage genome evolution, we performed long-term bacterium-phage (Streptococcus thermophilus-phage 2972) coevolution experiments. We found that in this species, CRISPR immunity drives fixation of single nucleotide polymorphisms that accumulate exclusively in phage genome regions targeted by CRISPR. Mutation rates in phage genomes highly exceed those of the host. The presence of multiple phages increased phage persistence by enabling recombination-based formation of chimeric phage genomes in which sequences heavily targeted by CRISPR were replaced. Collectively, our results establish CRISPR-Cas adaptive immunity as a key driver of phage genome evolution under the conditions studied and highlight the importance of multiple coexisting phages for persistence in natural systems. PMID:25900652

  13. The function and evolution of the Aspergillus genome

    PubMed Central

    Gibbons, John G.; Rokas, Antonis

    2012-01-01

    Species in the filamentous fungal genus Aspergillus display a wide diversity of lifestyles and are of great importance to humans. The decoding of genome sequences from a dozen species that vary widely in their degree of evolutionary affinity has galvanized studies of the function and evolution of the Aspergillus genome in clinical, industrial, and agricultural environments. Here, we synthesize recent key findings that shed light on the architecture of the Aspergillus genome, on the molecular foundations of the genus’ astounding dexterity and diversity in secondary metabolism, and on the genetic underpinnings of virulence in Aspergillus fumigatus, one of the most lethal fungal pathogens. Many of these insights dramatically expand our knowledge of fungal and microbial eukaryote genome evolution and function and argue that Aspergillus constitutes a superb model clade for the study of functional and comparative genomics. PMID:23084572

  14. Molecular Epidemiology of Human Rhinoviruses and Enteroviruses Highlights Their Diversity in Sub-Saharan Africa.

    PubMed

    L'Huillier, Arnaud G; Kaiser, Laurent; Petty, Tom J; Kilowoko, Mary; Kyungu, Esther; Hongoa, Philipina; Vieille, Gal; Turin, Lara; Genton, Blaise; D'Acremont, Valrie; Tapparel, Caroline

    2015-01-01

    Human rhinoviruses (HRVs) and enteroviruses (HEVs) belong to the Enterovirus genus and are the most frequent cause of infection worldwide, but data on their molecular epidemiology in Africa are scarce. To understand HRV and HEV molecular epidemiology in this setting, we enrolled febrile pediatric patients participating in a large prospective cohort assessing the causes of fever in Tanzanian children. Naso/oropharyngeal swabs were systematically collected and tested by real-time RT-PCR for HRV and HEV. Viruses from positive samples were sequenced and phylogenetic analyses were then applied to highlight the HRV and HEV types as well as recombinant or divergent strains. Thirty-eight percent (378/1005) of the enrolled children harboured an HRV or HEV infection. Although some types were predominant, many distinct types were co-circulating, including a vaccinal poliovirus, HEV-A71 and HEV-D68. Three HRV-A recombinants were identified: HRV-A36/HRV-A67, HRV-A12/HRV-A67 and HRV-A96/HRV-A61. Four divergent HRV strains were also identified: one HRV-B strain and three HRV-C strains. This is the first prospective study focused on HRV and HEV molecular epidemiology in sub-Saharan Africa. This systematic and thorough large screening with careful clinical data management confirms the wide genomic diversity of these viruses, brings new insights about their evolution and provides data about associated symptoms. PMID:26670243

  15. Molecular Epidemiology of Human Rhinoviruses and Enteroviruses Highlights Their Diversity in Sub-Saharan Africa

    PubMed Central

    L’Huillier, Arnaud G.; Kaiser, Laurent; Petty, Tom J.; Kilowoko, Mary; Kyungu, Esther; Hongoa, Philipina; Vieille, Gaël; Turin, Lara; Genton, Blaise; D’Acremont, Valérie; Tapparel, Caroline

    2015-01-01

    Human rhinoviruses (HRVs) and enteroviruses (HEVs) belong to the Enterovirus genus and are the most frequent cause of infection worldwide, but data on their molecular epidemiology in Africa are scarce. To understand HRV and HEV molecular epidemiology in this setting, we enrolled febrile pediatric patients participating in a large prospective cohort assessing the causes of fever in Tanzanian children. Naso/oropharyngeal swabs were systematically collected and tested by real-time RT-PCR for HRV and HEV. Viruses from positive samples were sequenced and phylogenetic analyses were then applied to highlight the HRV and HEV types as well as recombinant or divergent strains. Thirty-eight percent (378/1005) of the enrolled children harboured an HRV or HEV infection. Although some types were predominant, many distinct types were co-circulating, including a vaccinal poliovirus, HEV-A71 and HEV-D68. Three HRV-A recombinants were identified: HRV-A36/HRV-A67, HRV-A12/HRV-A67 and HRV-A96/HRV-A61. Four divergent HRV strains were also identified: one HRV-B strain and three HRV-C strains. This is the first prospective study focused on HRV and HEV molecular epidemiology in sub-Saharan Africa. This systematic and thorough large screening with careful clinical data management confirms the wide genomic diversity of these viruses, brings new insights about their evolution and provides data about associated symptoms. PMID:26670243

  16. Reductive genome evolution in Buchnera aphidicola.

    PubMed

    van Ham, Roeland C H J; Kamerbeek, Judith; Palacios, Carmen; Rausell, Carolina; Abascal, Federico; Bastolla, Ugo; Fernndez, Jose M; Jimnez, Luis; Postigo, Marina; Silva, Francisco J; Tamames, Javier; Viguera, Enrique; Latorre, Amparo; Valencia, Alfonso; Morn, Federico; Moya, Andrs

    2003-01-21

    We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Baizongia pistacea. This strain diverged 80-150 million years ago from the common ancestor of two previously sequenced Buchnera strains. Here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. As a consequence, the genome assembly unveiled intrapopulational variation, consisting of approximately 1,200 polymorphic sites. Comparison of the 618-kb (kbp) genome with the two other Buchnera genomes revealed a nearly perfect gene-order conservation, indicating that the onset of genomic stasis coincided closely with establishment of the symbiosis with aphids, approximately 200 million years ago. Extensive genome reduction also predates the synchronous diversification of Buchnera and its host; but, at a slower rate, gene loss continues among the extant lineages. A computational study of protein folding predicts that proteins in Buchnera, as well as proteins of other intracellular bacteria, are generally characterized by smaller folding efficiency compared with proteins of free living bacteria. These and other degenerative genomic features are discussed in light of compensatory processes and theoretical predictions on the long-term evolutionary fate of symbionts like Buchnera. PMID:12522265

  17. Genomic Diversity and Evolution of Bacillus subtilis.

    PubMed

    Yu, Gang; Wang, Xun Cheng; Tian, Wang Hong; Shi, Ji Chun; Wang, Bin; Ye, Qiang; Dong, Si Guo; Zeng, Ming; Wang, Jun Zhi

    2015-08-01

    Bacillus subtilis is the focus of both academic and industrial research. Previous studies have reported a number of sequence variations in different B. subtilis strains. To uncover the genetic variation and evolutionary pressure in B. subtilis strains, we performed whole genome sequencing of two B. subtilis isolates, KM and CGMCC63528. Comparative genomic analyses of these two strains with other B. subtilis strains identified high sequence variations including large insertions, deletions and SNPs. Most SNPs in genes were synonymous and the average frequency of synonymous mutations was significantly higher than that of the non-synonymous mutations. Pan-genome analysis of B. subtilis strains showed that the core genome had lower dN/dS values than the accessory genome. Whole genome comparisons of these two isolates with other B. subtilis strains showed that strains in different subspecies have similar dN/dS values. Nucleotide diversity analysis showed that spizizenii subspecies have higher nucleotide diversity than subtilis subspecies. Our results indicate that genes in B. subtilis strains are under high purifying selection pressure. The evolutionary pressure in different subspecies of B. subtilis is complex. PMID:26383601

  18. Genomic Evolution of Saccharomyces cerevisiae under Chinese Rice Wine Fermentation

    PubMed Central

    Li, Yudong; Zhang, Weiping; Zheng, Daoqiong; Zhou, Zhan; Yu, Wenwen; Zhang, Lei; Feng, Lifang; Liang, Xinle; Guan, Wenjun; Zhou, Jingwen; Chen, Jian; Lin, Zhenguo

    2014-01-01

    Rice wine fermentation represents a unique environment for the evolution of the budding yeast, Saccharomyces cerevisiae. To understand how the selection pressure shaped the yeast genome and gene regulation, we determined the genome sequence and transcriptome of a S. cerevisiae strain YHJ7 isolated from Chinese rice wine (Huangjiu), a popular traditional alcoholic beverage in China. By comparing the genome of YHJ7 to the lab strain S288c, a Japanese sake strain K7, and a Chinese industrial bioethanol strain YJSH1, we identified many genomic sequence and structural variations in YHJ7, which are mainly located in subtelomeric regions, suggesting that these regions play an important role in genomic evolution between strains. In addition, our comparative transcriptome analysis between YHJ7 and S288c revealed a set of differentially expressed genes, including those involved in glucose transport (e.g., HXT2, HXT7) and oxidoredutase activity (e.g., AAD10, ADH7). Interestingly, many of these genomic and transcriptional variations are directly or indirectly associated with the adaptation of YHJ7 strain to its specific niches. Our molecular evolution analysis suggested that Japanese sake strains (K7/UC5) were derived from Chinese rice wine strains (YHJ7) at least approximately 2,300 years ago, providing the first molecular evidence elucidating the origin of Japanese sake strains. Our results depict interesting insights regarding the evolution of yeast during rice wine fermentation, and provided a valuable resource for genetic engineering to improve industrial wine-making strains. PMID:25212861

  19. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

    PubMed Central

    Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

    2015-01-01

    To provide context for the diversifications of archosaurs, the group that includes crocodilians, dinosaurs and birds, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the relatively rapid evolution of bird genomes represents an autapomorphy within that clade. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

  20. Rickettsial evolution in the light of comparative genomics.

    PubMed

    Merhej, Vicky; Raoult, Didier

    2011-05-01

    Rickettsia are best known as strictly intracellular vector-borne bacteria that cause mild to severe diseases in humans and other animals. Recent advances in molecular tools and biological experiments have unveiled a wide diversity of Rickettsia spp. that include species with a broad host range and some species that act as endosymbiotic associates. Molecular phylogenies of Rickettsia spp. contain some ambiguities, such as the position of R. canadensis and relationships within the spotted fever group. In the modern era of genomics, with an ever-increasing number of sequenced genomes, there is enhanced interest in the use of whole-genome sequences to understand pathogenesis and assess evolutionary relationships among rickettsial species. Rickettsia have small genomes (1.1-1.5 Mb) as a result of reductive evolution. These genomes contain split genes, gene remnants and pseudogenes that, owing to the colinearity of some rickettsial genomes, may represent different steps of the genome degradation process. Genomics reveal extreme genome reduction and massive gene loss in highly vertebrate-pathogenic Rickettsia compared to less virulent or endosymbiotic species. Information gleaned from rickettsial genomics challenges traditional concepts of pathogenesis that focused primarily on the acquisition of virulence factors. Another intriguing phenomenon about the reduced rickettsial genomes concerns the large fraction of non-coding DNA and possible functionality of these "non-coding" sequences, because of the high conservation of these regions. Despite genome streamlining, Rickettsia spp. contain gene families, selfish DNA, repeat palindromic elements and genes encoding eukaryotic-like motifs. These features participate in sequence and functional diversity and may play a crucial role in adaptation to the host cell and pathogenesis. Genome analyses have identified a large fraction of mobile genetic elements, including plasmids, suggesting the possibility of lateral gene transfer in these intracellular bacteria. Phylogenetic analyses have identified several candidates for horizontal gene acquisition among Rickettsia spp. including tra, pat2, and genes encoding for the type IV secretion system and ATP/ADP translocase that may have been acquired from bacteria living in amoebae. Gene loss, gene duplication, DNA repeats and lateral gene transfer all have shaped rickettsial genome evolution. A comprehensive analysis of the entire genome, including genes and non-coding DNA, will help to unlock the mysteries of rickettsial evolution and pathogenesis. PMID:20716256

  1. Population genomics of intrapatient HIV-1 evolution.

    PubMed

    Zanini, Fabio; Brodin, Johanna; Thebo, Lina; Lanz, Christa; Bratt, Göran; Albert, Jan; Neher, Richard A

    2015-01-01

    Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are essential. We performed whole-genome deep sequencing of HIV-1 populations in 9 untreated patients, with 6-12 longitudinal samples per patient spanning 5-8 years of infection. The data can be accessed and explored via an interactive web application. We show that patterns of minor diversity are reproducible between patients and mirror global HIV-1 diversity, suggesting a universal landscape of fitness costs that control diversity. Reversions towards the ancestral HIV-1 sequence are observed throughout infection and account for almost one third of all sequence changes. Reversion rates depend strongly on conservation. Frequent recombination limits linkage disequilibrium to about 100bp in most of the genome, but strong hitch-hiking due to short range linkage limits diversity. PMID:26652000

  2. Mitochondrial genome evolution and the origin of eukaryotes.

    PubMed

    Lang, B F; Gray, M W; Burger, G

    1999-01-01

    Recent results from ancestral (minimally derived) protists testify to the tremendous diversity of the mitochondrial genome in various eukaryotic lineages, but also reinforce the view that mitochondria, descendants of an endosymbiotic alpha-Proteobacterium, arose only once in evolution. The serial endosymbiosis theory, currently the most popular hypothesis to explain the origin of mitochondria, postulates the capture of an alpha-proteobacterial endosymbiont by a nucleus-containing eukaryotic host resembling extant amitochondriate protists. New sequence data have challenged this scenario, instead raising the possibility that the origin of the mitochondrion was coincident with, and contributed substantially to, the origin of the nuclear genome of the eukaryotic cell. Defining more precisely the alpha-proteobacterial ancestry of the mitochondrial genome, and the contribution of the endosymbiotic event to the nuclear genome, will be essential for a full understanding of the origin and evolution of the eukaryotic cell as a whole. PMID:10690412

  3. Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

    PubMed Central

    El Baidouri, Moaine; Panaud, Olivier

    2013-01-01

    Long terminal repeat-retrotransposons (LTR-RTs) are the most abundant class of transposable elements (TEs) in plants. They strongly impact the structure, function, and evolution of their host genome, and, in particular, their role in genome size variation has been clearly established. However, the dynamics of the process through which LTR-RTs have differentially shaped plant genomes is still poorly understood because of a lack of comparative studies. Using a new robust and automated family classification procedure, we exhaustively characterized the LTR-RTs in eight plant genomes for which a high-quality sequence is available (i.e., Arabidopsis thaliana, A. lyrata, grapevine, soybean, rice, Brachypodium dystachion, sorghum, and maize). This allowed us to perform a comparative genome-wide study of the retrotranspositional landscape in these eight plant lineages from both monocots and dicots. We show that retrotransposition has recurrently occurred in all plant genomes investigated, regardless their size, and through bursts, rather than a continuous process. Moreover, in each genome, only one or few LTR-RT families have been active in the recent past, and the difference in genome size among the species studied could thus mostly be accounted for by the extent of the latest transpositional burst(s). Following these bursts, LTR-RTs are efficiently eliminated from their host genomes through recombination and deletion, but we show that the removal rate is not lineage specific. These new findings lead us to propose a new model of TE-driven genome evolution in plants. PMID:23426643

  4. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

    PubMed

    Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

    2014-12-12

    To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

  5. Polyploidy-associated genome modifications during land plant evolution

    PubMed Central

    Jiao, Yuannian; Paterson, Andrew H.

    2014-01-01

    The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more ‘particulate’ understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity. PMID:24958928

  6. Genome evolution: groping in the soil interstices.

    PubMed

    Minelli, Alessandro

    2015-03-01

    Centipedes are a very old lineage of terrestrial animals. The first completely sequenced myriapod genome reveals that the blind centipede Strigamia maritima has no gene for light-sensory proteins, lacks the canonical circadian clock and possesses unusual features related to chemosensory perception. PMID:25734267

  7. Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements

    PubMed Central

    Zhang, Cheng-Zhong; Leibowitz, Mitchell L.; Pellman, David

    2013-01-01

    Recent genome sequencing studies have identified several classes of complex genomic rearrangements that appear to be derived from a single catastrophic event. These discoveries identify ways that genomes can be altered in single large jumps rather than by many incremental steps. Here we compare and contrast these phenomena and examine the evidence that they arise all at once. We consider the impact of massive chromosomal change for the development of diseases such as cancer and for evolution more generally. Finally, we summarize current models for underlying mechanisms and discuss strategies for testing these models. PMID:24298051

  8. Evolution and function of genomic imprinting in plants.

    PubMed

    Rodrigues, Jessica A; Zilberman, Daniel

    2015-12-15

    Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings. PMID:26680300

  9. Identification of a Novel Human Rhinovirus C Type by Antibody Capture VIDISCA-454

    PubMed Central

    Jazaeri Farsani, Seyed Mohammad; Oude Munnink, Bas B.; Canuti, Marta; Deijs, Martin; Cotten, Matthew; Jebbink, Maarten F.; Verhoeven, Joost; Kellam, Paul; Loens, Katherine; Goossens, Herman; Ieven, Margareta; van der Hoek, Lia

    2015-01-01

    Causative agents for more than 30 percent of respiratory infections remain unidentified, suggesting that unknown respiratory pathogens might be involved. In this study, antibody capture VIDISCA-454 (virus discovery cDNA-AFLP combined with Roche 454 high-throughput sequencing) resulted in the discovery of a novel type of rhinovirus C (RV-C). The virus has an RNA genome of at least 7054 nt and carries the characteristics of rhinovirus C species. The gene encoding viral protein 1, which is used for typing, has only 81% nucleotide sequence identity with the closest known RV-C type, and, therefore, the virus represents the first member of a novel type, named RV-C54. PMID:25606972

  10. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    SciTech Connect

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  11. Dynamic Evolution of Rht-1 Homologous Regions in Grass Genomes

    PubMed Central

    Wu, Jing; Kong, Xiuying; Shi, Chao; Gu, Yongqiang; Jin, Cuiyun; Gao, Lizhi; Jia, Jizeng

    2013-01-01

    Hexaploid bread wheat contains A, B, and D three subgenomes with its well-characterized ancestral genomes existed at diploid and tetraploid levels, making the wheat act as a good model species for studying evolutionary genomic dynamics. Here, we performed intra- and inter-species comparative analyses of wheat and related grass genomes to examine the dynamics of homologous regions surrounding Rht-1, a well-known green revolution gene. Our results showed that the divergence of the two A genomes in the Rht-1 region from the diploid and tetraploid species is greater than that from the tetraploid and hexaploid wheat. The divergence of D genome between diploid and hexaploid is lower than those of A genome, suggesting that D genome diverged latter than others. The divergence among the A, B and D subgenomes was larger than that among different ploidy levels for each subgenome which mainly resulted from genomic structural variation of insertions and, perhaps deletions, of the repetitive sequences. Meanwhile, the repetitive sequences caused genome expansion further after the divergence of the three subgenomes. However, several conserved non-coding sequences were identified to be shared among the three subgenomes of wheat, suggesting that they may have played an important role to maintain the homolog of three subgenomes. This is a pilot study on evolutionary dynamics across the wheat ploids, subgenomes and differently related grasses. Our results gained new insights into evolutionary dynamics of Rht-1 region at sequence level as well as the evolution of wheat during the plolyploidization process. PMID:24086561

  12. Spatiotemporal Evolution of the Primary Glioblastoma Genome.

    PubMed

    Kim, Jinkuk; Lee, In-Hee; Cho, Hee Jin; Park, Chul-Kee; Jung, Yang-Soon; Kim, Yanghee; Nam, So Hee; Kim, Byung Sup; Johnson, Mark D; Kong, Doo-Sik; Seol, Ho Jun; Lee, Jung-Il; Joo, Kyeung Min; Yoon, Yeup; Park, Woong-Yang; Lee, Jeongwu; Park, Peter J; Nam, Do-Hyun

    2015-09-14

    Tumor recurrence following treatment is the major cause of mortality for glioblastoma multiforme (GBM) patients. Thus, insights on the evolutionary process at recurrence are critical for improved patient care. Here, we describe our genomic analyses of the initial and recurrent tumor specimens from each of 38 GBM patients. A substantial divergence in the landscape of driver alterations was associated with distant appearance of a recurrent tumor from the initial tumor, suggesting that the genomic profile of the initial tumor can mislead targeted therapies for the distally recurred tumor. In addition, in contrast to IDH1-mutated gliomas, IDH1-wild-type primary GBMs rarely developed hypermutation following temozolomide (TMZ) treatment, indicating low risk for TMZ-induced hypermutation for these tumors under the standard regimen. PMID:26373279

  13. The importance of genomic novelty in social evolution.

    PubMed

    Sumner, Seirian

    2014-01-01

    Insect societies dominate the natural world: They mould landscapes, sculpt habitats, pollinate plants, sow seeds and control pests. The secret to their success lies in the evolution of queen (reproductive) and worker (provisioner and carer) castes (Oster & Wilson 1978). A major problem in evolutionary biology is explaining the evolution of insect castes, particularly the workers (Darwin 1859). Next-generation sequencing technologies now make it possible to understand how genomic material is born, lost and reorganized in the evolution of alternative phenotypes. Such analyses are revealing a general role for novel (e.g. taxonomically restricted) genes in phenotypic innovations across the animal kingdom (Chen et al. 2013). In this issue of molecular ecology, Feldmeyer et al. (2014) provide overwhelming evidence for the importance of novel genes in caste evolution in an ant. Feldmeyer et al.'s study is important and exciting because it cements the role of genomic novelty, as well as conservation, firmly into the molecular jigsaw of social evolution. Evolution is eclectic in its exploitation of both old and new genomic material to generate replicated phenotypic innovations across the tree of life. PMID:24372753

  14. Population genomics of intrapatient HIV-1 evolution

    PubMed Central

    Zanini, Fabio; Brodin, Johanna; Thebo, Lina; Lanz, Christa; Bratt, Göran; Albert, Jan; Neher, Richard A

    2015-01-01

    Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are essential. We performed whole-genome deep sequencing of HIV-1 populations in 9 untreated patients, with 6-12 longitudinal samples per patient spanning 5-8 years of infection. The data can be accessed and explored via an interactive web application. We show that patterns of minor diversity are reproducible between patients and mirror global HIV-1 diversity, suggesting a universal landscape of fitness costs that control diversity. Reversions towards the ancestral HIV-1 sequence are observed throughout infection and account for almost one third of all sequence changes. Reversion rates depend strongly on conservation. Frequent recombination limits linkage disequilibrium to about 100bp in most of the genome, but strong hitch-hiking due to short range linkage limits diversity. DOI: http://dx.doi.org/10.7554/eLife.11282.001 PMID:26652000

  15. Pigmentation Pathway Evolution after Whole-Genome Duplication in Fish

    PubMed Central

    Brunet, Frdric; Volff, Jean-Nicolas; Schartl, Manfred

    2009-01-01

    Whole-genome duplications (WGDs) have occurred repeatedly in the vertebrate lineage, but their evolutionary significance for phenotypic evolution remains elusive. Here, we have investigated the impact of the fish-specific genome duplication (FSGD) on the evolution of pigmentation pathways in teleost fishes. Pigmentation and color patterning are among the most diverse traits in teleosts, and their pigmentary system is the most complex of all vertebrate groups. Using a comparative genomic approach including phylogenetic and synteny analyses, the evolution of 128 vertebrate pigmentation genes in five teleost genomes following the FSGD has been reconstructed. We show that pigmentation genes have been preferentially retained in duplicate after the FSGD, so that teleosts have 30% more pigmentation genes compared with tetrapods. This is significantly higher than genome-wide estimates of FSGD gene duplicate retention in teleosts. Large parts of the melanocyte regulatory network have been retained in two copies after the FSGD. Duplicated pigmentation genes follow general evolutionary patterns such as the preservation of protein complex stoichiometries and the overrepresentation of developmental genes among retained duplicates. These results suggest that the FSGD has made an important contribution to the evolution of teleost-specific features of pigmentation, which include novel pigment cell types or the division of existing pigment cell types into distinct subtypes. Furthermore, we have observed species-specific differences in duplicate retention and evolution that might contribute to pigmentary diversity among teleosts. Our study therefore strongly supports the hypothesis that WGDs have promoted the increase of complexity and diversity during vertebrate phenotypic evolution. PMID:20333216

  16. Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

    PubMed Central

    2013-01-01

    Background Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. Results We determined that TEs comprise ~25% of the genome. The predominant class of TEs (~12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. Conclusions Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group. PMID:24088337

  17. Insights into hominid evolution from the gorilla genome sequence

    PubMed Central

    Scally, Aylwyn; Dutheil, Julien Y.; Hillier, LaDeana W.; Jordan, Greg E.; Goodhead, Ian; Herrero, Javier; Hobolth, Asger; Lappalainen, Tuuli; Mailund, Thomas; Marques-Bonet, Tomas; McCarthy, Shane; Montgomery, Stephen H.; Schwalie, Petra C.; Tang, Y. Amy; Ward, Michelle C.; Xue, Yali; Yngvadottir, Bryndis; Alkan, Can; Andersen, Lars N.; Ayub, Qasim; Ball, Edward V.; Beal, Kathryn; Bradley, Brenda J.; Chen, Yuan; Clee, Chris M.; Fitzgerald, Stephen; Graves, Tina A.; Gu, Yong; Heath, Paul; Heger, Andreas; Karakoc, Emre; Kolb-Kokocinski, Anja; Laird, Gavin K.; Lunter, Gerton; Meader, Stephen; Mort, Matthew; Mullikin, James C.; Munch, Kasper; OConnor, Timothy D.; Phillips, Andrew D.; Prado-Martinez, Javier; Rogers, Anthony S.; Sajjadian, Saba; Schmidt, Dominic; Shaw, Katy; Simpson, Jared T.; Stenson, Peter D.; Turner, Daniel J.; Vigilant, Linda; Vilella, Albert J.; Whitener, Weldon; Zhu, Baoli; Cooper, David N.; de Jong, Pieter; Dermitzakis, Emmanouil T.; Eichler, Evan E.; Flicek, Paul; Goldman, Nick; Mundy, Nicholas I.; Ning, Zemin; Odom, Duncan T.; Ponting, Chris P.; Quail, Michael A.; Ryder, Oliver A.; Searle, Stephen M.; Warren, Wesley C.; Wilson, Richard K.; Schierup, Mikkel H.; Rogers, Jane; Tyler-Smith, Chris; Durbin, Richard

    2012-01-01

    Summary Gorillas are humans closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution. PMID:22398555

  18. The influence of the accessory genome on bacterial pathogen evolution

    PubMed Central

    Vinatzer, Boris; Arnold, Dawn L; Dorus, Steve; Murillo, Jesús

    2011-01-01

    Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens' frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorize the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution. PMID:22016845

  19. Ancient population genomics and the study of evolution

    PubMed Central

    Parks, M.; Subramanian, S.; Baroni, C.; Salvatore, M. C.; Zhang, G.; Millar, C. D.; Lambert, D. M.

    2015-01-01

    Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution. PMID:25487332

  20. Ancient population genomics and the study of evolution.

    PubMed

    Parks, M; Subramanian, S; Baroni, C; Salvatore, M C; Zhang, G; Millar, C D; Lambert, D M

    2015-01-19

    Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution. PMID:25487332

  1. The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants

    SciTech Connect

    Grigoriev, Igor V.; Banks, Jo Ann; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Bowman, John L.; Gribskov, Michael; dePamphilis, Claude; Albert, Victor A.; Aono, Naoki; Aoyama, Tsuyoshi; Ambrose, Barbara A.; Ashton, Neil W.; Axtell, Michael J.; Barker, Elizabeth; Barker, Michael S.; Bennetzen, Jeffrey L.; Bonawitz, Nicholas D.; Chapple, Clint; Cheng, Chaoyang; Correa, Luiz Gustavo Guedes; Dacre, Michael; DeBarry, Jeremy; Dreyer, Ingo; Elias, Marek; Engstrom, Eric M.; Estelle, Mark; Feng, Liang; Finet, Cedric; Floyd, Sandra K.; Frommer, Wolf B.; Fujita, Tomomichi; Gramzow, Lydia; Gutensohn, Michael; Harholt, Jesper; Hattori, Mitsuru; Heyl, Alexander; Hirai, Tadayoshi; Hiwatashi, Yuji; Ishikawa, Masaki; Iwata, Mineko; Karol, Kenneth G.; Koehler, Barbara; Kolukisaoglu, Uener; Kubo, Minoru; Kurata, Tetsuya; Lalonde, Sylvie; Li, Kejie; Li, Ying; Litt, Amy; Lyons, Eric; Manning, Gerard; Maruyama, Takeshi; Michael, Todd P.; Mikami, Koji; Miyazaki, Saori; Morinaga, Shin-ichi; Murata, Takashi; Mueller-Roeber, Bernd; Nelson, David R.; Obara, Mari; Oguri, Yasuko; Olmstead, Richard G.; Onodera, Naoko; Petersen, Bent Larsen; Pils, Birgit; Prigge, Michael; Rensing, Stefan A.; Riano-Pachon, Diego Mauricio; Roberts, Alison W.; Sato, Yoshikatsu; Scheller, Henrik Vibe; Schulz, Burkhard; Schulz, Christian; Shakirov, Eugene V.; Shibagaki, Nakako; Shinohara, Naoki; Shippen, Dorothy E.; Sorensen, Iben; Sotooka, Ryo; Sugimoto, Nagisa; Sugita, Mamoru; Sumikawa, Naomi; Tanurdzic, Milos; Theilsen, Gunter; Ulvskov, Peter; Wakazuki, Sachiko; Weng, Jing-Ke; Willats, William W.G.T.; Wipf, Daniel; Wolf, Paul G.; Yang, Lixing; Zimmer, Andreas D.; Zhu, Qihui; Mitros, Therese; Hellsten, Uffe; Loque, Dominique; Otillar, Robert; Salamov, Asaf; Schmutz, Jeremy; Shapiro, Harris; Lindquist, Erika; Lucas, Susan; Rokhsar, Daniel

    2011-04-28

    We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by comparative genomics identify genes that likely played important roles in the early evolution of vascular plants and their subsequent evolution

  2. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

    PubMed Central

    Berthelot, Camille; Brunet, Frédéric; Chalopin, Domitille; Juanchich, Amélie; Bernard, Maria; Noël, Benjamin; Bento, Pascal; Da Silva, Corinne; Labadie, Karine; Alberti, Adriana; Aury, Jean-Marc; Louis, Alexandra; Dehais, Patrice; Bardou, Philippe; Montfort, Jérôme; Klopp, Christophe; Cabau, Cédric; Gaspin, Christine; Thorgaard, Gary H.; Boussaha, Mekki; Quillet, Edwige; Guyomard, René; Galiana, Delphine; Bobe, Julien; Volff, Jean-Nicolas; Genêt, Carine; Wincker, Patrick; Jaillon, Olivier; Crollius, Hugues Roest; Guiguen, Yann

    2014-01-01

    Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions. PMID:24755649

  3. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes

    PubMed Central

    Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

    2014-01-01

    Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. PMID:25523484

  4. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.

    PubMed

    Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

    2014-01-01

    Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. PMID:25523484

  5. Genome-wide signatures of convergent evolution in echolocating mammals.

    PubMed

    Parker, Joe; Tsagkogeorga, Georgia; Cotton, James A; Liu, Yuan; Provero, Paolo; Stupka, Elia; Rossiter, Stephen J

    2013-10-10

    Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes. However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures. Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution, although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized. PMID:24005325

  6. Experimental rhinovirus infection in human volunteers exposed to ozone

    SciTech Connect

    Henderson, F.W.; Dubovi, E.J.; Harder, S.; Seal, E. Jr.; Graham, D.

    1988-05-01

    We studied 24 young adult male volunteers experimentally inoculated with type 39 rhinovirus to determine whether the course of viral infection was modified by exposure to moderate levels of ozone (0.3 ppm for 6 h per day) over the 5 days after virus inoculation. No differences in rhinovirus titers in nasal secretions, recruitment of neutrophils into nasal secretions, levels of interferon in nasal lavage fluid, in vitro lymphocyte proliferative responses to rhinovirus antigen, or levels of convalescent serum neutralizing antibody to type 39 rhinovirus were demonstrated in relation to ozone exposure. The level and pattern of ozone exposure used in this experiment had no demonstrable adverse effects on the immune responses necessary to limit and terminate rhinovirus infection of the upper respiratory tract.

  7. Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits

    PubMed Central

    Hu, Jianqiang; Han, Danxiang; Wang, Hui; Zeng, Xiaowei; Jing, Xiaoyan; Zhou, Qian; Su, Xiaoquan; Chang, Xingzhi; Wang, Anhui; Wang, Wei; Jia, Jing; Wei, Li; Xin, Yi; Qiao, Yinghe; Huang, Ranran; Chen, Jie; Han, Bo; Yoon, Kangsup; Hill, Russell T.; Zohar, Yonathan; Chen, Feng; Hu, Qiang; Xu, Jian

    2014-01-01

    Oleaginous microalgae are promising feedstock for biofuels, yet the genetic diversity, origin and evolution of oleaginous traits remain largely unknown. Here we present a detailed phylogenomic analysis of five oleaginous Nannochloropsis species (a total of six strains) and one time-series transcriptome dataset for triacylglycerol (TAG) synthesis on one representative strain. Despite small genome sizes, high coding potential and relative paucity of mobile elements, the genomes feature small cores of ca. 2,700 protein-coding genes and a large pan-genome of >38,000 genes. The six genomes share key oleaginous traits, such as the enrichment of selected lipid biosynthesis genes and certain glycoside hydrolase genes that potentially shift carbon flux from chrysolaminaran to TAG synthesis. The eleven type II diacylglycerol acyltransferase genes (DGAT-2) in every strain, each expressed during TAG synthesis, likely originated from three ancient genomes, including the secondary endosymbiosis host and the engulfed green and red algae. Horizontal gene transfers were inferred in most lipid synthesis nodes with expanded gene doses and many glycoside hydrolase genes. Thus multiple genome pooling and horizontal genetic exchange, together with selective inheritance of lipid synthesis genes and species-specific gene loss, have led to the enormous genetic apparatus for oleaginousness and the wide genomic divergence among present-day Nannochloropsis. These findings have important implications in the screening and genetic engineering of microalgae for biofuels. PMID:24415958

  8. [Adaptive evolution of the Homo mitochondrial genome].

    PubMed

    Maliarchuk, B A

    2011-01-01

    Adaptive evolution of 12 protein-coding mitochondrial genes in members of genus Homo (Denisova hominin (H. sp. Altai), Neandertals (H. neanderthalensis) and modern humans (H. sapiens)) has been evaluated by assessing the pattern of changes in the physicochemical properties of amino acid replacements during the primate evolution. It has been found that in the Homo molecular adaptation (positive destabilizing selection) become apparent in the form of 12 radical amino acid replacements accompanied by statistically significant (P < 0.001) changes of physicochemical properties that probably had the functional consequences. These replacements have occurred on the stage of a common ancestor of the Homo (in CO2 and CytB genes) as well as with the appearance of the common ancestor of Neandertals and modern humans (in CO1 and ND5 genes). Radical amino acid replacements were mainly revealed in the cytochrome c oxidase complex IV and cytochrome bc1 complex III, thus coinciding with general trend of increasing of non-synonymous changes in mtDNA genes coding subunits of complexes III and IV proteins in anthropoid primates. PMID:22393781

  9. Genomic perspectives on the evolution and spread of bacterial pathogens.

    PubMed

    Bentley, Stephen D; Parkhill, Julian

    2015-12-22

    Since the first complete sequencing of a free-living organism, Haemophilus influenzae, genomics has been used to probe both the biology of bacterial pathogens and their evolution. Single-genome approaches provided information on the repertoire of virulence determinants and host-interaction factors, and, along with comparative analyses, allowed the proposal of hypotheses to explain the evolution of many of these traits. These analyses suggested many bacterial pathogens to be of relatively recent origin and identified genome degradation as a key aspect of host adaptation. The advent of very-high-throughput sequencing has allowed for detailed phylogenetic analysis of many important pathogens, revealing patterns of global and local spread, and recent evolution in response to pressure from therapeutics and the human immune system. Such analyses have shown that bacteria can evolve and transmit very rapidly, with emerging clones showing adaptation and global spread over years or decades. The resolution achieved with whole-genome sequencing has shown considerable benefits in clinical microbiology, enabling accurate outbreak tracking within hospitals and across continents. Continued large-scale sequencing promises many further insights into genetic determinants of drug resistance, virulence and transmission in bacterial pathogens. PMID:26702036

  10. Moments of genome evolution by Double Cut-and-Join

    PubMed Central

    2015-01-01

    We study statistical estimators of the number of genomic events separating two genomes under a Double Cut-and Join (DCJ) rearrangement model, by a method of moment estimation. We first propose an exact, closed, analytically invertible formula for the expected number of breakpoints after a given number of DCJs. This improves over the heuristic, recursive and computationally slower previously proposed one. Then we explore the analogies of genome evolution by DCJ with evolution of binary sequences under substitutions, permutations under transpositions, and random graphs. Each of these are presented in the literature with intuitive justifications, and are used to import results from better known fields. We formalize the relations by proving a correspondence between moments in sequence and genome evolution, provided substitutions appear four by four in the corresponding model. Eventually we prove a bounded error on two estimators of the number of cycles in the breakpoint graph after a given number of rearrangements, by an analogy with cycles in permutations and components in random graphs. PMID:26451469

  11. Genomic perspectives on the evolution and spread of bacterial pathogens

    PubMed Central

    Bentley, Stephen D.

    2015-01-01

    Since the first complete sequencing of a free-living organism, Haemophilus influenzae, genomics has been used to probe both the biology of bacterial pathogens and their evolution. Single-genome approaches provided information on the repertoire of virulence determinants and host-interaction factors, and, along with comparative analyses, allowed the proposal of hypotheses to explain the evolution of many of these traits. These analyses suggested many bacterial pathogens to be of relatively recent origin and identified genome degradation as a key aspect of host adaptation. The advent of very-high-throughput sequencing has allowed for detailed phylogenetic analysis of many important pathogens, revealing patterns of global and local spread, and recent evolution in response to pressure from therapeutics and the human immune system. Such analyses have shown that bacteria can evolve and transmit very rapidly, with emerging clones showing adaptation and global spread over years or decades. The resolution achieved with whole-genome sequencing has shown considerable benefits in clinical microbiology, enabling accurate outbreak tracking within hospitals and across continents. Continued large-scale sequencing promises many further insights into genetic determinants of drug resistance, virulence and transmission in bacterial pathogens. PMID:26702036

  12. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Rieseberg, Loren [University of British Columbia

    2013-01-15

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  13. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Rieseberg, Loren

    2012-03-21

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  14. A unifying model of genome evolution under parsimony

    PubMed Central

    2014-01-01

    Background Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. Results We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph G, a finite set of AVGs describe all parsimonious interpretations of G, and this set can be explored with a few sampling moves. Conclusion This theoretical study describes a model in which the inference of genome rearrangements and phylogeny can be unified under parsimony. PMID:24946830

  15. Plastid genome evolution in mycoheterotrophic Ericaceae.

    PubMed

    Braukmann, Thomas; Stefanović, Saša

    2012-05-01

    Unlike parasitic plants, which are linked to their hosts directly through haustoria, mycoheterotrophic (MHT) plants derive all or part of their water and nutrients from autothrophs via fungal mycorrhizal intermediaries. Ericaceae, the heather family, are a large and diverse group of plants known to form elaborate symbiotic relationships with mycorrhizal fungi. Using PHYA sequence data, we first investigated relationships among mycoheterotrophic Ericaceae and their close autotrophic relatives. Phylogenetic results suggest a minimum of two independent origins of MHT within this family. Additionally, a comparative investigation of plastid genomes (plastomes) grounded within this phylogenetic framework was conducted using a slot-blot Southern hybridization approach. This survey encompassed numerous lineages of Ericaceae with different life histories and trophic levels, including multiple representatives from mixotrophic Pyroleae and fully heterotrophic Monotropeae and Pterosporeae. Fifty-four probes derived from all categories of protein coding genes typically found within the plastomes of flowering plants were used. Our results indicate that the holo-mycoheterotrophic Ericaceae exhibit extensive loss of genes relating to photosynthetic function and expression of the plastome but retain genes with possible functions outside photosynthesis. Mixotrophic taxa tend to retain most genes relating to photosynthetic functions but are varied regarding the plastid ndh gene content. This investigation extends previous inferences that the loss of the NDH complex occurs prior to becoming holo-heterotrophic and it shows that the pattern of gene losses among mycoheterotrophic Ericaceae is similar to that of haustorial parasites. Additionally, we identify the most desirable candidate species for entire plastome sequencing. PMID:22442035

  16. Genomics and the evolution, pathogenesis, and diagnosis of tuberculosis

    PubMed Central

    Ernst, Joel D.; Trevejo-Nuñez, Giraldina; Banaiee, Niaz

    2007-01-01

    Tuberculosis kills nearly 2 million people annually, and current approaches to tuberculosis control are expensive, have limited efficacy, and are vulnerable to being overcome by extensively drug-resistant strains of Mycobacterium tuberculosis. Determination of the genome sequence of M. tuberculosis has revolutionized tuberculosis research, contributed to major advances in the understanding of the evolution and pathogenesis of M. tuberculosis, and facilitated development of new diagnostic tests with increased specificity for tuberculosis. In this review, we describe some of the major progress in tuberculosis research that has resulted from knowledge of the genome sequence and note some of the problems that remain unsolved. PMID:17607348

  17. Genomic and comparative genomic analyses of Rickettsia heilongjiangensis provide insight into its evolution and pathogenesis.

    PubMed

    Duan, Changsong; Xiong, Xiaolu; Qi, Yong; Gong, Wenping; Jiao, Jun; Wen, Bohai

    2014-08-01

    Rickettsia heilongjiangensis, the causative agent of far eastern spotted fever, is an obligate intracellular gram-negative bacterium that belongs to the spotted fever group rickettsiae. To understand the evolution and pathogenesis of R. heilongjiangensis, we analyzed its genome and compared it with other rickettsial genomes available in GenBank. The R. heilongjiangensis chromosome contains 1333 genes, including 1297 protein coding genes and 36 RNA coding genes. The genome also contains 121 pseudogenes, 54 insertion sequences, and 39 tandem repeats. Sixteen genes encoding the major components of the type IV secretion systems were identified in the R. heilongjiangensis genome. In total, 37 β-barrel outer membrane proteins were predicted in the genome, eight of which have been previously confirmed to be outer membrane proteins. In addition, 266 potential virulence factor genes, seven partially deleted antibiotic resistance genes, and a genomic island were identified in the genome. The codon usage in the genome is compatible with its low GC content, and the amino acid usage shows apparent bias. A comparative genomic analysis showed that R. heilongjiangensis and R. japonica share one unique fragment that may be a target sequence for a diagnostic assay. The orthologs of 37 genes of R. heilongjiangensis were found in pathogenic R. rickettsii str. Sheila Smith but not in non-pathogenic R. rickettsii str. Iowa, which may explain why R. heilongjiangensis is pathogenic. Pan-genome analysis showed that R. heilongjiangensis and 42 other rickettsiae strains share 693 core genes with a pan-genome size of 4837 genes. The pan-genome-based phylogeny showed that R. heilongjiangensis was closely related to R. japonica. PMID:24924907

  18. Rearrangement and evolution of mitochondrial genomes in parrots.

    PubMed

    Eberhard, Jessica R; Wright, Timothy F

    2016-01-01

    Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One potential cause for this compositional asymmetry is that parrots have unusually slow mtDNA replication. If this is the case, then any replicative advantage provided by having a second control region could result in selection for maintenance of both control regions once duplicated. PMID:26291569

  19. The human genome and the human control of natural evolution.

    PubMed

    Sakamoto, H

    2001-10-01

    Recent advances in research on the Human Genome are provoking many critical problems in the global policy regarding the future status of human beings as well as in that of the whole life system on the earth, and consequently, these advances provoke the serious bioethical and philosophical questions. Firstly, how can we comprehend that we are going to have the complete technology to manipulate the system of the human genome and other non-human genomes? Though no science and technology can be complete, we will, I believe, take possession of an almost complete gene technology in the early stage of the next Century. Gene technology will soon fall into the hands of human beings instead of rendering in the province of God. Secondly, which gene technologies will we actually realize and utilize in the early stages of the 21st Century? Most probably, we will adopt these technologies to health care to treat some apparent bodily diseases, for instance, cancer, hemophilia, ADA deficiency, and so forth, and sooner or later we will adopt gene therapy to germ lines, which, in the long run, suggests the possibility of a future "artificial evolution" instead of the "natural evolution" of the past. Thirdly, how is the new concept of "artificial evolution" justified ethically? I believe this kind of manmade evolution is the only way for human beings to survive into the future global environment. There cannot be any serious ethical objection against the idea of artificial evolution. Fourthly, what is the background philosophy for the concept of "artificial evolution"? I will discuss the nature of modern European humanism with individual dignity and fundamental human rights which has led the philosophy of modern culture and modern society, and I will conclude by suggesting that we should abolish an essential part of modern humanism and newly devise some alternative philosophy to fit the new Millennium. PMID:15011660

  20. Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

    PubMed Central

    2010-01-01

    Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon hemoglobin genes involves the loss of a single hemoglobin gene cluster after the whole genome duplication (WGD) at the base of the teleost radiation but prior to the salmonid-specific WGD, which then produced the duplicated copies seen today. We also propose that the relatively high number of hemoglobin genes as well as the presence of non-Bohr β hemoglobin genes may be due to the dynamic life history of salmon and the diverse environmental conditions that the species encounters. Data deposition: BACs S0155C07 and S0079J05 (fps135): GenBank GQ898924; BACs S0055H05 and S0014B03 (fps1046): GenBank GQ898925 PMID:20923558

  1. Reduction and Expansion in Microsporidian Genome Evolution: New Insights from Comparative Genomics

    PubMed Central

    Heinz, Eva; Watson, Andrew K.; Foster, Peter G.; Sendra, Kacper M.; Heaps, Sarah E.; Hirt, Robert P.; Martin Embley, T.

    2013-01-01

    Microsporidia are an abundant group of obligate intracellular parasites of other eukaryotes, including immunocompromised humans, but the molecular basis of their intracellular lifestyle and pathobiology are poorly understood. New genomes from a taxonomically broad range of microsporidians, complemented by published expression data, provide an opportunity for comparative analyses to identify conserved and lineage-specific patterns of microsporidian genome evolution that have underpinned this success. In this study, we infer that a dramatic bottleneck in the last common microsporidian ancestor (LCMA) left a small conserved core of genes that was subsequently embellished by gene family expansion driven by gene acquisition in different lineages. Novel expressed protein families represent a substantial fraction of sequenced microsporidian genomes and are significantly enriched for signals consistent with secretion or membrane location. Further evidence of selection is inferred from the gain and reciprocal loss of functional domains between paralogous genes, for example, affecting transport proteins. Gene expansions among transporter families preferentially affect those that are located on the plasma membrane of model organisms, consistent with recruitment to plug conserved gaps in microsporidian biosynthesis and metabolism. Core microsporidian genes shared with other eukaryotes are enriched in orthologs that, in yeast, are highly expressed, highly connected, and often essential, consistent with strong negative selection against further reduction of the conserved gene set since the LCMA. Our study reveals that microsporidian genome evolution is a highly dynamic process that has balanced constraint, reductive evolution, and genome expansion during adaptation to an extraordinarily successful obligate intracellular lifestyle. PMID:24259309

  2. Bordetella pertussis evolution in the (functional) genomics era.

    PubMed

    Belcher, Thomas; Preston, Andrew

    2015-11-01

    The incidence of whooping cough caused by Bordetella pertussis in many developed countries has risen dramatically in recent years. This has been linked to the use of an acellular pertussis vaccine. In addition, it is thought that B. pertussis is adapting under acellular vaccine mediated immune selection pressure, towards vaccine escape. Genomics-based approaches have revolutionized the ability to resolve the fine structure of the global B. pertussis population and its evolution during the era of vaccination. Here, we discuss the current picture of B. pertussis evolution and diversity in the light of the current resurgence, highlight import questions raised by recent studies in this area and discuss the role that functional genomics can play in addressing current knowledge gaps. PMID:26297914

  3. Tracing Monotreme Venom Evolution in the Genomics Era

    PubMed Central

    Whittington, Camilla M.; Belov, Katherine

    2014-01-01

    The monotremes (platypuses and echidnas) represent one of only four extant venomous mammalian lineages. Until recently, monotreme venom was poorly understood. However, the availability of the platypus genome and increasingly sophisticated genomic tools has allowed us to characterize platypus toxins, and provides a means of reconstructing the evolutionary history of monotreme venom. Here we review the physiology of platypus and echidna crural (venom) systems as well as pharmacological and genomic studies of monotreme toxins. Further, we synthesize current ideas about the evolution of the venom system, which in the platypus is likely to have been retained from a venomous ancestor, whilst being lost in the echidnas. We also outline several research directions and outstanding questions that would be productive to address in future research. An improved characterization of mammalian venoms will not only yield new toxins with potential therapeutic uses, but will also aid in our understanding of the way that this unusual trait evolves. PMID:24699339

  4. Genomics of alternative splicing: evolution, development and pathophysiology.

    PubMed

    Gamazon, Eric R; Stranger, Barbara E

    2014-06-01

    Alternative splicing is a major cellular mechanism in metazoans for generating proteomic diversity. A large proportion of protein-coding genes in multicellular organisms undergo alternative splicing, and in humans, it has been estimated that nearly 90 % of protein-coding genes-much larger than expected-are subject to alternative splicing. Genomic analyses of alternative splicing have illuminated its universal role in shaping the evolution of genomes, in the control of developmental processes, and in the dynamic regulation of the transcriptome to influence phenotype. Disruption of the splicing machinery has been found to drive pathophysiology, and indeed reprogramming of aberrant splicing can provide novel approaches to the development of molecular therapy. This review focuses on the recent progress in our understanding of alternative splicing brought about by the unprecedented explosive growth of genomic data and highlights the relevance of human splicing variation on disease and therapy. PMID:24378600

  5. The Amphimedon queenslandica genome and the evolution of animal complexity

    SciTech Connect

    Srivastava, Mansi; Simakov, Oleg; Chapman, Jarrod; Fahey, Bryony; Gauthier, Marie E.A.; Mitros, Therese; Richards, Gemma S.; Conaco, Cecilia; Dacre, Michael; Hellsten, Uffe; Larroux, Claire; Putnam, Nicholas H.; Stanke, Mario; Adamska, Maja; Darling, Aaron; Degnan, Sandie M.; Oakley, Todd H.; Plachetzki, David C.; Zhai, Yufeng; Adamski, Marcin; Calcino, Andrew; Cummins, Scott F.; Goodstein, David M.; Harris, Christina; Jackson, Daniel J.; Leys, Sally P.; Shu, Shengqiang; Woodcroft, Ben J.; Vervoort, Michel; Kosik, Kenneth S.; Manning, Gerard; Degnan, Bernard M.; Rokhsar, Daniel S.

    2010-07-01

    Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sponge sequence reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion, and diversification of pan-metazoan transcription factor, signaling pathway, and structural genes. This diverse 'toolkit' of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic and germ cell specification, cell adhesion, innate immunity, and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.

  6. Tracing monotreme venom evolution in the genomics era.

    PubMed

    Whittington, Camilla M; Belov, Katherine

    2014-04-01

    The monotremes (platypuses and echidnas) represent one of only four extant venomous mammalian lineages. Until recently, monotreme venom was poorly understood. However, the availability of the platypus genome and increasingly sophisticated genomic tools has allowed us to characterize platypus toxins, and provides a means of reconstructing the evolutionary history of monotreme venom. Here we review the physiology of platypus and echidna crural (venom) systems as well as pharmacological and genomic studies of monotreme toxins. Further, we synthesize current ideas about the evolution of the venom system, which in the platypus is likely to have been retained from a venomous ancestor, whilst being lost in the echidnas. We also outline several research directions and outstanding questions that would be productive to address in future research. An improved characterization of mammalian venoms will not only yield new toxins with potential therapeutic uses, but will also aid in our understanding of the way that this unusual trait evolves. PMID:24699339

  7. Genomic and epigenomic co-evolution in follicular lymphomas.

    PubMed

    Loeffler, M; Kreuz, M; Haake, A; Hasenclever, D; Trautmann, H; Arnold, C; Winter, K; Koch, K; Klapper, W; Scholtysik, R; Rosolowski, M; Hoffmann, S; Ammerpohl, O; Szczepanowski, M; Herrmann, D; Kppers, R; Pott, C; Siebert, R

    2015-02-01

    Follicular lymphoma (FL) with a t(14;18) is a B-cell neoplasm clinically characterized by multiple recurrencies. In order to investigate the clonal evolution of this lymphoma, we studied paired primary and relapse tumor samples from 33 patients with recurrent non-transformed t(14;18)-positive FL. We reconstructed phylogenetic trees of the evolution by taking advantage of the activation-induced cytidine deaminase (AID)-mediated somatic hypermutation (SHM) active in the germinal center reaction using sequences of the clonal VHDHJH rearrangements of the immunoglobulin heavy chain (IGH) locus. Mutational analysis of the IGH locus showed evidence for ongoing somatic mutation and for counter-selection of mutations affecting the BCR conformation during tumor evolution. We further followed evolutionary divergence by targeted sequencing of gene loci affected by aberrant SHM as well as of known driver genes of lymphomagenesis, and by array-based genome-wide chromosomal imbalance and DNA methylation analysis. We observed a wide spectrum of evolutionary patterns ranging from almost no evolution to divergent evolution within recurrent non-transformed t(14;18) FL. Remarkably, we observed a correlation of the magnitude of evolutionary divergence across all genetic and epigenetic levels suggesting co-evolution. The distribution of coding mutations in driver genes and the correlation with SHM suggest CREBBP and AID to be potential modifiers of genetic and epigenetic co-evolution in FL. PMID:25027518

  8. Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes.

    PubMed

    McCauley, David E

    2013-12-01

    Plant mitochondrial genomes are usually transmitted to the progeny from the maternal parent. However, cases of paternal transmission are known and are perhaps more common than once thought. This review will consider recent evidence, both direct and indirect, of paternal transmission (leakage) of the mitochondrial genome of seed plants, especially in natural populations, and how this can result in offspring that carry a mixture of maternally and paternally derived copies of the genome; a type of heteroplasmy. It will further consider how this heteroplasmy facilitates recombination between genetically distinct partners; a process that can enhance mitochondrial genotypic diversity. This will then form the basis for a discussion of five evolutionary questions that arise from these observations. Questions include how plant mitochondrial genome evolution can be placed on a sexual to asexual continuum, whether cytoplasmic male sterility (CMS) facilitates the evolution of paternal leakage, whether paternal leakage is more likely in populations undergoing admixture, how leakage influences patterns of gene flow, and whether heteroplasmy occurs in natural populations at a frequency greater than predicted by crossing experiments. It is proposed that each of these questions offers fertile ground for future research on a diversity of plant species. PMID:23952142

  9. Photosynthetic evolution in parasitic plants: insight from the chloroplast genome.

    PubMed

    Bungard, Ralph A

    2004-03-01

    Despite the enormous diversity in plant form, structure and growth environment across the seed-bearing plants (angiosperms and gymnosperms), the chloroplast genome has, with few exceptions, remained remarkably conserved. This conservation suggests the existence of universal evolutionary selection pressures associated with photosynthesis-the primary function of chloroplasts. The stark exceptions to this conservation occur in parasitic angiosperms, which have escaped the dominant model by evolving the capacity to obtain some or all of their carbon (and nutrients) from their plant hosts. The consequence of this evolution to parasitism is a relaxation of the evolutionary constraints associated with the need to maintain photosynthetic function, the very function that drove early stages of the ancient symbiotic relationship that produced the contemporary chloroplast. Extreme examples of reductionism among parasitic angiosperms reveals major alterations in chloroplast function with the loss of photosynthetic capacity and, with that, massive alterations in chloroplast genome content. This review highlights emerging patterns in reported gene loss and gene retention in the chloroplast genomes of parasitic plants. Some gene losses appear to occur in the early stages of parasitic evolution, even before the loss of photosynthetic capacity, like the chlororespiratory (ndh) genes. This contrasts with unexpected gene retentions, like that of the rbcL gene responsible for photosynthetic carbon dioxide fixation, and belies current understanding of gene function. The review relates gene retention to current knowledge of protein function and gene processing that has implications to broader aspects of genome conservation in organelles. PMID:14988925

  10. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes

    PubMed Central

    Sun, Yan-Bo; Xiong, Zi-Jun; Xiang, Xue-Yan; Liu, Shi-Ping; Zhou, Wei-Wei; Tu, Xiao-Long; Zhong, Li; Wang, Lu; Wu, Dong-Dong; Zhang, Bao-Lin; Zhu, Chun-Ling; Yang, Min-Min; Chen, Hong-Man; Li, Fang; Zhou, Long; Feng, Shao-Hong; Huang, Chao; Zhang, Guo-Jie; Irwin, David; Hillis, David M.; Murphy, Robert W.; Yang, Huan-Ming; Che, Jing; Wang, Jun; Zhang, Ya-Ping

    2015-01-01

    The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies. PMID:25733869

  11. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.

    PubMed

    Sun, Yan-Bo; Xiong, Zi-Jun; Xiang, Xue-Yan; Liu, Shi-Ping; Zhou, Wei-Wei; Tu, Xiao-Long; Zhong, Li; Wang, Lu; Wu, Dong-Dong; Zhang, Bao-Lin; Zhu, Chun-Ling; Yang, Min-Min; Chen, Hong-Man; Li, Fang; Zhou, Long; Feng, Shao-Hong; Huang, Chao; Zhang, Guo-Jie; Irwin, David; Hillis, David M; Murphy, Robert W; Yang, Huan-Ming; Che, Jing; Wang, Jun; Zhang, Ya-Ping

    2015-03-17

    The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies. PMID:25733869

  12. Evaluation of Virucidal Compounds for Inactivation of Rhinovirus on Hands

    PubMed Central

    Hendley, J. Owen; Mika, Leonard A.; Gwaltney, Jack M.

    1978-01-01

    Antimicrobial liquids and foams were applied to the hands to determine their virucidal activity against rhinoviruses. Dilute solutions (1%) of iodine in ethyl alcohol or in water were most effective in causing inactivation of rhinovirus when applied immediately after viral contamination. Iodine also had a residual virucidal activity which persisted on the hands for up to 1 h. Less effective inactivation of rhinovirus was observed with foams containing 0.23% hexachlorophene and 58% ethyl alcohol and another containing 0.2% benzalkonium chloride and 50% ethyl alcohol. Ethyl alcohol alone or in a mixture with benzyl alcohol was the least effective preparation tested. PMID:215080

  13. Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes

    PubMed Central

    Fan, Shaohua; Meyer, Axel

    2014-01-01

    African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile Tilapia (Oreochromis niloticus), a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the Tilapia genome as a reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), inversions and deletions. In total, around 18.8, 17.7, 17.0, and 17.0 million SNPs, 2.3, 2.2, 1.4, and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710, and 2634 deletions were inferred to have evolved in N. brichardi, A. burtoni, P. nyererei, and M. zebra, respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes. PMID:24917883

  14. Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes.

    PubMed

    Fan, Shaohua; Meyer, Axel

    2014-01-01

    African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile Tilapia (Oreochromis niloticus), a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the Tilapia genome as a reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), inversions and deletions. In total, around 18.8, 17.7, 17.0, and 17.0 million SNPs, 2.3, 2.2, 1.4, and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710, and 2634 deletions were inferred to have evolved in N. brichardi, A. burtoni, P. nyererei, and M. zebra, respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes. PMID:24917883

  15. Molecular cytogenetic and genomic insights into chromosomal evolution

    PubMed Central

    Ruiz-Herrera, A; Farr, M; Robinson, T J

    2012-01-01

    This review summarizes aspects of the extensive literature on the patterns and processes underpinning chromosomal evolution in vertebrates and especially placental mammals. It highlights the growing synergy between molecular cytogenetics and comparative genomics, particularly with respect to fully or partially sequenced genomes, and provides novel insights into changes in chromosome number and structure across deep division of the vertebrate tree of life. The examination of basal numbers in the deeper branches of the vertebrate tree suggest a haploid (n) chromosome number of 1013 in an ancestral vertebrate, with modest increases in tetrapods and amniotes most probably by chromosomal fissioning. Information drawn largely from cross-species chromosome painting in the data-dense Placentalia permits the confident reconstruction of an ancestral karyotype comprising n=23 chromosomes that is similarly retained in Boreoeutheria. Using in silico genome-wide scans that include the newly released frog genome we show that of the nine ancient syntenies detected in conserved karyotypes of extant placentals (thought likely to reflect the structure of ancestral chromosomes), the human syntenic segmental associations 3p/21, 4pq/8p, 7a/16p, 14/15, 12qt/22q and 12pq/22qt predate the divergence of tetrapods. These findings underscore the enhanced quality of ancestral reconstructions based on the integrative molecular cytogenetic and comparative genomic approaches that collectively highlight a pattern of conserved syntenic associations that extends back ?360 million years ago. PMID:22108627

  16. Loss of Genetic Redundancy in Reductive Genome Evolution

    PubMed Central

    Pereira-Leal, Jos B.

    2011-01-01

    Biological systems evolved to be functionally robust in uncertain environments, but also highly adaptable. Such robustness is partly achieved by genetic redundancy, where the failure of a specific component through mutation or environmental challenge can be compensated by duplicate components capable of performing, to a limited extent, the same function. Highly variable environments require very robust systems. Conversely, predictable environments should not place a high selective value on robustness. Here we test this hypothesis by investigating the evolutionary dynamics of genetic redundancy in extremely reduced genomes, found mostly in intracellular parasites and endosymbionts. By combining data analysis with simulations of genome evolution we show that in the extensive gene loss suffered by reduced genomes there is a selective drive to keep the diversity of protein families while sacrificing paralogy. We show that this is not a by-product of the known drivers of genome reduction and that there is very limited convergence to a common core of families, indicating that the repertoire of protein families in reduced genomes is the result of historical contingency and niche-specific adaptations. We propose that our observations reflect a loss of genetic redundancy due to a decreased selection for robustness in a predictable environment. PMID:21379323

  17. The evolution of genome compression and genomic novelty in RNA viruses

    PubMed Central

    Belshaw, Robert; Pybus, Oliver G.; Rambaut, Andrew

    2007-01-01

    The genomes of RNA viruses are characterized by their extremely small size and extremely high mutation rates (typically 10 kb and 10−4/base/replication cycle, respectively), traits that are thought to be causally linked. One aspect of their small size is the genome compression caused by the use of overlapping genes (where some nucleotides code for two genes). Using a comparative analysis of all known RNA viral species, we show that viruses with larger genomes tend to have less gene overlap. We provide a numerical model to show how a high mutation rate could lead to gene overlap, and we discuss the factors that might explain the observed relationship between gene overlap and genome size. We also propose a model for the evolution of gene overlap based on the co-opting of previously unused ORFs, which gives rise to two types of overlap: (1) the creation of novel genes inside older genes, predominantly via +1 frameshifts, and (2) the incremental increase in overlap between originally contiguous genes, with no frameshift preference. Both types of overlap are viewed as the creation of genomic novelty under pressure for genome compression. Simulations based on our model generate the empirical size distributions of overlaps and explain the observed frameshift preferences. We suggest that RNA viruses are a good model system for the investigation of general evolutionary relationship between genome attributes such as mutational robustness, mutation rate, and size. PMID:17785537

  18. Pentatricopeptide repeat proteins constrain genome evolution in chloroplasts.

    PubMed

    Hayes, Michael L; Mulligan, R Michael

    2011-07-01

    Higher plants encode hundreds of pentatricopeptide repeat proteins (PPRs) that are involved in several types of RNA processing reactions. Most PPR genes are predicted to be targeted to chloroplasts or mitochondria, and many are known to affect organellar gene expression. In some cases, RNA binding has been directly demonstrated, and the sequences of the cis-elements are known. In this work, we demonstrate that RNA cis-elements recognized by PPRs are constrained in chloroplast genome evolution. Cis-elements for two PPR genes and several RNA editing sites were analyzed for sequence changes by pairwise nucleotide substitution frequency, pairwise indel frequency, and maximum likelihood (ML) phylogenetic distances. All three of these analyses demonstrated that sequences within the cis-element are highly conserved compared with surrounding sequences. In addition, we have compared sequences around chloroplast editing sites and homologous sequences in species that lack an editing site due to the presence of a genomic T. Cis-elements for RNA editing sites are highly conserved in angiosperms; by contrast, comparable sequences around a genomically encoded T exhibit higher rates of nucleotide substitution, higher frequencies of indels, and greater ML distances. The loss in requirement for editing to create the ndhD start codon has resulted in the conversion of the PPR gene responsible for editing that site to a pseudogene. We show that organellar dependence on nuclear-encoded PPR proteins for gene expression has constrained the evolution of cis-elements that are required at the level of RNA processing. Thus, the expansion of the PPR gene family in plants has had a dramatic effect on the evolution of plant organelle genomes. PMID:21263042

  19. Reconstructing the Evolution of Brachypodium Genomes Using Comparative Chromosome Painting

    PubMed Central

    Betekhtin, Alexander; Jenkins, Glyn; Hasterok, Robert

    2014-01-01

    Brachypodium distachyon is a model for the temperate cereals and grasses and has a biology, genomics infrastructure and cytogenetic platform fit for purpose. It is a member of a genus with fewer than 20 species, which have different genome sizes, basic chromosome numbers and ploidy levels. The phylogeny and interspecific relationships of this group have not to date been resolved by sequence comparisons and karyotypical studies. The aims of this study are not only to reconstruct the evolution of Brachypodium karyotypes to resolve the phylogeny, but also to highlight the mechanisms that shape the evolution of grass genomes. This was achieved through the use of comparative chromosome painting (CCP) which hybridises fluorescent, chromosome-specific probes derived from B. distachyon to homoeologous meiotic chromosomes of its close relatives. The study included five diploids (B. distachyon 2n = 10, B. sylvaticum 2n = 18, B. pinnatum 2n = 16; 2n = 18, B. arbuscula 2n = 18 and B. stacei 2n = 20) three allotetraploids (B. pinnatum 2n = 28, B. phoenicoides 2n = 28 and B. hybridum 2n = 30), and two species of unknown ploidy (B. retusum 2n = 38 and B. mexicanum 2n = 40). On the basis of the patterns of hybridisation and incorporating published data, we propose two alternative, but similar, models of karyotype evolution in the genus Brachypodium. According to the first model, the extant genome of B. distachyon derives from B. mexicanum or B. stacei by several rounds of descending dysploidy, and the other diploids evolve from B. distachyon via ascending dysploidy. The allotetraploids arise by interspecific hybridisation and chromosome doubling between B. distachyon and other diploids. The second model differs from the first insofar as it incorporates an intermediate 2n = 18 species between the B. mexicanum or B. stacei progenitors and the dysploidic B. distachyon. PMID:25493646

  20. The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq

    PubMed Central

    Renaut, Sébastien; Grassa, Christopher J.; Moyers, Brook T.; Kane, Nolan C.; Rieseberg, Loren H.

    2012-01-01

    Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq) to refine our understanding of the population genomics of wild species of sunflowers (Helianthus spp.) and the factors that affect rates of protein evolution. We aligned 35 GB of transcriptome sequencing data and identified 433,257 polymorphic sites (SNPs) in a reference transcriptome comprising 16,312 genes. Using SNP markers, we identified strong population clustering largely corresponding to the three species analyzed here (Helianthus annuus, H. petiolaris, H. debilis), with one distinct early generation hybrid. Then, we calculated the proportions of adaptive substitution fixed by selection (alpha) and identified gene ontology categories with elevated values of alpha. The “response to biotic stimulus” category had the highest mean alpha across the three interspecific comparisons, implying that natural selection imposed by other organisms plays an important role in driving protein evolution in wild sunflowers. Finally, we examined the relationship between protein evolution (dN/dS ratio) and several genomic factors predicted to co-vary with protein evolution (gene expression level, divergence and specificity, genetic divergence [FST], and nucleotide diversity pi). We find that variation in rates of protein divergence was correlated with gene expression level and specificity, consistent with results from a broad range of taxa and timescales. This would in turn imply that these factors govern protein evolution both at a microevolutionary and macroevolutionary timescale. Our results contribute to a general understanding of the determinants of rates of protein evolution and the impact of selection on patterns of polymorphism and divergence. PMID:24832509

  1. Genomes and geography: genomic insights into the evolution and phylogeography of the genus Schistosoma

    PubMed Central

    2011-01-01

    Blood flukes within the genus Schistosoma still remain a major cause of disease in the tropics and subtropics and the study of their evolution has been an area of major debate and research. With the advent of modern molecular and genomic approaches deeper insights have been attained not only into the divergence and speciation of these worms, but also into the historic movement of these parasites from Asia into Africa, via migration and dispersal of definitive and snail intermediate hosts. This movement was subsequently followed by a radiation of Schistosoma species giving rise to the S. mansoni and S. haematobium groups, as well as the S. indicum group that reinvaded Asia. Each of these major evolutionary events has been marked by distinct changes in genomic structure evident in differences in mitochondrial gene order and nuclear chromosomal architecture between the species associated with Asia and Africa. Data from DNA sequencing, comparative molecular genomics and karyotyping are indicative of major constitutional genomic events which would have become fixed in the ancestral populations of these worms. Here we examine how modern genomic techniques may give a more in depth understanding of the evolution of schistosomes and highlight the complexity of speciation and divergence in this group. PMID:21736723

  2. The genome diversity and karyotype evolution of mammals

    PubMed Central

    2011-01-01

    The past decade has witnessed an explosion of genome sequencing and mapping in evolutionary diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosome regions from more than a few species is still not possible. The intense focus on building of comparative maps for companion (dog and cat), laboratory (mice and rat) and agricultural (cattle, pig, and horse) animals has traditionally been used as a means to understand the underlying basis of disease-related or economically important phenotypes. However, these maps also provide an unprecedented opportunity to use multispecies analysis as a tool for inferring karyotype evolution. Comparative chromosome painting and related techniques are now considered to be the most powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization (FISH) on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders. In most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. The number of rearrangements that have become fixed in evolutionary history seems comparatively low, bearing in mind the 180 million years of the mammalian radiation. Comparative chromosome maps record the history of karyotype changes that have occurred during evolution. The aim of this review is to provide an overview of these recent advances in our endeavor to decipher the karyotype evolution of mammals by integrating the published results together with some of our latest unpublished results. PMID:21992653

  3. Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution

    PubMed Central

    Cai, Hui; Thompson, Rebecca; Budinich, Mateo F.; Broadbent, Jeff R.

    2009-01-01

    Lactobacillus casei is remarkably adaptable to diverse habitats and widely used in the food industry. To reveal the genomic features that contribute to its broad ecological adaptability and examine the evolution of the species, the genome sequence of L. casei ATCC 334 is analyzed and compared with other sequenced lactobacilli. This analysis reveals that ATCC 334 contains a high number of coding sequences involved in carbohydrate utilization and transcriptional regulation, reflecting its requirement for dealing with diverse environmental conditions. A comparison of the genome sequences of ATCC 334 to L. casei BL23 reveals 12 and 19 genomic islands, respectively. For a broader assessment of the genetic variability within L. casei, gene content of 21 L. casei strains isolated from various habitats (cheeses, n = 7; plant materials, n = 8; and human sources, n = 6) was examined by comparative genome hybridization with an ATCC 334-based microarray. This analysis resulted in identification of 25 hypervariable regions. One of these regions contains an overrepresentation of genes involved in carbohydrate utilization and transcriptional regulation and was thus proposed as a lifestyle adaptation island. Differences in L. casei genome inventory reveal both gene gain and gene decay. Gene gain, via acquisition of genomic islands, likely confers a fitness benefit in specific habitats. Gene decay, that is, loss of unnecessary ancestral traits, is observed in the cheese isolates and likely results in enhanced fitness in the dairy niche. This study gives the first picture of the stable versus variable regions in L. casei and provides valuable insights into evolution, lifestyle adaptation, and metabolic diversity of L. casei. PMID:20333194

  4. Thermodynamic basis for the emergence of genomes during prebiotic evolution.

    PubMed

    Woo, Hyung-June; Vijaya Satya, Ravi; Reifman, Jaques

    2012-05-01

    The RNA world hypothesis views modern organisms as descendants of RNA molecules. The earliest RNA molecules must have been random sequences, from which the first genomes that coded for polymerase ribozymes emerged. The quasispecies theory by Eigen predicts the existence of an error threshold limiting genomic stability during such transitions, but does not address the spontaneity of changes. Following a recent theoretical approach, we applied the quasispecies theory combined with kinetic/thermodynamic descriptions of RNA replication to analyze the collective behavior of RNA replicators based on known experimental kinetics data. We find that, with increasing fidelity (relative rate of base-extension for Watson-Crick versus mismatched base pairs), replications without enzymes, with ribozymes, and with protein-based polymerases are above, near, and below a critical point, respectively. The prebiotic evolution therefore must have crossed this critical region. Over large regions of the phase diagram, fitness increases with increasing fidelity, biasing random drifts in sequence space toward 'crystallization.' This region encloses the experimental nonenzymatic fidelity value, favoring evolutions toward polymerase sequences with ever higher fidelity, despite error rates above the error catastrophe threshold. Our work shows that experimentally characterized kinetics and thermodynamics of RNA replication allow us to determine the physicochemical conditions required for the spontaneous crystallization of biological information. Our findings also suggest that among many potential oligomers capable of templated replication, RNAs may have evolved to form prebiotic genomes due to the value of their nonenzymatic fidelity. PMID:22693440

  5. Genome duplication and the evolution of conspecific pollen precedence

    PubMed Central

    Baldwin, Sarah J.; Husband, Brian C.

    2011-01-01

    Conspecific pollen precedence can be a strong reproductive barrier between polyploid and diploid species, but the role of genome multiplication in the evolution of this barrier has not been investigated. Here, we examine the direct effect of genome duplication on the evolution of pollen siring success in tetraploid Chamerion angustifolium. To separate the effects of genome duplication from selection after duplication, we compared pollen siring success of synthesized tetraploids (neotetraploids) with that of naturally occurring tetraploids by applying 2x, 4x (neo or established) or 2x + 4x pollen to diploid and tetraploid flowers. Seed set increased in diploids and decreased in both types of tetraploids as the proportion of pollen from diploid plants increased. Based on offspring ploidy from mixed-ploidy pollinations, pollen of the maternal ploidy always sired the majority of offspring but was strongest in established tetraploids and weakest in neotetraploids. Pollen from established tetraploids had significantly higher siring rates than neotetraploids when deposited on diploid (4xest = 47.2%, 4xneo = 27.1%) and on tetraploid recipients (4xest = 91.9%, 4xneo = 56.0%). Siring success of established tetraploids exceeded that of neotetraploids despite having similar pollen production per anther and pollen diameter. Our results suggest that, while pollen precedence can arise in association with the duplication event, the strength of polyploid siring success evolves after the duplication event. PMID:21123263

  6. Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution

    PubMed Central

    Woo, Hyung-June; Vijaya Satya, Ravi; Reifman, Jaques

    2012-01-01

    The RNA world hypothesis views modern organisms as descendants of RNA molecules. The earliest RNA molecules must have been random sequences, from which the first genomes that coded for polymerase ribozymes emerged. The quasispecies theory by Eigen predicts the existence of an error threshold limiting genomic stability during such transitions, but does not address the spontaneity of changes. Following a recent theoretical approach, we applied the quasispecies theory combined with kinetic/thermodynamic descriptions of RNA replication to analyze the collective behavior of RNA replicators based on known experimental kinetics data. We find that, with increasing fidelity (relative rate of base-extension for Watson-Crick versus mismatched base pairs), replications without enzymes, with ribozymes, and with protein-based polymerases are above, near, and below a critical point, respectively. The prebiotic evolution therefore must have crossed this critical region. Over large regions of the phase diagram, fitness increases with increasing fidelity, biasing random drifts in sequence space toward crystallization. This region encloses the experimental nonenzymatic fidelity value, favoring evolutions toward polymerase sequences with ever higher fidelity, despite error rates above the error catastrophe threshold. Our work shows that experimentally characterized kinetics and thermodynamics of RNA replication allow us to determine the physicochemical conditions required for the spontaneous crystallization of biological information. Our findings also suggest that among many potential oligomers capable of templated replication, RNAs may have evolved to form prebiotic genomes due to the value of their nonenzymatic fidelity. PMID:22693440

  7. Stress-Induced Modulators of Repeat Instability and Genome Evolution

    PubMed Central

    Fonville, Natalie C.; Ward, R. Matthew; Mittelman, David

    2012-01-01

    Evolution hinges on the ability of organisms to adapt to their environment. A key regulator of adaptability is mutation rate, which must be balanced to maintain genome fidelity while permitting sufficient plasticity to cope with environmental changes. Multiple mechanisms govern an organism's mutation rate. Constitutive mechanisms include mutator alleles that drive global, permanent increases in mutation rates, but these changes are confined to the subpopulation that carries the mutator allele. Other mechanisms focus mutagenesis in time and space to improve the chances that adaptive mutations can spread through the population. For example, environmental stress can induce mechanisms that transiently relax the fidelity of DNA repair to bring about a temporary increase in mutation rates during times when an organism experiences a reduced fitness for its surroundings, as has been demonstrated for double-strand break repair in Escherichia coli. Still, other mechanisms control the spatial distribution of mutations by directing changes to especially mutable sequences in the genome. In eukaryotic cells, for example, the stress-sensitive chaperone Hsp90 can regulate the length of trinucleotide repeats to fine-tune gene function and can regulate the mobility of transposable elements to enable larger functional changes. Here, we review the regulation of mutation rate, with special emphasis on the roles of tandem repeats and environmental stress in genome evolution. PMID:22248541

  8. Genomes of the T4-related bacteriophages as windows on microbial genome evolution

    PubMed Central

    2010-01-01

    The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or "Core Genome" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature. PMID:21029436

  9. Genome Size, Karyotype Polymorphism and Chromosomal Evolution in Trypanosoma cruzi

    PubMed Central

    Barros, Roberto Moraes; Cortez, Danielle R.; Santos, Michele F.; Cordero, Esteban M.; Ruiz, Jeronimo Conceiao; Goldenberg, Samuel; Teixeira, Marta M. G.; da Silveira, Jos Franco

    2011-01-01

    Background The Trypanosoma cruzi genome was sequenced from a hybrid strain (CL Brener). However, high allelic variation and the repetitive nature of the genome have prevented the complete linear sequence of chromosomes being determined. Determining the full complement of chromosomes and establishing syntenic groups will be important in defining the structure of T. cruzi chromosomes. A large amount of information is now available for T. cruzi and Trypanosoma brucei, providing the opportunity to compare and describe the overall patterns of chromosomal evolution in these parasites. Methodology/Principal Findings The genome sizes, repetitive DNA contents, and the numbers and sizes of chromosomes of nine strains of T. cruzi from four lineages (TcI, TcII, TcV and TcVI) were determined. The genome of the TcI group was statistically smaller than other lineages, with the exception of the TcI isolate Tc1161 (Jos-IMT). Satellite DNA content was correlated with genome size for all isolates, but this was not accompanied by simultaneous amplification of retrotransposons. Regardless of chromosomal polymorphism, large syntenic groups are conserved among T. cruzi lineages. Duplicated chromosome-sized regions were identified and could be retained as paralogous loci, increasing the dosage of several genes. By comparing T. cruzi and T. brucei chromosomes, homologous chromosomal regions in T. brucei were identified. Chromosomes Tb9 and Tb11 of T. brucei share regions of syntenic homology with three and six T. cruzi chromosomal bands, respectively. Conclusions Despite genome size variation and karyotype polymorphism, T. cruzi lineages exhibit conservation of chromosome structure. Several syntenic groups are conserved among all isolates analyzed in this study. The syntenic regions are larger than expected if rearrangements occur randomly, suggesting that they are conserved owing to positive selection. Mapping of the syntenic regions on T. cruzi chromosomal bands provides evidence for the occurrence of fusion and split events involving T. brucei and T. cruzi chromosomes. PMID:21857989

  10. Rates of phenotypic and genomic evolution during the Cambrian explosion.

    PubMed

    Lee, Michael S Y; Soubrier, Julien; Edgecombe, Gregory D

    2013-10-01

    The near-simultaneous appearance of most modern animal body plans (phyla) ~530 million years ago during the Cambrian explosion is strong evidence for a brief interval of rapid phenotypic and genetic innovation, yet the exact speed and nature of this grand adaptive radiation remain debated. Crucially, rates of morphological evolution in the past (i.e., in ancestral lineages) can be inferred from phenotypic differences among living organisms-just as molecular evolutionary rates in ancestral lineages can be inferred from genetic divergences. We here employed Bayesian and maximum likelihood phylogenetic clock methods on an extensive anatomical and genomic data set for arthropods, the most diverse phylum in the Cambrian and today. Assuming an Ediacaran origin for arthropods, phenotypic evolution was ~4 times faster, and molecular evolution ~5.5 times faster, during the Cambrian explosion compared to all subsequent parts of the Phanerozoic. These rapid evolutionary rates are robust to assumptions about the precise age of arthropods. Surprisingly, these fast early rates do not change substantially even if the radiation of arthropods is compressed entirely into the Cambrian (~542 mega-annum [Ma]) or telescoped into the Cryogenian (~650 Ma). The fastest inferred rates are still consistent with evolution by natural selection and with data from living organisms, potentially resolving "Darwin's dilemma." However, evolution during the Cambrian explosion was unusual (compared to the subsequent Phanerozoic) in that fast rates were present across many lineages. PMID:24035543

  11. Phylostratigraphic bias creates spurious patterns of genome evolution.

    PubMed

    Moyers, Bryan A; Zhang, Jianzhi

    2015-01-01

    Phylostratigraphy is a method for dating the evolutionary emergence of a gene or gene family by identifying its homologs across the tree of life, typically by using BLAST searches. Applying this method to all genes in a species, or genomic phylostratigraphy, allows investigation of genome-wide patterns in new gene origination at different evolutionary times and thus has been extensively used. However, gene age estimation depends on the challenging task of detecting distant homologs via sequence similarity, which is expected to have differential accuracies for different genes. Here, we evaluate the accuracy of phylostratigraphy by realistic computer simulation with parameters estimated from genomic data, and investigate the impact of its error on findings of genome evolution. We show that 1) phylostratigraphy substantially underestimates gene age for a considerable fraction of genes, 2) the error is especially serious when the protein evolves rapidly, is short, and/or its most conserved block of sites is small, and 3) these errors create spurious nonuniform distributions of various gene properties among age groups, many of which cannot be predicted a priori. Given the high likelihood that conclusions about gene age are faulty, we advocate the use of realistic simulation to determine if observations from phylostratigraphy are explainable, at least qualitatively, by a null model of biased measurement, and in all cases, critical evaluation of results. PMID:25312911

  12. Genomic diversity and evolution within the species Streptococcus agalactiae.

    PubMed

    Brochet, Mathieu; Couvé, Elisabeth; Zouine, Mohamed; Vallaeys, Tatiana; Rusniok, Christophe; Lamy, Marie-Cécile; Buchrieser, Carmen; Trieu-Cuot, Patrick; Kunst, Frank; Poyart, Claire; Glaser, Philippe

    2006-04-01

    Streptococcus agalactiae is a leading cause of invasive infections in neonates, and responsible for bovine mastitis. It is also a commensal bacterium adapted to asymptomatic colonization of the mammalian gut and of the genitourinary tract. Here, we report the analysis of a collection of 75 strains of human and animal origin by using serotyping, multilocus sequence typing, whole genome DNA-array hybridizations and sequence comparison of putatively virulence-associated loci. Although the most variable parts of the genome are the previously predicted genomic islands, significant genetic variations were present in the genome backbone. Evolution within genes encoding surface and secreted proteins and those involved in the biosynthesis of different capsular types is mainly due to recombination events leading to the replacement of a locus of several genes or to the allelic exchange of the internal part of a gene. These two processes, which led to a broad diversity of surface protein patterns, are probably involved in the diversity of interactions with the host and its immune system. According to gene content comparisons and phylogeny, recent gene replacements by horizontal gene transfer may occur but are rare events. Although specific gene patterns, with respect to the origin of the strains and the epidemiological characteristics, were not identified, we show that the recently described hypervirulent ST-17 lineage is a homogeneous group. The study highlights for the first time that this lineage contains a specific and conserved set of surface proteins, probably accounting for its high capacity to cause infections in newborns. PMID:16529966

  13. Camelid genomes reveal evolution and adaptation to desert environments.

    PubMed

    Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

    2014-01-01

    Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments. PMID:25333821

  14. The structure of the protein universe and genome evolution.

    PubMed

    Koonin, Eugene V; Wolf, Yuri I; Karev, Georgy P

    2002-11-14

    Despite the practically unlimited number of possible protein sequences, the number of basic shapes in which proteins fold seems not only to be finite, but also to be relatively small, with probably no more than 10,000 folds in existence. Moreover, the distribution of proteins among these folds is highly non-homogeneous -- some folds and superfamilies are extremely abundant, but most are rare. Protein folds and families encoded in diverse genomes show similar size distributions with notable mathematical properties, which also extend to the number of connections between domains in multidomain proteins. All these distributions follow asymptotic power laws, such as have been identified in a wide variety of biological and physical systems, and which are typically associated with scale-free networks. These findings suggest that genome evolution is driven by extremely general mechanisms based on the preferential attachment principle. PMID:12432406

  15. Nitrifier genomics and evolution of the nitrogen cycle.

    PubMed

    Klotz, Martin G; Stein, Lisa Y

    2008-01-01

    Advances in technology have tremendously increased high throughput whole genome-sequencing efforts, many of which have included prokaryotes that facilitate processes in the extant nitrogen cycle. Molecular genetic and evolutionary analyses of these genomes paired with advances in postgenomics, biochemical and physiological experimentation have enabled scientists to reevaluate existing geochemical and oceanographic data for improved characterization of the extant nitrogen cycle as well as its evolution since the primordial era of planet Earth. Based on the literature and extensive new data relevant to aerobic and anaerobic ammonia oxidation (ANAMMOX), the natural history of the nitrogen-cycle has been redrawn with emphasis on the early roles of incomplete denitrification and ammonification as driving forces for emergence of ANAMMOX as the foundation for a complete nitrogen cycle, and concluding with emergence of nitrification in the oxic era. PMID:18031536

  16. The genomic signatures of Shigella evolution, adaptation and geographical spread.

    PubMed

    The, Hao Chung; Thanh, Duy Pham; Holt, Kathryn E; Thomson, Nicholas R; Baker, Stephen

    2016-04-01

    Shigella spp. are some of the key pathogens responsible for the global burden of diarrhoeal disease. These facultative intracellular bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Escherichia coli and Salmonella spp. The genus Shigella comprises four different species, each consisting of several serogroups, all of which show phenotypic similarity, including invasive pathogenicity. DNA sequencing suggests that this similarity results from the convergent evolution of different Shigella spp. founders. Here, we review the evolutionary relationships between Shigella spp. and E . coli, and we highlight how the genomic plasticity of these bacteria and their acquisition of a distinctive virulence plasmid have enabled the development of such highly specialized pathogens. Furthermore, we discuss the insights that genotyping and whole-genome sequencing have provided into the phylogenetics and intercontinental spread of Shigella spp. PMID:26923111

  17. The Opossum genome reveals further evidence for regulatory evolution in mammalian diversification

    PubMed Central

    Lemos, Bernardo

    2007-01-01

    The sequencing of the euchromatic genome of a marsupial, the opossum Monodelphis domestica, identifies shared and unique features of marsupial and placental genomes and reveals a prominent role for the evolution of non-protein-coding elements. PMID:17688679

  18. The Complete Chloroplast and Mitochondrial Genome Sequences of Boea hygrometrica: Insights into the Evolution of Plant Organellar Genomes

    PubMed Central

    Wang, Xumin; Deng, Xin; Zhang, Xiaowei; Hu, Songnian; Yu, Jun

    2012-01-01

    The complete nucleotide sequences of the chloroplast (cp) and mitochondrial (mt) genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae) have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147) with a 72% coding sequence, and the larger mitochondrial genome have less genes (65) with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC) and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage. PMID:22291979

  19. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes.

    PubMed

    Zhang, Tongwu; Fang, Yongjun; Wang, Xumin; Deng, Xin; Zhang, Xiaowei; Hu, Songnian; Yu, Jun

    2012-01-01

    The complete nucleotide sequences of the chloroplast (cp) and mitochondrial (mt) genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae) have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147) with a 72% coding sequence, and the larger mitochondrial genome have less genes (65) with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC) and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage. PMID:22291979

  20. Perspective: transposable elements, parasitic DNA, and genome evolution.

    PubMed

    Kidwell, M G; Lisch, D R

    2001-01-01

    The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as "selfish DNA" and "junk DNA" may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum, endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions. PMID:11263730

  1. Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

    PubMed Central

    Griffin, Darren K; Robertson, Lindsay B; Tempest, Helen G; Vignal, Alain; Fillon, Valérie; Crooijmans, Richard PMA; Groenen, Martien AM; Deryusheva, Svetlana; Gaginskaya, Elena; Carré, Wilfrid; Waddington, David; Talbot, Richard; Völker, Martin; Masabanda, Julio S; Burt, Dave W

    2008-01-01

    Background Comparative genomics is a powerful means of establishing inter-specific relationships between gene function/location and allows insight into genomic rearrangements, conservation and evolutionary phylogeny. The availability of the complete sequence of the chicken genome has initiated the development of detailed genomic information in other birds including turkey, an agriculturally important species where mapping has hitherto focused on linkage with limited physical information. No molecular study has yet examined conservation of avian microchromosomes, nor differences in copy number variants (CNVs) between birds. Results We present a detailed comparative cytogenetic map between chicken and turkey based on reciprocal chromosome painting and mapping of 338 chicken BACs to turkey metaphases. Two inter-chromosomal changes (both involving centromeres) and three pericentric inversions have been identified between chicken and turkey; and array CGH identified 16 inter-specific CNVs. Conclusion This is the first study to combine the modalities of zoo-FISH and array CGH between different avian species. The first insight into the conservation of microchromosomes, the first comparative cytogenetic map of any bird and the first appraisal of CNVs between birds is provided. Results suggest that avian genomes have remained relatively stable during evolution compared to mammalian equivalents. PMID:18410676

  2. Evolution of Prdm Genes in Animals: Insights from Comparative Genomics

    PubMed Central

    Vervoort, Michel; Meulemeester, David; Béhague, Julien; Kerner, Pierre

    2016-01-01

    Prdm genes encode transcription factors with a subtype of SET domain known as the PRDF1-RIZ (PR) homology domain and a variable number of zinc finger motifs. These genes are involved in a wide variety of functions during animal development. As most Prdm genes have been studied in vertebrates, especially in mice, little is known about the evolution of this gene family. We searched for Prdm genes in the fully sequenced genomes of 93 different species representative of all the main metazoan lineages. A total of 976 Prdm genes were identified in these species. The number of Prdm genes per species ranges from 2 to 19. To better understand how the Prdm gene family has evolved in metazoans, we performed phylogenetic analyses using this large set of identified Prdm genes. These analyses allowed us to define 14 different subfamilies of Prdm genes and to establish, through ancestral state reconstruction, that 11 of them are ancestral to bilaterian animals. Three additional subfamilies were acquired during early vertebrate evolution (Prdm5, Prdm11, and Prdm17). Several gene duplication and gene loss events were identified and mapped onto the metazoan phylogenetic tree. By studying a large number of nonmetazoan genomes, we confirmed that Prdm genes likely constitute a metazoan-specific gene family. Our data also suggest that Prdm genes originated before the diversification of animals through the association of a single ancestral SET domain encoding gene with one or several zinc finger encoding genes. PMID:26560352

  3. Cubozoan genome illuminates functional diversification of opsins and photoreceptor evolution.

    PubMed

    Liegertov, Michaela; Pergner, Ji?; Kozmikov, Iryna; Fabian, Peter; Pombinho, Antonio R; Strnad, Hynek; Pa?es, Jan; Vl?ek, ?estmr; Bart?n?k, Petr; Kozmik, Zbyn?k

    2015-01-01

    Animals sense light primarily by an opsin-based photopigment present in a photoreceptor cell. Cnidaria are arguably the most basal phylum containing a well-developed visual system. The evolutionary history of opsins in the animal kingdom has not yet been resolved. Here, we study the evolution of animal opsins by genome-wide analysis of the cubozoan jellyfish Tripedalia cystophora, a cnidarian possessing complex lens-containing eyes and minor photoreceptors. A large number of opsin genes with distinct tissue- and stage-specific expression were identified. Our phylogenetic analysis unequivocally classifies cubozoan opsins as a sister group to c-opsins and documents lineage-specific expansion of the opsin gene repertoire in the cubozoan genome. Functional analyses provided evidence for the use of the Gs-cAMP signaling pathway in a small set of cubozoan opsins, indicating the possibility that the majority of other cubozoan opsins signal via distinct pathways. Additionally, these tests uncovered subtle differences among individual opsins, suggesting possible fine-tuning for specific photoreceptor tasks. Based on phylogenetic, expression and biochemical analysis we propose that rapid lineage- and species-specific duplications of the intron-less opsin genes and their subsequent functional diversification promoted evolution of a large repertoire of both visual and extraocular photoreceptors in cubozoans. PMID:26154478

  4. Complex prokaryotic genome structure: rapid evolution of chromosome II.

    PubMed

    Bavishi, Anish; Abhishek, Ankur; Lin, Lin; Choudhary, Madhusudan

    2010-09-01

    Although many bacteria with two chromosomes have been sequenced, the roles of such complex genome structuring are still unclear. To uncover levels of chromosome I (CI) and chromosome II (CII) sequence divergence, Mauve 2.2.0 was used to align the CI- and CII-specific sequences of bacteria with complex genome structuring in two sets of comparisons: the first set was conducted among the CI and CII of bacterial strains of the same species, while the second set was conducted among the CI and CII of species in Alphaproteobacteria that possess two chromosomes. The analyses revealed a rapid evolution of CII-specific DNA sequences compared with CI-specific sequences in a majority of organisms. In addition, levels of protein divergence between CI-specific and CII-specific genes were determined using phylogenetic analyses and confirmed the DNA alignment findings. Analysis of synonymous and nonsynonymous substitutions revealed that the structural and functional constraints on CI and CII genes are not significantly different. Also, horizontal gene transfer estimates in selected organisms demonstrated that CII in many species has acquired higher levels of horizontally transferred segments than CI. In summary, rapid evolution of CII may perform particular roles for organisms such as aiding in adapting to specialized niches. PMID:20924417

  5. Evolution of Prdm Genes in Animals: Insights from Comparative Genomics.

    PubMed

    Vervoort, Michel; Meulemeester, David; Bhague, Julien; Kerner, Pierre

    2016-03-01

    Prdm genes encode transcription factors with a subtype of SET domain known as the PRDF1-RIZ (PR) homology domain and a variable number of zinc finger motifs. These genes are involved in a wide variety of functions during animal development. As most Prdm genes have been studied in vertebrates, especially in mice, little is known about the evolution of this gene family. We searched for Prdm genes in the fully sequenced genomes of 93 different species representative of all the main metazoan lineages. A total of 976 Prdm genes were identified in these species. The number of Prdm genes per species ranges from 2 to 19. To better understand how the Prdm gene family has evolved in metazoans, we performed phylogenetic analyses using this large set of identified Prdm genes. These analyses allowed us to define 14 different subfamilies of Prdm genes and to establish, through ancestral state reconstruction, that 11 of them are ancestral to bilaterian animals. Three additional subfamilies were acquired during early vertebrate evolution (Prdm5, Prdm11, and Prdm17). Several gene duplication and gene loss events were identified and mapped onto the metazoan phylogenetic tree. By studying a large number of nonmetazoan genomes, we confirmed that Prdm genes likely constitute a metazoan-specific gene family. Our data also suggest that Prdm genes originated before the diversification of animals through the association of a single ancestral SET domain encoding gene with one or several zinc finger encoding genes. PMID:26560352

  6. Comparative Genomics Provide Insights into Evolution of Trichoderma Nutrition Style

    PubMed Central

    Xie, Bin-Bin; Qin, Qi-Long; Shi, Mei; Chen, Lei-Lei; Shu, Yan-Li; Luo, Yan; Wang, Xiao-Wei; Rong, Jin-Cheng; Gong, Zhi-Ting; Li, Dan; Sun, Cai-Yun; Liu, Gui-Ming; Dong, Xiao-Wei; Pang, Xiu-Hua; Huang, Feng; Liu, Weifeng; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Song, Xiao-Yan

    2014-01-01

    Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei (Tr), including glycoside hydrolases and nonribosomal peptide synthetase–polyketide synthase. Homology and phylogenetic analyses suggest that a large number of nutrition-related genes, including GH18 chitinases, β-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum (Tl) and Tr. dN/dS (ω) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in Tl and Tr, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma. PMID:24482532

  7. Genomics in Coccidioides: insights into evolution, ecology, and pathogenesis.

    PubMed

    Whiston, Emily; Taylor, John W

    2014-02-01

    Coccidioides immitis and C. posadasii, the causative agents of the mammalian disease coccidioidomycosis, are dimorphic fungal pathogens distributed throughout desert-like environments in North and South America. Coccidioides spp. are members of the Onygenales, a diverse group of pathogenic and nonpathogenic fungi. Recently, full genomes have been published for Coccidioides and a number of other Onygenales species. Phylogenomic comparisons and additional studies in Coccidioides population genomics and gene expression have shed light on the ecology and pathogenesis of Coccidioides and the other medically important species in this clade. Observed patterns of gene family expansion/contraction and evidence of gene flow have provided insight to the evolution of Coccidioides and greatly broadened our understanding of the diversity and sources of genetic variation found in fungi. In the future, expansion of the number of sequenced isolates from all populations will allow deeper insight into the evolutionary processes that have shaped this unique human pathogen. In addition, deep sequencing of isolates from a single Coccidioides population and pairing of those data with phenotype information on growth and pathogenicity for genome-wide association analysis will allow researchers to find genes responsible for any phenotype, virulence included, that shows variation in the population. PMID:24576996

  8. Genomic Determinants of Protein Evolution and Polymorphism in Arabidopsis

    PubMed Central

    Slotte, Tanja; Bataillon, Thomas; Hansen, Troels T.; St. Onge, Kate; Wright, Stephen I.; Schierup, Mikkel H.

    2011-01-01

    Recent results from Drosophila suggest that positive selection has a substantial impact on genomic patterns of polymorphism and divergence. However, species with smaller population sizes and/or stronger population structure may not be expected to exhibit Drosophila-like patterns of sequence variation. We test this prediction and identify determinants of levels of polymorphism and rates of protein evolution using genomic data from Arabidopsis thaliana and the recently sequenced Arabidopsis lyrata genome. We find that, in contrast to Drosophila, there is no negative relationship between nonsynonymous divergence and silent polymorphism at any spatial scale examined. Instead, synonymous divergence is a major predictor of silent polymorphism, which suggests variation in mutation rate as the main determinant of silent variation. Variation in rates of protein divergence is mainly correlated with gene expression level and breadth, consistent with results for a broad range of taxa, and map-based estimates of recombination rate are only weakly correlated with nonsynonymous divergence. Variation in mutation rates and the strength of purifying selection seem to be major drivers of patterns of polymorphism and divergence in Arabidopsis. Nevertheless, a model allowing for varying negative and positive selection by functional gene category explains the data better than a homogeneous model, implying the action of positive selection on a subset of genes. Genes involved in disease resistance and abiotic stress display high proportions of adaptive substitution. Our results are important for a general understanding of the determinants of rates of protein evolution and the impact of selection on patterns of polymorphism and divergence. PMID:21926095

  9. Tracing the evolution of streptophyte algae and their mitochondrial genome.

    PubMed

    Turmel, Monique; Otis, Christian; Lemieux, Claude

    2013-01-01

    Six monophyletic groups of charophycean green algae are recognized within the Streptophyta. Although incongruent with earlier studies based on genes from three cellular compartments, chloroplast and nuclear phylogenomic analyses have resolved identical relationships among these groups, placing the Zygnematales or the Zygnematales + Coleochaetales as sister to land plants. The present investigation aimed at determining whether this consensus view is supported by the mitochondrial genome and at gaining insight into mitochondrial DNA (mtDNA) evolution within and across streptophyte algal lineages and during the transition toward the first land plants. We present here the newly sequenced mtDNAs of representatives of the Klebsormidiales (Entransia fimbriata and Klebsormidium spec.) and Zygnematales (Closterium baillyanum and Roya obtusa) and compare them with their homologs in other charophycean lineages as well as in selected embryophyte and chlorophyte lineages. Our results indicate that important changes occurred at the levels of genome size, gene order, and intron content within the Zygnematales. Although the representatives of the Klebsormidiales display more similarity in genome size and intron content, gene order seems more fluid and gene losses more frequent than in other charophycean lineages. In contrast, the two members of the Charales display an extremely conservative pattern of mtDNA evolution. Collectively, our analyses of gene order and gene content and the phylogenies we inferred from 40 mtDNA-encoded proteins failed to resolve the relationships among the Zygnematales, Coleochaetales, and Charales; however, they are consistent with previous phylogenomic studies in favoring that the morphologically complex Charales are not sister to land plants. PMID:24022472

  10. Tracing the Evolution of Streptophyte Algae and Their Mitochondrial Genome

    PubMed Central

    Turmel, Monique; Otis, Christian; Lemieux, Claude

    2013-01-01

    Six monophyletic groups of charophycean green algae are recognized within the Streptophyta. Although incongruent with earlier studies based on genes from three cellular compartments, chloroplast and nuclear phylogenomic analyses have resolved identical relationships among these groups, placing the Zygnematales or the Zygnematales + Coleochaetales as sister to land plants. The present investigation aimed at determining whether this consensus view is supported by the mitochondrial genome and at gaining insight into mitochondrial DNA (mtDNA) evolution within and across streptophyte algal lineages and during the transition toward the first land plants. We present here the newly sequenced mtDNAs of representatives of the Klebsormidiales (Entransia fimbriata and Klebsormidium spec.) and Zygnematales (Closterium baillyanum and Roya obtusa) and compare them with their homologs in other charophycean lineages as well as in selected embryophyte and chlorophyte lineages. Our results indicate that important changes occurred at the levels of genome size, gene order, and intron content within the Zygnematales. Although the representatives of the Klebsormidiales display more similarity in genome size and intron content, gene order seems more fluid and gene losses more frequent than in other charophycean lineages. In contrast, the two members of the Charales display an extremely conservative pattern of mtDNA evolution. Collectively, our analyses of gene order and gene content and the phylogenies we inferred from 40 mtDNA-encoded proteins failed to resolve the relationships among the Zygnematales, Coleochaetales, and Charales; however, they are consistent with previous phylogenomic studies in favoring that the morphologically complex Charales are not sister to land plants. PMID:24022472

  11. Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

    PubMed Central

    2011-01-01

    Background The genome of Helicobacter pylori, an oncogenic bacterium in the human stomach, rapidly evolves and shows wide geographical divergence. The high incidence of stomach cancer in East Asia might be related to bacterial genotype. We used newly developed comparative methods to follow the evolution of East Asian H. pylori genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains. Results A phylogenetic tree of concatenated well-defined core genes supported divergence of the East Asian lineage (hspEAsia; Japanese and Korean) from the European lineage ancestor, and then from the Amerind lineage ancestor. Phylogenetic profiling revealed a large difference in the repertoire of outer membrane proteins (including oipA, hopMN, babABC, sabAB and vacA-2) through gene loss, gain, and mutation. All known functions associated with molybdenum, a rare element essential to nearly all organisms that catalyzes two-electron-transfer oxidation-reduction reactions, appeared to be inactivated. Two pathways linking acetyl~CoA and acetate appeared intact in some Japanese strains. Phylogenetic analysis revealed greater divergence between the East Asian (hspEAsia) and the European (hpEurope) genomes in proteins in host interaction, specifically virulence factors (tip?), outer membrane proteins, and lipopolysaccharide synthesis (human Lewis antigen mimicry) enzymes. Divergence was also seen in proteins in electron transfer and translation fidelity (miaA, tilS), a DNA recombinase/exonuclease that recognizes genome identity (addA), and DNA/RNA hybrid nucleases (rnhAB). Positively selected amino acid changes between hspEAsia and hpEurope were mapped to products of cagA, vacA, homC (outer membrane protein), sotB (sugar transport), and a translation fidelity factor (miaA). Large divergence was seen in genes related to antibiotics: frxA (metronidazole resistance), def (peptide deformylase, drug target), and ftsA (actin-like, drug target). Conclusions These results demonstrate dramatic genome evolution within a species, especially in likely host interaction genes. The East Asian strains appear to differ greatly from the European strains in electron transfer and redox reactions. These findings also suggest a model of adaptive evolution through proteome diversification and selection through modulation of translational fidelity. The results define H. pylori East Asian lineages and provide essential information for understanding their pathogenesis and designing drugs and therapies that target them. PMID:21575176

  12. Insights into the genome evolution of Yersinia pestis through whole genome comparison with Yersinia pseudotuberculosis

    SciTech Connect

    Souza, B; Stoutland, P; Derbise, A; Georgescu, A; Elliott, J; Land, M; Marceau, M; Motin, V; Hinnebusch, J; Simonet, M; Medigue, C; Dacheux, D; Chenal-Francisque, V; Regala, W; Brubaker, R R; Carniel, E; Chain, P; Verguez, L; Fowler, J; Garcia, E; Lamerdin, J; Hauser, L; Larimer, F

    2004-01-24

    Yersinia pestis, the causative agent of plague, is a highly uniform clone that diverged recently from the enteric pathogen Yersinia pseudotuberculosis. Despite their close genetic relationship, they differ radically in their pathogenicity and transmission. Here we report the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome comparisons to available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world reveals 32 Y. pestis chromosomal genes that, together with the two Y. pestis-specific plasmids, represent the only new genetic material in Y. pestis acquired since the divergence from Y. pseudotuberculosis. In contrast, 149 new pseudogenes (doubling the previous estimate) and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis. Extensive IS-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of pre-existing gene expression pathways appear to be more important than acquisition of new genes in the evolution of Y. pestis. These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.

  13. Impact of Small Repeat Sequences on Bacterial Genome Evolution

    PubMed Central

    Delihas, Nicholas

    2011-01-01

    Intergenic regions of prokaryotic genomes carry multiple copies of terminal inverted repeat (TIR) sequences, the nonautonomous miniature inverted-repeat transposable element (MITE). In addition, there are the repetitive extragenic palindromic (REP) sequences that fold into a small stem loop rich in GC bonding. And the clustered regularly interspaced short palindromic repeats (CRISPRs) display similar small stem loops but are an integral part of a complex genetic element. Other classes of repeats such as the REP2 element do not have TIRs but show other signatures. With the current availability of a large number of whole-genome sequences, many new repeat elements have been discovered. These sequences display diverse properties. Some show an intimate linkage to integrons, and at least one encodes a small RNA. Many repeats are found fused with chromosomal open reading frames, and some are located within protein coding sequences. Small repeat units appear to work hand in hand with the transcriptional and/or post-transcriptional apparatus of the cell. Functionally, they are multifaceted, and this can range from the control of gene expression, the facilitation of host/pathogen interactions, or stimulation of the mammalian immune system. The CRISPR complex displays dramatic functions such as an acquired immune system that defends against invading viruses and plasmids. Evolutionarily, mobile repeat elements may have influenced a cycle of active versus inactive genes in ancestral organisms, and some repeats are concentrated in regions of the chromosome where there is significant genomic plasticity. Changes in the abundance of genomic repeats during the evolution of an organism may have resulted in a benefit to the cell or posed a disadvantage, and some present day species may reflect a purification process. The diverse structure, eclectic functions, and evolutionary aspects of repeat elements are described. PMID:21803768

  14. Sequence analysis of a bovine rhinovirus type 1 strain RS3x

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine rhinoviruses, known to cause clinical and subclinical upper respiratory infections in bovines worldwide, include three serotypes. Bovine rhinovirus (BRV) 1, 2 and 3 were originally classified as tentative members of the genus Rhinovirus (family Picornaviridae), however, in 2008 this genus was...

  15. Parallel Evolution of the Genetic Code in Arthropod Mitochondrial Genomes

    PubMed Central

    Posada, David; Knight, Robin D; Zardoya, Rafael

    2006-01-01

    The genetic code provides the translation table necessary to transform the information contained in DNA into the language of proteins. In this table, a correspondence between each codon and each amino acid is established: tRNA is the main adaptor that links the two. Although the genetic code is nearly universal, several variants of this code have been described in a wide range of nuclear and organellar systems, especially in metazoan mitochondria. These variants are generally found by searching for conserved positions that consistently code for a specific alternative amino acid in a new species. We have devised an accurate computational method to automate these comparisons, and have tested it with 626 metazoan mitochondrial genomes. Our results indicate that several arthropods have a new genetic code and translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code). We have investigated the evolution of the genetic code in the arthropods and found several events of parallel evolution in which the AGG codon was reassigned between serine and lysine. Our analyses also revealed correlated evolution between the arthropod genetic codes and the tRNA-Lys/-Ser, which show specific point mutations at the anticodons. These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments. PMID:16620150

  16. Carbocisteine inhibits rhinovirus infection in human tracheal epithelial cells.

    PubMed

    Yasuda, H; Yamaya, M; Sasaki, T; Inoue, D; Nakayama, K; Yamada, M; Asada, M; Yoshida, M; Suzuki, T; Nishimura, H; Sasaki, H

    2006-07-01

    The aim of the study was to examine the effects of a mucolytic drug, carbocisteine, on rhinovirus (RV) infection in the airways. Human tracheal epithelial cells were infected with a major-group RV, RV14. RV14 infection increased virus titres and the cytokine content of supernatants. Carbocisteine reduced supernatant virus titres, the amount of RV14 RNA in cells, cell susceptibility to RV infection and supernatant cytokine concentrations, including interleukin (IL)-6 and IL-8, after RV14 infection. Carbocisteine reduced the expression of mRNA encoding intercellular adhesion molecule (ICAM)-1, the receptor for the major group of RVs. It also reduced the supernatant concentration of a soluble form of ICAM-1, the number and fluorescence intensity of acidic endosomes in the cells before RV infection, and nuclear factor-kappaB activation by RV14. Carbocisteine also reduced the supernatant virus titres of the minor group RV, RV2, although carbocisteine did not reduce the expression of mRNA encoding a low density lipoprotein receptor, the receptor for RV2. These results suggest that carbocisteine inhibits rhinovirus 2 infection by blocking rhinovirus RNA entry into the endosomes, and inhibits rhinovirus 14 infection by the same mechanism as well as by reducing intercellular adhesion molecule-1 levels. Carbocisteine may modulate airway inflammation by reducing the production of cytokines in rhinovirus infection. PMID:16510461

  17. Conditions for the evolution of gene clusters in bacterial genomes.

    PubMed

    Ballouz, Sara; Francis, Andrew R; Lan, Ruiting; Tanaka, Mark M

    2010-02-01

    Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour gene clusters through a variety of mechanisms, such as increased efficiency of coregulation. An alternative and controversial hypothesis is the selfish operon model, which asserts that clustered arrangements of genes are more easily transferred to other species, thus improving the prospects for survival of the cluster. According to another hypothesis (the persistence model), genes that are in close proximity are less likely to be disrupted by deletions. Here we develop computational models to study the conditions under which gene clusters can evolve and persist. First, we examine the selfish operon model by re-implementing the simulation and running it under a wide range of conditions. Second, we introduce and study a Moran process in which there is natural selection for gene clustering and rearrangement occurs by genome inversion events. Finally, we develop and study a model that includes selection and inversion, which tracks the occurrence and fixation of rearrangements. Surprisingly, gene clusters fail to evolve under a wide range of conditions. Factors that promote the evolution of gene clusters include a low number of genes in the pathway, a high population size, and in the case of the selfish operon model, a high horizontal transfer rate. The computational analysis here has shown that the evolution of gene clusters can occur under both direct and indirect selection as long as certain conditions hold. Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters. PMID:20168992

  18. Rapid evolution of cheating mitochondrial genomes in small yeast populations.

    PubMed

    Jasmin, Jean-Nicolas; Zeyl, Clifford

    2014-01-01

    Outcrossed sex exposes genes to competition with their homologues, allowing alleles that transmit more often than their competitors to spread despite organismal fitness costs. Mitochondrial populations in species with biparental inheritance are thought to be especially susceptible to such cheaters because they lack strict transmission rules like meiosis or maternal inheritance. Yet the interaction between mutation and natural selection in the evolution of cheating mitochondrial genomes has not been tested experimentally. Using yeast experimental populations, we show that although cheaters were rare in a large sample of spontaneous respiratory-deficient mitochondrial mutations (petites), cheaters evolve under experimentally enforced outcrossing even when mutation supply and selection are restricted by repeatedly bottlenecking populations. PMID:24372606

  19. Gene frequency distributions reject a neutral model of genome evolution.

    PubMed

    Lobkovsky, Alexander E; Wolf, Yuri I; Koonin, Eugene V

    2013-01-01

    Evolution of prokaryotes involves extensive loss and gain of genes, which lead to substantial differences in the gene repertoires even among closely related organisms. Through a wide range of phylogenetic depths, gene frequency distributions in prokaryotic pangenomes bear a characteristic, asymmetrical U-shape, with a core of (nearly) universal genes, a "shell" of moderately common genes, and a "cloud" of rare genes. We employ mathematical modeling to investigate evolutionary processes that might underlie this universal pattern. Gene frequency distributions for almost 400 groups of 10 bacterial or archaeal species each over a broad range of evolutionary distances were fit to steady-state, infinite allele models based on the distribution of gene replacement rates and the phylogenetic tree relating the species in each group. The fits of the theoretical frequency distributions to the empirical ones yield model parameters and estimates of the goodness of fit. Using the Akaike Information Criterion, we show that the neutral model of genome evolution, with the same replacement rate for all genes, can be confidently rejected. Of the three tested models with purifying selection, the one in which the distribution of replacement rates is derived from a stochastic population model with additive per-gene fitness yields the best fits to the data. The selection strength estimated from the fits declines with evolutionary divergence while staying well outside the neutral regime. These findings indicate that, unlike some other universal distributions of genomic variables, for example, the distribution of paralogous gene family membership, the gene frequency distribution is substantially affected by selection. PMID:23315380

  20. Proteases of human rhinovirus: role in infection.

    PubMed

    Jensen, Lora M; Walker, Erin J; Jans, David A; Ghildyal, Reena

    2015-01-01

    Human rhinoviruses (HRV) are the major etiological agents of the common cold and asthma exacerbations, with significant worldwide health and economic impact. Although large-scale population vaccination has proved successful in limiting or even eradicating many viruses, the more than 100 distinct serotypes mean that conventional vaccination is not a feasible strategy to combat HRV. An alternative strategy is to target conserved viral proteins such as the HRV proteases, 2A(pro) and 3C(pro), the focus of this review. Necessary for host cell shutoff, virus replication, and pathogenesis, 2A(pro) and 3C(pro) are clearly viable drug targets, and indeed, 3C(pro) has been successfully targeted for treating the common cold in experimental infection. 2A(pro) and 3C(pro) are crucial for virus replication due to their role in polyprotein processing as well as cleavage of key cellular proteins to inhibit cellular transcription and translation. Intriguingly, the action of the HRV proteases also disrupts nucleocytoplasmic trafficking, contributing to HRV cytopathic effects. Improved understanding of the protease-cell interactions should enable new therapeutic approaches to be identified for drug development. PMID:25261311

  1. Stability domains of actin genes and genomic evolution

    NASA Astrophysics Data System (ADS)

    Carlon, E.; Dkhissi, A.; Malki, M. Lejard; Blossey, R.

    2007-11-01

    In eukaryotic genes, the protein coding sequence is split into several fragments, the exons, separated by noncoding DNA stretches, the introns. Prokaryotes do not have introns in their genomes. We report calculations of the stability domains of actin genes for various organisms in the animal, plant, and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes, all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e., before intron insertion. Common stability boundaries are found in evolutionarily distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general, the boundaries correspond with intron positions in the actins of vertebrates and other animals, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae, and animals have introns in positions separated by one nucleotide only, which identifies a hot spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamically driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for intron insertion in plants and animals.

  2. Tertiary endosymbiosis driven genome evolution in dinoflagellate algae.

    PubMed

    Yoon, Hwan Su; Hackett, Jeremiah D; Van Dolah, Frances M; Nosenko, Tetyana; Lidie, Kristy L; Bhattacharya, Debashish

    2005-05-01

    Dinoflagellates are important aquatic primary producers and cause "red tides." The most widespread plastid (photosynthetic organelle) in these algae contains the unique accessory pigment peridinin. This plastid putatively originated via a red algal secondary endosymbiosis and has some remarkable features, the most notable being a genome that is reduced to 1-3 gene minicircles with about 14 genes (out of an original 130-200) remaining in the organelle and a nuclear-encoded proteobacterial Form II Rubisco. The "missing" plastid genes are relocated to the nucleus via a massive transfer unequaled in other photosynthetic eukaryotes. The fate of these characters is unknown in a number of dinoflagellates that have replaced the peridinin plastid through tertiary endosymbiosis. We addressed this issue in the fucoxanthin dinoflagellates (e.g., Karenia brevis) that contain a captured haptophyte plastid. Our multiprotein phylogenetic analyses provide robust support for the haptophyte plastid replacement and are consistent with a red algal origin of the chromalveolate plastid. We then generated an expressed sequence tag (EST) database of 5,138 unique genes from K. brevis and searched for nuclear genes of plastid function. The EST data indicate the loss of the ancestral peridinin plastid characters in K. brevis including the transferred plastid genes and Form II Rubisco. These results underline the remarkable ability of dinoflagellates to remodel their genomes through endosymbiosis and the considerable impact of this process on cell evolution. PMID:15746017

  3. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As a major step toward understanding the biology and evolution of ruminants, the cattle genome was sequenced to ~7x coverage using a combined whole genome shotgun and BAC skim approach. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs found in seven mammalian...

  4. Convergence of ion channel genome content in early animal evolution

    PubMed Central

    Liebeskind, Benjamin J.; Hillis, David M.; Zakon, Harold H.

    2015-01-01

    Multicellularity has evolved multiple times, but animals are the only multicellular lineage with nervous systems. This fact implies that the origin of nervous systems was an unlikely event, yet recent comparisons among extant taxa suggest that animal nervous systems may have evolved multiple times independently. Here, we use ancestral gene content reconstruction to track the timing of gene family expansions for the major families of ion-channel proteins that drive nervous system function. We find that animals with nervous systems have broadly similar complements of ion-channel types but that these complements likely evolved independently. We also find that ion-channel gene family evolution has included large loss events, two of which were immediately followed by rounds of duplication. Ctenophores, cnidarians, and bilaterians underwent independent bouts of gene expansion in channel families involved in synaptic transmission and action potential shaping. We suggest that expansions of these family types may represent a genomic signature of expanding nervous system complexity. Ancestral nodes in which nervous systems are currently hypothesized to have originated did not experience large expansions, making it difficult to distinguish among competing hypotheses of nervous system origins and suggesting that the origin of nerves was not attended by an immediate burst of complexity. Rather, the evolution of nervous system complexity appears to resemble a slow fuse in stem animals followed by many independent bouts of gene gain and loss. PMID:25675537

  5. Adaptive immunity to rhinoviruses: sex and age matter

    PubMed Central

    2010-01-01

    Background Rhinoviruses (RV) are key triggers in acute asthma exacerbations. Previous studies suggest that men suffer from infectious diseases more frequently and with greater severity than women. Additionally, the immune response to most infections and vaccinations decreases with age. Most immune function studies do not account for such differences, therefore the aim of this study was to determine if the immune response to rhinovirus varies with sex or age. Methods Blood mononuclear cells were isolated from 63 healthy individuals and grouped by sex and age (?50 years old and ?52 years old). Cells were cultured with rhinovirus 16 at a multiplicity of infection of 1. The chemokine IP-10 was measured at 24 h as an index of innate immunity while IFN? and IL-13 were measured at 5 days as an index of adaptive immunity. Results Rhinovirus induced IFN? and IL-13 was significantly higher in ?50 year old women than in age matched men (p < 0.02 and p < 0.05) and ?52 year old women (p < 0.02 and p > 0.005). There was no sex or age based difference in rhinovirus induced IP-10 expression. Both IFN? and IL-13 were negatively correlated with age in women but not in men. Conclusions This study suggests that pre-menopausal women have a stronger adaptive immune response to rhinovirus infection than men and older people, though the mechanisms responsible for these differences remain to be determined. Our findings highlight the importance of gender and age balance in clinical studies and in the development of new treatments and vaccines. PMID:21194432

  6. The adaptive evolution of the mammalian mitochondrial genome

    PubMed Central

    da Fonseca, Rute R; Johnson, Warren E; O'Brien, Stephen J; Ramos, Maria João; Antunes, Agostinho

    2008-01-01

    Background The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures. Results Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas). Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas. Conclusion Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation. PMID:18318906

  7. Rates of genome evolution and branching order from whole genome analysis.

    PubMed

    Huttley, Gavin A; Wakefield, Matthew J; Easteal, Simon

    2007-08-01

    Accurate estimation of any phylogeny is important as a framework for evolutionary analysis of form and function at all levels of organization from sequence to whole organism. Using alignments of nonrepetitive components of opossum, human, mouse, rat, and dog genomes we evaluated two alternative tree topologies for eutherian evolution. We show with very high confidence that there is a basal split between rodents (as represented by the mouse and rat) and a branch joining primates (as represented by humans) and carnivores (as represented by dogs), consistent with some but not the most widely accepted mammalian phylogenies. The result was robust to substitution model choice with equivalent inference returned from a spectrum of models ranging from a general time reversible model, a model that treated nucleotides as either purines and pyrimidines, and variants of these that incorporated rate heterogeneity among sites. By determining this particular branching order we are able to show that the rate of molecular evolution is almost identical in rodent and carnivore lineages and that sequences evolve approximately 11%-14% faster in these lineages than in the primate lineage. In addition by applying the chicken as outgroup the analyses suggested that the rate of evolution in all eutherian lineages is approximately 30% slower than in the opossum lineage. This pattern of relative rates is inconsistent with the hypothesis that generation time is an important determinant of substitution rates and, by implication, mutation rates. Possible factors causing rate differences between the lineages include differences in DNA repair and replication enzymology, and shifts in nucleotide pools. Our analysis demonstrates the importance of using multiple sequences from across the genome to estimate phylogeny and relative evolutionary rate in order to reduce the influence of distorting local effects evident even in relatively long sequences. PMID:17494028

  8. Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution

    PubMed Central

    Filée, Jonathan

    2015-01-01

    Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for five groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the different losses. In addition, each lineage displays specific patterns of genome evolution. Mimiviridae (megaviruses and mimiviruses) and Chlorella Phycodnaviruses evolved mainly by duplications and losses of genes belonging to large paralogous families (including movements of diverse mobiles genetic elements), whereas Micromonas and Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral gene transfers. Taken together, these data support an accordion-like model of evolution in which GV genomes have undergone successive steps of gene gain and gene loss, accrediting the hypothesis that genome gigantism appears early, before the diversification of the different GV lineages. PMID:26136734

  9. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates.

    PubMed

    Yuan, Bo; Liu, Pengfei; Gupta, Aditya; Beck, Christine R; Tejomurtula, Anusha; Campbell, Ian M; Gambin, Tomasz; Simmons, Alexandra D; Withers, Marjorie A; Harris, R Alan; Rogers, Jeffrey; Schwartz, David C; Lupski, James R

    2015-12-01

    Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases-about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual's susceptibility to acquiring disease-associated alleles. PMID:26641089

  10. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates

    PubMed Central

    Yuan, Bo; Liu, Pengfei; Gupta, Aditya; Beck, Christine R.; Tejomurtula, Anusha; Campbell, Ian M.; Gambin, Tomasz; Simmons, Alexandra D.; Withers, Marjorie A.; Harris, R. Alan; Rogers, Jeffrey; Schwartz, David C.; Lupski, James R.

    2015-01-01

    Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases—about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles. PMID:26641089

  11. Avian picornaviruses: molecular evolution, genome diversity and unusual genome features of a rapidly expanding group of viruses in birds.

    PubMed

    Boros, kos; Pankovics, Pter; Reuter, Gbor

    2014-12-01

    Picornaviridae is one of the most diverse families of viruses infecting vertebrate species. In contrast to the relative small number of mammal species compared to other vertebrates, the abundance of mammal-infecting picornaviruses was significantly overrepresented among the presently known picornaviruses. Therefore most of the current knowledge about the genome diversity/organization patterns and common genome features were based on the analysis of mammal-infecting picornaviruses. Beside the well known reservoir role of birds in case of several emerging viral pathogens, little is known about the diversity of picornaviruses circulating among birds, although in the last decade the number of known avian picornavirus species with complete genome was increased from one to at least 15. However, little is known about the geographic distribution, host spectrum or pathogenic potential of the recently described picornaviruses of birds. Despite the low number of known avian picornaviruses, the phylogenetic and genome organization diversity of these viruses were remarkable. Beside the common L-4-3-4 and 4-3-4 genome layouts unusual genome patterns (3-4-4; 3-5-4, 3-6-4; 3-8-4) with variable, multicistronic 2A genome regions were found among avian picornaviruses. The phylogenetic and genomic analysis revealed the presence of several conserved structures at the untranslated regions among phylogenetically distant avian and non-avian picornaviruses as well as at least five different avian picornavirus phylogenetic clusters located in every main picornavirus lineage with characteristic genome layouts which suggests the complex evolution history of these viruses. Based on the remarkable genetic diversity of the few known avian picornaviruses, the emergence of further divergent picornaviruses causing challenges in the current taxonomy and also in the understanding of the evolution and genome organization of picornaviruses will be strongly expected. In this review we would like to summarize the current knowledge about the taxonomy, pathogenic potential, phylogenetic/genomic diversity and evolutional relationship of avian picornaviruses. PMID:25278047

  12. Comparative genomics and evolution of proteins involved in RNA metabolism

    PubMed Central

    Anantharaman, Vivek; Koonin, Eugene V.; Aravind, L.

    2002-01-01

    RNA metabolism, broadly defined as the compendium of all processes that involve RNA, including transcription, processing and modification of transcripts, translation, RNA degradation and its regulation, is the central and most evolutionarily conserved part of cell physiology. A comprehensive, genome-wide census of all enzymatic and non-enzymatic protein domains involved in RNA metabolism was conducted by using sequence profile analysis and structural comparisons. Proteins related to RNA metabolism comprise from 3 to 11% of the complete protein repertoire in bacteria, archaea and eukaryotes, with the greatest fraction seen in parasitic bacteria with small genomes. Approximately one-half of protein domains involved in RNA metabolism are present in most, if not all, species from all three primary kingdoms and are traceable to the last universal common ancestor (LUCA). The principal features of LUCAs RNA metabolism system were reconstructed by parsimony-based evolutionary analysis of all relevant groups of orthologous proteins. This reconstruction shows that LUCA possessed not only the basal translation system, but also the principal forms of RNA modification, such as methylation, pseudouridylation and thiouridylation, as well as simple mechanisms for polyadenylation and RNA degradation. Some of these ancient domains form paralogous groups whose evolution can be traced back in time beyond LUCA, towards low-specificity proteins, which probably functioned as cofactors for ribozymes within the RNA world framework. The main lineage-specific innovations of RNA metabolism systems were identified. The most notable phase of innovation in RNA metabolism coincides with the advent of eukaryotes and was brought about by the merge of the archaeal and bacterial systems via mitochondrial endosymbiosis, but also involved emergence of several new, eukaryote-specific RNA-binding domains. Subsequent, vast expansions of these domains mark the origin of alternative splicing in animals and probably in plants. In addition to the reconstruction of the evolutionary history of RNA metabolism, this analysis produced numerous functional predictions, e.g. of previously undetected enzymes of RNA modification. PMID:11917006

  13. Evolution of Linear Mitochondrial Genomes in Medusozoan Cnidarians

    PubMed Central

    Kayal, Ehsan; Bentlage, Bastian; Collins, Allen G.; Pirro, Stacy; Lavrov, Dennis V.

    2012-01-01

    In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans. PMID:22113796

  14. Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

    PubMed Central

    Page, Justin T.; Huynh, Mark D.; Liechty, Zach S.; Grupp, Kara; Stelly, David; Hulse, Amanda M.; Ashrafi, Hamid; Van Deynze, Allen; Wendel, Jonathan F.; Udall, Joshua A.

    2013-01-01

    Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton. PMID:23979935

  15. Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes

    PubMed Central

    Suh, Alexander; Churakov, Gennady; Ramakodi, Meganathan P.; Platt, Roy N.; Jurka, Jerzy; Kojima, Kenji K.; Caballero, Juan; Smit, Arian F.; Vliet, Kent A.; Hoffmann, Federico G.; Brosius, Jrgen; Green, Richard E.; Braun, Edward L.; Ray, David A.; Schmitz, Jrgen

    2015-01-01

    Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians. PMID:25503085

  16. Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.

    PubMed

    Suh, Alexander; Churakov, Gennady; Ramakodi, Meganathan P; Platt, Roy N; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Smit, Arian F; Vliet, Kent A; Hoffmann, Federico G; Brosius, Jürgen; Green, Richard E; Braun, Edward L; Ray, David A; Schmitz, Jürgen

    2015-01-01

    Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians. PMID:25503085

  17. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution.

    PubMed

    Slack, Kerryn E; Jones, Craig M; Ando, Tatsuro; Harrison, G L Abby; Fordyce, R Ewan; Arnason, Ulfur; Penny, David

    2006-06-01

    Testing models of macroevolution, and especially the sufficiency of microevolutionary processes, requires good collaboration between molecular biologists and paleontologists. We report such a test for events around the Late Cretaceous by describing the earliest penguin fossils, analyzing complete mitochondrial genomes from an albatross, a petrel, and a loon, and describe the gradual decline of pterosaurs at the same time modern birds radiate. The penguin fossils comprise four naturally associated skeletons from the New Zealand Waipara Greensand, a Paleocene (early Tertiary) formation just above a well-known Cretaceous/Tertiary boundary site. The fossils, in a new genus (Waimanu), provide a lower estimate of 61-62 Ma for the divergence between penguins and other birds and thus establish a reliable calibration point for avian evolution. Combining fossil calibration points, DNA sequences, maximum likelihood, and Bayesian analysis, the penguin calibrations imply a radiation of modern (crown group) birds in the Late Cretaceous. This includes a conservative estimate that modern sea and shorebird lineages diverged at least by the Late Cretaceous about 74 +/- 3 Ma (Campanian). It is clear that modern birds from at least the latest Cretaceous lived at the same time as archaic birds including Hesperornis, Ichthyornis, and the diverse Enantiornithiformes. Pterosaurs, which also coexisted with early crown birds, show notable changes through the Late Cretaceous. There was a decrease in taxonomic diversity, and small- to medium-sized species disappeared well before the end of the Cretaceous. A simple reading of the fossil record might suggest competitive interactions with birds, but much more needs to be understood about pterosaur life histories. Additional fossils and molecular data are still required to help understand the role of biotic interactions in the evolution of Late Cretaceous birds and thus to test that the mechanisms of microevolution are sufficient to explain macroevolution. PMID:16533822

  18. Orthopoxvirus Genome Evolution: The Role of Gene Loss

    PubMed Central

    Hendrickson, Robert Curtis; Wang, Chunlin; Hatcher, Eneida L.; Lefkowitz, Elliot J.

    2010-01-01

    Poxviruses are highly successful pathogens, known to infect a variety of hosts. The family Poxviridae includes Variola virus, the causative agent of smallpox, which has been eradicated as a public health threat but could potentially reemerge as a bioterrorist threat. The risk scenario includes other animal poxviruses and genetically engineered manipulations of poxviruses. Studies of orthologous gene sets have established the evolutionary relationships of members within the Poxviridae family. It is not clear, however, how variations between family members arose in the past, an important issue in understanding how these viruses may vary and possibly produce future threats. Using a newly developed poxvirus-specific tool, we predicted accurate gene sets for viruses with completely sequenced genomes in the genus Orthopoxvirus. Employing sensitive sequence comparison techniques together with comparison of syntenic gene maps, we established the relationships between all viral gene sets. These techniques allowed us to unambiguously identify the gene loss/gain events that have occurred over the course of orthopoxvirus evolution. It is clear that for all existing Orthopoxvirus species, no individual species has acquired protein-coding genes unique to that species. All existing species contain genes that are all present in members of the species Cowpox virus and that cowpox virus strains contain every gene present in any other orthopoxvirus strain. These results support a theory of reductive evolution in which the reduction in size of the core gene set of a putative ancestral virus played a critical role in speciation and confining any newly emerging virus species to a particular environmental (host or tissue) niche. PMID:21994715

  19. GenomicusPlants: A Web Resource to Study Genome Evolution in Flowering Plants

    PubMed Central

    Louis, Alexandra; Murat, Florent; Salse, Jrme; Roest Crollius, Hugues

    2015-01-01

    Comparative genomics combined with phylogenetic reconstructions are powerful approaches to study the evolution of genes and genomes. However, the current rapid expansion of the volume of genomic information makes it increasingly difficult to interrogate, integrate and synthesize comparative genome data while taking into account the maximum breadth of information available. GenomicusPlants (http://www.genomicus.biologie.ens.fr/genomicus-plants) is an extension of the Genomicus webserver that addresses this issue by allowing users to explore flowering plant genomes in an intuitive way, across the broadest evolutionary scales. Extant genomes of 26 flowering plants can be analyzed, as well as 23 ancestral reconstructed genomes. Ancestral gene order provides a long-term chronological view of gene order evolution, greatly facilitating comparative genomics and evolutionary studies. Four main interfaces (views) are available where: (i) PhyloView combines phylogenetic trees with comparisons of genomic loci across any number of genomes; (ii) AlignView projects loci of interest against all other genomes to visualize its topological conservation; (iii) MatrixView compares two genomes in a classical dotplot representation; and (iv) Karyoview visualizes chromosome karyotypes painted with colours of another genome of interest. All four views are interconnected and benefit from many customizable features. PMID:25432975

  20. GenomicusPlants: a web resource to study genome evolution in flowering plants.

    PubMed

    Louis, Alexandra; Murat, Florent; Salse, Jrme; Crollius, Hugues Roest

    2015-01-01

    Comparative genomics combined with phylogenetic reconstructions are powerful approaches to study the evolution of genes and genomes. However, the current rapid expansion of the volume of genomic information makes it increasingly difficult to interrogate, integrate and synthesize comparative genome data while taking into account the maximum breadth of information available. GenomicusPlants (http://www.genomicus.biologie.ens.fr/genomicus-plants) is an extension of the Genomicus webserver that addresses this issue by allowing users to explore flowering plant genomes in an intuitive way, across the broadest evolutionary scales. Extant genomes of 26 flowering plants can be analyzed, as well as 23 ancestral reconstructed genomes. Ancestral gene order provides a long-term chronological view of gene order evolution, greatly facilitating comparative genomics and evolutionary studies. Four main interfaces ('views') are available where: (i) PhyloView combines phylogenetic trees with comparisons of genomic loci across any number of genomes; (ii) AlignView projects loci of interest against all other genomes to visualize its topological conservation; (iii) MatrixView compares two genomes in a classical dotplot representation; and (iv) Karyoview visualizes chromosome karyotypes 'painted' with colours of another genome of interest. All four views are interconnected and benefit from many customizable features. PMID:25432975

  1. 21 CFR 866.3490 - Rhinovirus serological reagents.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Rhinovirus serological reagents. 866.3490 Section 866.3490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3490...

  2. 21 CFR 866.3490 - Rhinovirus serological reagents.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Rhinovirus serological reagents. 866.3490 Section 866.3490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3490...

  3. 21 CFR 866.3490 - Rhinovirus serological reagents.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Rhinovirus serological reagents. 866.3490 Section 866.3490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3490...

  4. 21 CFR 866.3490 - Rhinovirus serological reagents.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Rhinovirus serological reagents. 866.3490 Section 866.3490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3490...

  5. 21 CFR 866.3490 - Rhinovirus serological reagents.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Rhinovirus serological reagents. 866.3490 Section 866.3490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3490...

  6. An Exercise in Molecular Epidemiology: Human Rhinovirus Prevalence and Genetics

    ERIC Educational Resources Information Center

    Albright, Catherine J.; Hall, David J.

    2011-01-01

    Human rhinovirus (HRV) is one of the most common human respiratory pathogens and is responsible for the majority of upper respiratory illnesses. Recently, a phylogeny was constructed from all known American Type Culture Collection (ATCC) HRV sequences. From this study, three HRV classifications (HRVA, HRVB, and HRVC) were determined and techniques

  7. An Exercise in Molecular Epidemiology: Human Rhinovirus Prevalence and Genetics

    ERIC Educational Resources Information Center

    Albright, Catherine J.; Hall, David J.

    2011-01-01

    Human rhinovirus (HRV) is one of the most common human respiratory pathogens and is responsible for the majority of upper respiratory illnesses. Recently, a phylogeny was constructed from all known American Type Culture Collection (ATCC) HRV sequences. From this study, three HRV classifications (HRVA, HRVB, and HRVC) were determined and techniques…

  8. Natural transformation and genome evolution in Streptococcus pneumoniae.

    PubMed

    Straume, Daniel; Stamss, Gro Anita; Hvarstein, Leiv Sigve

    2015-07-01

    Streptococcus pneumoniae is a frequent colonizer of the human nasopharynx that has the potential to cause severe infections such as pneumonia, bacteremia and meningitis. Despite considerable efforts to reduce the burden of pneumococcal disease, it continues to be a major public health problem. After the Second World War, antimicrobial therapy was introduced to fight pneumococcal infections, followed by the first effective vaccines more than half a century later. These clinical interventions generated a selection pressure that drove the evolution of vaccine-escape mutants and strains that were highly resistant against antibiotics. The remarkable ability of S. pneumoniae to acquire drug resistance and evade vaccine pressure is due to its recombination-mediated genetic plasticity. S. pneumoniae is competent for natural genetic transformation, a property that enables the pneumococcus to acquire new traits by taking up naked DNA from the environment and incorporating it into its genome through homologous recombination. In the present paper, we review current knowledge on pneumococcal transformation, and discuss how the pneumococcus uses this mechanism to adapt and survive under adverse and fluctuating conditions. PMID:25445643

  9. The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution

    PubMed Central

    Heinz, Eva; Williams, Tom A.; Nakjang, Sirintra; Noël, Christophe J.; Swan, Daniel C.; Goldberg, Alina V.; Harris, Simon R.; Weinmaier, Thomas; Markert, Stephanie; Becher, Dörte; Bernhardt, Jörg; Dagan, Tal; Hacker, Christian; Lucocq, John M.; Schweder, Thomas; Rattei, Thomas; Hall, Neil; Hirt, Robert P.; Embley, T. Martin

    2012-01-01

    The dynamics of reductive genome evolution for eukaryotes living inside other eukaryotic cells are poorly understood compared to well-studied model systems involving obligate intracellular bacteria. Here we present 8.5 Mb of sequence from the genome of the microsporidian Trachipleistophora hominis, isolated from an HIV/AIDS patient, which is an outgroup to the smaller compacted-genome species that primarily inform ideas of evolutionary mode for these enormously successful obligate intracellular parasites. Our data provide detailed information on the gene content, genome architecture and intergenic regions of a larger microsporidian genome, while comparative analyses allowed us to infer genomic features and metabolism of the common ancestor of the species investigated. Gene length reduction and massive loss of metabolic capacity in the common ancestor was accompanied by the evolution of novel microsporidian-specific protein families, whose conservation among microsporidians, against a background of reductive evolution, suggests they may have important functions in their parasitic lifestyle. The ancestor had already lost many metabolic pathways but retained glycolysis and the pentose phosphate pathway to provide cytosolic ATP and reduced coenzymes, and it had a minimal mitochondrion (mitosome) making Fe-S clusters but not ATP. It possessed bacterial-like nucleotide transport proteins as a key innovation for stealing host-generated ATP, the machinery for RNAi, key elements of the early secretory pathway, canonical eukaryotic as well as microsporidian-specific regulatory elements, a diversity of repetitive and transposable elements, and relatively low average gene density. Microsporidian genome evolution thus appears to have proceeded in at least two major steps: an ancestral remodelling of the proteome upon transition to intracellular parasitism that involved reduction but also selective expansion, followed by a secondary compaction of genome architecture in some, but not all, lineages. PMID:23133373

  10. Reductive genome evolution at both ends of the bacterial population size spectrum.

    PubMed

    Batut, Brnice; Knibbe, Carole; Marais, Gabriel; Daubin, Vincent

    2014-12-01

    Bacterial genomes show substantial variations in size. The smallest bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. In this Opinion article, we discuss the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum. PMID:25220308

  11. Differential cleavage of IRES trans-acting factors (ITAFs) in cells infected by human rhinovirus.

    PubMed

    Chase, Amanda J; Semler, Bert L

    2014-01-20

    Human rhinovirus (HRV) is a major causative agent of the common cold, and thus has several important health implications. As a member of the picornavirus family, HRV has a small genomic RNA that utilizes several host cell proteins for RNA replication. Host proteins poly(rC) binding protein 2 (PCBP2) and polypyrimidine tract binding protein (PTB) are cleaved by a viral proteinase during the course of infection by the related picornavirus, poliovirus. The cleavage of PCBP2 and PTB inhibits poliovirus translation and has been proposed to mediate a switch in poliovirus template usage from translation to RNA replication. HRV RNA replication also requires a switch in template usage from translation to RNA replication; however, the mechanism is not yet known. We demonstrate that PCBP2 and PTB are differentially cleaved during HRV infection in different cell lines, suggesting that HRV utilizes a mechanism distinct from PCBP2 or PTB cleavage to mediate a switch in template usage. PMID:24418535

  12. Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes.

    PubMed

    Kang, Zhen; Zhang, Junli; Jin, Peng; Yang, Sen

    2015-01-01

    Owing to our limited understanding of the relationship between sequence and function and the interaction between intracellular pathways and regulatory systems, the rational design of enzyme-coding genes and de novo assembly of a brand-new artificial genome for a desired functionality or phenotype are difficult to achieve. As an alternative approach, directed evolution has been widely used to engineer genomes and enzyme-coding genes. In particular, significant developments toward DNA synthesis, DNA assembly (in vitro or in vivo), recombination-mediated genetic engineering, and high-throughput screening techniques in the field of synthetic biology have been matured and widely adopted, enabling rapid semi-rational genome engineering to generate variants with desired properties. In this commentary, these novel tools and their corresponding applications in the directed evolution of genomes and enzymes are discussed. Moreover, the strategies for genome engineering and rapid in vitro enzyme evolution are also proposed. PMID:25621864

  13. Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

    PubMed Central

    2010-01-01

    Background The bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii, both of which carry homologous virulence gene clusters such as the prfA cluster and clusters of internalin genes. Initial evidence for multiple deletions of the prfA cluster during the evolution of Listeria indicates that this genus provides an interesting model for studying the evolution of virulence and also presents practical challenges with regard to definition of pathogenic strains. Results To better understand genome evolution and evolution of virulence characteristics in Listeria, we used a next generation sequencing approach to generate draft genomes for seven strains representing Listeria species or clades for which genome sequences were not available. Comparative analyses of these draft genomes and six publicly available genomes, which together represent the main Listeria species, showed evidence for (i) a pangenome with 2,032 core and 2,918 accessory genes identified to date, (ii) a critical role of gene loss events in transition of Listeria species from facultative pathogen to saprotroph, even though a consistent pattern of gene loss seemed to be absent, and a number of isolates representing non-pathogenic species still carried some virulence associated genes, and (iii) divergence of modern pathogenic and non-pathogenic Listeria species and strains, most likely circa 47 million years ago, from a pathogenic common ancestor that contained key virulence genes. Conclusions Genome evolution in Listeria involved limited gene loss and acquisition as supported by (i) a relatively high coverage of the predicted pan-genome by the observed pan-genome, (ii) conserved genome size (between 2.8 and 3.2 Mb), and (iii) a highly syntenic genome. Limited gene loss in Listeria did include loss of virulence associated genes, likely associated with multiple transitions to a saprotrophic lifestyle. The genus Listeria thus provides an example of a group of bacteria that appears to evolve through a loss of virulence rather than acquisition of virulence characteristics. While Listeria includes a number of species-like clades, many of these putative species include clades or strains with atypical virulence associated characteristics. This information will allow for the development of genetic and genomic criteria for pathogenic strains, including development of assays that specifically detect pathogenic Listeria strains. PMID:21126366

  14. The scope and strength of sex-specific selection in genome evolution

    PubMed Central

    Wright, A E; Mank, J E

    2013-01-01

    Males and females share the vast majority of their genomes and yet are often subject to different, even conflicting, selection. Genomic and transcriptomic developments have made it possible to assess sex-specific selection at the molecular level, and it is clear that sex-specific selection shapes the evolutionary properties of several genomic characteristics, including transcription, post-transcriptional regulation, imprinting, genome structure and gene sequence. Sex-specific selection is strongly influenced by mating system, which also causes neutral evolutionary changes that affect different regions of the genome in different ways. Here, we synthesize theoretical and molecular work in order to provide a cohesive view of the role of sex-specific selection and mating system in genome evolution. We also highlight the need for a combined approach, incorporating both genomic data and experimental phenotypic studies, in order to understand precisely how sex-specific selection drives evolutionary change across the genome. PMID:23848139

  15. The Cambrian explosion triggered by critical turning point in genome size evolution.

    PubMed

    Li, Dirson Jian; Zhang, Shengli

    2010-02-01

    The Cambrian explosion is a grand challenge to science today and involves multidisciplinary study. This event is generally believed as a result of genetic innovations, environmental factors and ecological interactions, even though there are many conflicts on nature and timing of metazoan origins. The crux of the matter is that an entire roadmap of the evolution is missing to discern the biological complexity transition and to evaluate the critical role of the Cambrian explosion in the overall evolutionary context. Here, we calculate the time of the Cambrian explosion by a "C-value clock"; our result quite fits the fossil records. We clarify that the intrinsic reason of genome evolution determined the Cambrian explosion. A general formula for evaluating genome size of different species has been found, by which the genome size evolution can be illustrated. The Cambrian explosion, as a major transition of biological complexity, essentially corresponds to a critical turning point in genome size evolution. PMID:20074549

  16. The Laccaria and Tuber Genomes Reveal Unique Signatures of Mycorrhizal Symbiosis Evolution (2010 JGI User Meeting)

    SciTech Connect

    Knapp, Steve

    2010-03-24

    Francis Martin from the French agricultural research institute INRA talks on how "The Laccaria and Tuber genomes reveal unique signatures of mycorrhizal symbiosis evolution" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  17. Genomic inferences from Afrotheria and the evolution of elephants.

    PubMed

    Roca, Alfred L; O'Brien, Stephen J

    2005-12-01

    Recent genetic studies have established that African forest and savanna elephants are distinct species with dissociated cytonuclear genomic patterns, and have identified Asian elephants from Borneo and Sumatra as conservation priorities. Representative of Afrotheria, a superordinal clade encompassing six eutherian orders, the African savanna elephant was among the first mammals chosen for whole-genome sequencing to provide a comparative understanding of the human genome. Elephants have large and complex brains and display advanced levels of social structure, communication, learning and intelligence. The elephant genome sequence might prove useful for comparative genomic studies of these advanced traits, which have appeared independently in only three mammalian orders: primates, cetaceans and proboscideans. PMID:16226885

  18. Evolution of developmentally regulated genome rearrangements in eukaryotes.

    PubMed

    Zufall, Rebecca A; Robinson, Tessa; Katz, Laura A

    2005-09-15

    Developmentally regulated genome rearrangements (DRGR)--processes that alter genomes either in specific cells or during specific life cycle stages--are widespread throughout eukaryotes. This contrasts with the view that genome structure and content remain essentially constant throughout an organism's life cycle. Here we review three categories of developmentally regulated genome processing in eukaryotes: genome-wide rearrangements, targeted rearrangements, and a special case of amplification of ribosomal DNA genes. Mapping these types of DRGR onto eukaryotic phylogeny indicates that each type of processing is found in multiple independent lineages. We propose that such genome rearrangements were present within the last common ancestor of extant eukaryotes, and that future research will yield evidence of homologous epigenetic mechanisms underlying genome processing among diverse eukaryotes. PMID:16032699

  19. Capsid Protein VP4 of Human Rhinovirus Induces Membrane Permeability by the Formation of a Size-Selective Multimeric Pore

    PubMed Central

    Panjwani, Anusha; Strauss, Mike; Gold, Sarah; Wenham, Hannah; Jackson, Terry; Chou, James J.; Rowlands, David J.; Stonehouse, Nicola J.; Hogle, James M.; Tuthill, Tobias J.

    2014-01-01

    Non-enveloped viruses must deliver their viral genome across a cell membrane without the advantage of membrane fusion. The mechanisms used to achieve this remain poorly understood. Human rhinovirus, a frequent cause of the common cold, is a non-enveloped virus of the picornavirus family, which includes other significant pathogens such as poliovirus and foot-and-mouth disease virus. During picornavirus cell entry, the small myristoylated capsid protein VP4 is released from the virus, interacts with the cell membrane and is implicated in the delivery of the viral RNA genome into the cytoplasm to initiate replication. In this study, we have produced recombinant C-terminal histidine-tagged human rhinovirus VP4 and shown it can induce membrane permeability in liposome model membranes. Dextran size-exclusion studies, chemical crosslinking and electron microscopy demonstrated that VP4 forms a multimeric membrane pore, with a channel size consistent with transfer of the single-stranded RNA genome. The membrane permeability induced by recombinant VP4 was influenced by pH and was comparable to permeability induced by infectious virions. These findings present a molecular mechanism for the involvement of VP4 in cell entry and provide a model system which will facilitate exploration of VP4 as a novel antiviral target for the picornavirus family. PMID:25102288

  20. Capsid protein VP4 of human rhinovirus induces membrane permeability by the formation of a size-selective multimeric pore.

    PubMed

    Panjwani, Anusha; Strauss, Mike; Gold, Sarah; Wenham, Hannah; Jackson, Terry; Chou, James J; Rowlands, David J; Stonehouse, Nicola J; Hogle, James M; Tuthill, Tobias J

    2014-08-01

    Non-enveloped viruses must deliver their viral genome across a cell membrane without the advantage of membrane fusion. The mechanisms used to achieve this remain poorly understood. Human rhinovirus, a frequent cause of the common cold, is a non-enveloped virus of the picornavirus family, which includes other significant pathogens such as poliovirus and foot-and-mouth disease virus. During picornavirus cell entry, the small myristoylated capsid protein VP4 is released from the virus, interacts with the cell membrane and is implicated in the delivery of the viral RNA genome into the cytoplasm to initiate replication. In this study, we have produced recombinant C-terminal histidine-tagged human rhinovirus VP4 and shown it can induce membrane permeability in liposome model membranes. Dextran size-exclusion studies, chemical crosslinking and electron microscopy demonstrated that VP4 forms a multimeric membrane pore, with a channel size consistent with transfer of the single-stranded RNA genome. The membrane permeability induced by recombinant VP4 was influenced by pH and was comparable to permeability induced by infectious virions. These findings present a molecular mechanism for the involvement of VP4 in cell entry and provide a model system which will facilitate exploration of VP4 as a novel antiviral target for the picornavirus family. PMID:25102288

  1. How Evolution of Genomes Is Reflected in Exact DNA Sequence Match Statistics

    PubMed Central

    Massip, Florian; Sheinman, Michael; Schbath, Sophie; Arndt, Peter F.

    2015-01-01

    Genome evolution is shaped by a multitude of mutational processes, including point mutations, insertions, and deletions of DNA sequences, as well as segmental duplications. These mutational processes can leave distinctive qualitative marks in the statistical features of genomic DNA sequences. One such feature is the match length distribution (MLD) of exactly matching sequence segments within an individual genome or between the genomes of related species. These have been observed to exhibit characteristic power law decays in many species. Here, we show that simple dynamical models consisting solely of duplication and mutation processes can already explain the characteristic features of MLDs observed in genomic sequences. Surprisingly, we find that these features are largely insensitive to details of the underlying mutational processes and do not necessarily rely on the action of natural selection. Our results demonstrate how analyzing statistical features of DNA sequences can help us reveal and quantify the different mutational processes that underlie genome evolution. PMID:25398628

  2. Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life

    PubMed Central

    Hao, Da-Cheng; Xiao, Pei-Gen

    2015-01-01

    Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources. PMID:26461812

  3. The genome sequence of taurine cattle: A window to ruminant biology and evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (ma...

  4. Evolution of Weediness and Invasiveness: Charting the Course for Weed Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic bases of weedy and invasive traits and their evolution remain poorly understood, but genomic approaches offer tremendous promise for elucidating these important features of weed biology. However, the genomic tools and resources available for weeds are currently relatively meager compared...

  5. Biology, genome organization, and evolution of parvoviruses in marine shrimp.

    PubMed

    Dhar, Arun K; Robles-Sikisaka, Refugio; Saksmerprome, Vanvimon; Lakshman, Dilip K

    2014-01-01

    As shrimp aquaculture has evolved from a subsistent farming activity to an economically important global industry, viral diseases have also become a serious threat to the sustainable growth and productivity of this industry. Parvoviruses represent an economically important group of viruses that has greatly affected shrimp aquaculture. In the early 1980s, an outbreak of a shrimp parvovirus, infectious hypodermal and hematopoietic necrosis virus (IHHNV), led to the collapse of penaeid shrimp farming in the Americas. Since then, considerable progress has been made in characterizing the parvoviruses of shrimp and developing diagnostic methods aimed to preventing the spread of diseases caused by these viruses. To date, four parvoviruses are known that infect shrimp; these include IHHNV, hepatopancreatic parvovirus (HPV), spawner-isolated mortality virus (SMV), and lymphoid organ parvo-like virus. Due to the economic repercussions that IHHNV and HPV outbreaks have caused to shrimp farming over the years, studies have been focused mostly on these two pathogens, while information on SMV and LPV remains limited. IHHNV was the first shrimp virus to be sequenced and the first for which highly sensitive diagnostic methods were developed. IHHNV-resistant lines of shrimp were also developed to mitigate the losses caused by this virus. While the losses due to IHHNV have been largely contained in recent years, reports of HPV-induced mortalities in larval stages in hatchery and losses due to reduced growth have increased. This review presents a comprehensive account of the history and current knowledge on the biology, diagnostics methods, genomic features, mechanisms of evolution, and management strategies of shrimp parvoviruses. We also highlighted areas where research efforts should be focused in order to gain further insight on the mechanisms of parvoviral pathogenicity in shrimp that will help to prevent future losses caused by these viruses. PMID:24751195

  6. Hidden Markov models for evolution and comparative genomics analysis.

    PubMed

    Bykova, Nadezda A; Favorov, Alexander V; Mironov, Andrey A

    2013-01-01

    The problem of reconstruction of ancestral states given a phylogeny and data from extant species arises in a wide range of biological studies. The continuous-time Markov model for the discrete states evolution is generally used for the reconstruction of ancestral states. We modify this model to account for a case when the states of the extant species are uncertain. This situation appears, for example, if the states for extant species are predicted by some program and thus are known only with some level of reliability; it is common for bioinformatics field. The main idea is formulation of the problem as a hidden Markov model on a tree (tree HMM, tHMM), where the basic continuous-time Markov model is expanded with the introduction of emission probabilities of observed data (e.g. prediction scores) for each underlying discrete state. Our tHMM decoding algorithm allows us to predict states at the ancestral nodes as well as to refine states at the leaves on the basis of quantitative comparative genomics. The test on the simulated data shows that the tHMM approach applied to the continuous variable reflecting the probabilities of the states (i.e. prediction score) appears to be more accurate then the reconstruction from the discrete states assignment defined by the best score threshold. We provide examples of applying our model to the evolutionary analysis of N-terminal signal peptides and transcription factor binding sites in bacteria. The program is freely available at http://bioinf.fbb.msu.ru/~nadya/tHMM and via web-service at http://bioinf.fbb.msu.ru/treehmmweb. PMID:23762278

  7. Hidden Markov Models for Evolution and Comparative Genomics Analysis

    PubMed Central

    Bykova, Nadezda A.; Favorov, Alexander V.; Mironov, Andrey A.

    2013-01-01

    The problem of reconstruction of ancestral states given a phylogeny and data from extant species arises in a wide range of biological studies. The continuous-time Markov model for the discrete states evolution is generally used for the reconstruction of ancestral states. We modify this model to account for a case when the states of the extant species are uncertain. This situation appears, for example, if the states for extant species are predicted by some program and thus are known only with some level of reliability; it is common for bioinformatics field. The main idea is formulation of the problem as a hidden Markov model on a tree (tree HMM, tHMM), where the basic continuous-time Markov model is expanded with the introduction of emission probabilities of observed data (e.g. prediction scores) for each underlying discrete state. Our tHMM decoding algorithm allows us to predict states at the ancestral nodes as well as to refine states at the leaves on the basis of quantitative comparative genomics. The test on the simulated data shows that the tHMM approach applied to the continuous variable reflecting the probabilities of the states (i.e. prediction score) appears to be more accurate then the reconstruction from the discrete states assignment defined by the best score threshold. We provide examples of applying our model to the evolutionary analysis of N-terminal signal peptides and transcription factor binding sites in bacteria. The program is freely available at http://bioinf.fbb.msu.ru/~nadya/tHMM and via web-service at http://bioinf.fbb.msu.ru/treehmmweb. PMID:23762278

  8. Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication.

    PubMed

    Amores, Angel; Catchen, Julian; Ferrara, Allyse; Fontenot, Quenton; Postlethwait, John H

    2011-08-01

    Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F(1) offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. Thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F(1) dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing. PMID:21828280

  9. Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication

    PubMed Central

    Amores, Angel; Catchen, Julian; Ferrara, Allyse; Fontenot, Quenton; Postlethwait, John H.

    2011-01-01

    Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F1 offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. Thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F1 dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing. PMID:21828280

  10. Effectiveness of hand sanitizers with and without organic acids for removal of rhinovirus from hands.

    PubMed

    Turner, Ronald B; Fuls, Janice L; Rodgers, Nancy D

    2010-03-01

    These studies evaluated the effectiveness of ethanol hand sanitizers with or without organic acids to remove detectable rhinovirus from the hands and prevent experimental rhinovirus infection. Ethanol hand sanitizers were significantly more effective than hand washing with soap and water. The addition of organic acids to the ethanol provided residual virucidal activity that persisted for at least 4 h. Whether these treatments will reduce rhinovirus infection in the natural setting remains to be determined. PMID:20047916

  11. Effectiveness of Hand Sanitizers with and without Organic Acids for Removal of Rhinovirus from Hands ?

    PubMed Central

    Turner, Ronald B.; Fuls, Janice L.; Rodgers, Nancy D.

    2010-01-01

    These studies evaluated the effectiveness of ethanol hand sanitizers with or without organic acids to remove detectable rhinovirus from the hands and prevent experimental rhinovirus infection. Ethanol hand sanitizers were significantly more effective than hand washing with soap and water. The addition of organic acids to the ethanol provided residual virucidal activity that persisted for at least 4 h. Whether these treatments will reduce rhinovirus infection in the natural setting remains to be determined. PMID:20047916

  12. Gnolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts

    PubMed Central

    Sherman, David; Durrens, Pascal; Beyne, Emmanuelle; Nikolski, Macha; Souciet, Jean-Luc

    2004-01-01

    The Gnolevures online database (http://cbi.labri.fr/Genolevures/) provides data and tools to facilitate comparative genomic studies on hemiascomycetous yeasts. Now, four complete genome sequences recently determined (Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, Yarrowia lipolytica) have been added to the partial sequences of 13 species previously analysed by a random approach. The database also includes the reference genome Saccharomyces cerevisiae. Data are presented with a focus on relations between genes and genomes: conservation of genes and gene families, speciation, chromosomal reorganization and synteny. The Gnolevures site includes a community area for specific studies by members of the international community. PMID:14681422

  13. Life History Evolution and Genome Size in Subtribe Oncidiinae (Orchidaceae)

    PubMed Central

    CHASE, MARK W.; HANSON, LYNDA; ALBERT, VICTOR A.; WHITTEN, W. MARK; WILLIAMS, NORRIS H.

    2005-01-01

    Background and Aims Within Oncidiinae, there are several groups of species that are effectively annuals, and we wished to see if these species had smaller genome sizes than average for the subtribe. Methods Fifty-four genome size estimates (50 of which are new) for species in subtribe Oncidiinae (Orchidaceae) were examined for the first time in a phylogenetic context to evaluate hypotheses concerning genome sizes and life history traits. Results and Conclusions Within the limits of still relatively sparse sampling, the species that are effectively annuals do appear to have smaller genome sizes than average. However, the genome sizes of their immediate sister group are also small, indicating that changes in genome size preceded the change in life history traits. Genome sizes and chromosome numbers also do not correlate; some slowly growing species have lower chromosome numbers but large genomes and vice versa. Based on a survey of the literature on orchids, it is also clear that epiphytic species have smaller genome sizes than do terrestrial species, which could be an effect of different water relations or the fact that most terrestrial orchids are geophytic or have distinct growth and dormancy phases. PMID:15596466

  14. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.

    PubMed

    Li, Fuguang; Fan, Guangyi; Lu, Cairui; Xiao, Guanghui; Zou, Changsong; Kohel, Russell J; Ma, Zhiying; Shang, Haihong; Ma, Xiongfeng; Wu, Jianyong; Liang, Xinming; Huang, Gai; Percy, Richard G; Liu, Kun; Yang, Weihua; Chen, Wenbin; Du, Xiongming; Shi, Chengcheng; Yuan, Youlu; Ye, Wuwei; Liu, Xin; Zhang, Xueyan; Liu, Weiqing; Wei, Hengling; Wei, Shoujun; Huang, Guodong; Zhang, Xianlong; Zhu, Shuijin; Zhang, He; Sun, Fengming; Wang, Xingfen; Liang, Jie; Wang, Jiahao; He, Qiang; Huang, Leihuan; Wang, Jun; Cui, Jinjie; Song, Guoli; Wang, Kunbo; Xu, Xun; Yu, John Z; Zhu, Yuxian; Yu, Shuxun

    2015-05-01

    Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum. PMID:25893780

  15. Networks of lexical borrowing and lateral gene transfer in language and genome evolution

    PubMed Central

    List, Johann-Mattis; Nelson-Sathi, Shijulal; Geisler, Hans; Martin, William

    2014-01-01

    Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution. PMID:24375688

  16. The Early Stage of Bacterial Genome-Reductive Evolution in the Host

    PubMed Central

    Ulrich, Ricky L.; Yu, Yan; Nierman, William C.; Kim, Heenam Stanley

    2010-01-01

    The equine-associated obligate pathogen Burkholderia mallei was developed by reductive evolution involving a substantial portion of the genome from Burkholderia pseudomallei, a free-living opportunistic pathogen. With its short history of divergence (?3.5 myr), B. mallei provides an excellent resource to study the early steps in bacterial genome reductive evolution in the host. By examining 20 genomes of B. mallei and B. pseudomallei, we found that stepwise massive expansion of IS (insertion sequence) elements ISBma1, ISBma2, and IS407A occurred during the evolution of B. mallei. Each element proliferated through the sites where its target selection preference was met. Then, ISBma1 and ISBma2 contributed to the further spread of IS407A by providing secondary insertion sites. This spread increased genomic deletions and rearrangements, which were predominantly mediated by IS407A. There were also nucleotide-level disruptions in a large number of genes. However, no significant signs of erosion were yet noted in these genes. Intriguingly, all these genomic modifications did not seriously alter the gene expression patterns inherited from B. pseudomallei. This efficient and elaborate genomic transition was enabled largely through the formation of the highly flexible IS-blended genome and the guidance by selective forces in the host. The detailed IS intervention, unveiled for the first time in this study, may represent the key component of a general mechanism for early bacterial evolution in the host. PMID:20523904

  17. Patterns of Genome Evolution among the Microsporidian Parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi

    PubMed Central

    Morrison, Hilary G.; Feng, Xiaochuan; Weiss, Louis M.; Tzipori, Saul; Keeling, Patrick J.

    2007-01-01

    Background Microsporidia are intracellular parasites that are highly-derived relatives of fungi. They have compacted genomes and, despite a high rate of sequence evolution, distantly related species can share high levels of gene order conservation. To date, only two species have been analysed in detail, and data from one of these largely consists of short genomic fragments. It is therefore difficult to determine how conservation has been maintained through microsporidian evolution, and impossible to identify whether certain regions are more prone to genomic stasis. Principal Findings Here, we analyse three large fragments of the Enterocytozoon bieneusi genome (in total 429 kbp), a species of medical significance. A total of 296 ORFs were identified, annotated and their context compared with Encephalitozoon cuniculi and Antonospora locustae. Overall, a high degree of conservation was found between all three species, and interestingly the level of conservation was similar in all three pairwise comparisons, despite the fact that A. locustae is more distantly related to E. cuniculi and E. bieneusi than either are to each other. Conclusions/Significance Any two genes that are found together in any pair of genomes are more likely to be conserved in the third genome as well, suggesting that a core of genes tends to be conserved across the entire group. The mechanisms of rearrangments identified among microsporidian genomes were consistent with a very slow evolution of their architecture, as opposed to the very rapid sequence evolution reported for these parasites. PMID:18060071

  18. Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments.

    PubMed

    Jerison, Elizabeth R; Desai, Michael M

    2015-12-01

    Microbial evolution experiments enable us to watch adaptation in real time, and to quantify the repeatability and predictability of evolution by comparing identical replicate populations. Further, we can resurrect ancestral types to examine changes over evolutionary time. Until recently, experimental evolution has been limited to measuring phenotypic changes, or to tracking a few genetic markers over time. However, recent advances in sequencing technology now make it possible to extensively sequence clones or whole-population samples from microbial evolution experiments. Here, we review recent work exploiting these techniques to understand the genomic basis of evolutionary change in experimental systems. We first focus on studies that analyze the dynamics of genome evolution in microbial systems. We then survey work that uses observations of sequence evolution to infer aspects of the underlying fitness landscape, concentrating on the epistatic interactions between mutations and the constraints these interactions impose on adaptation. PMID:26370471

  19. The tomato genome sequence provides insight into fleshy fruit evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of the inbred tomato cultivar ‘Heinz 1706’ was sequenced and assembled using a combination of Sanger and “next generation” technologies. The predicted genome size is ~900 Mb, consistent with prior estimates, of which 760 Mb were assembled in 91 scaffolds aligned to the 12 tomato chromosom...

  20. Identification of host miRNAs that may limit human rhinovirus replication

    PubMed Central

    Bondanese, Victor Paky; Francisco-Garcia, Ana; Bedke, Nicole; Davies, Donna E; Sanchez-Elsner, Tilman

    2014-01-01

    AIM: To test whether the replication of human rhinovirus (HRV) is regulated by microRNAs in human bronchial epithelial cells. METHODS: For the present study, the human cell line BEAS-2B (derived from normal human bronchial epithelial cells) was adopted. DICER knock-down, by siRNA transfection in BEAS-2B cells, was performed in order to inhibit microRNA maturation globally. Alternatively, antisense oligonucleotides (anti-miRs) were transfected to inhibit the activity of specific microRNAs. Cells were infected with HRV-1B. Viral replication was assessed by measuring the genomic viral RNA by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Association between microRNA-induced-silencing-complex and viral RNA was detected by Ago2 co-immunoprecipitation followed by RT-qPCR. Targetscan v.6 was used to predict microRNA target sites on several HRV strains. RESULTS: Here, we show that microRNAs affect replication of HRV-1B. DICER knock-down significantly reduced the expression of mature microRNAs in a bronchial epithelial cell line (BEAS-2B) and in turn, increased the synthesis of HRV-1B RNA. Additionally, HRV-1B RNA co-immunoprecipitated with argonaute 2 protein, an important effector for microRNA activity suggesting that microRNAs bind to viral RNA during infection. In order to identify specific microRNAs involved in this interaction, we employed bioinformatics analysis, and selected a group of microRNAs that have been reported to be under-expressed in asthmatic bronchial epithelial cells and were predicted to target different strains of rhinoviruses (HRV-1B, -16, -14, -27). Our results suggest that, out of this group of microRNAs, miR-128 and miR-155 contribute to the innate defense against HRV-1B: transfection of specific anti-miRs increased viral replication, as anticipated in-silico. CONCLUSION: Taken together, our results suggest that pathological changes in microRNA expression, as already reported for asthma or chronic obstructive pulmonary disease have the potential to affect Rhinovirus replication and therefore may play a role in virus-induced exacerbations. PMID:25426267

  1. DNA Transposons and the Evolution of Eukaryotic Genomes

    PubMed Central

    Feschotte, Cédric; Pritham, Ellen J.

    2007-01-01

    Transposable elements are mobile genetic units that exhibit broad diversity in their structure and transposition mechanisms. Transposable elements occupy a large fraction of many eukaryotic genomes and their movement and accumulation represent a major force shaping the genes and genomes of almost all organisms. This review focuses on DNA-mediated or class 2 transposons and emphasizes how this class of elements is distinguished from other types of mobile elements in terms of their structure, amplification dynamics, and genomic effect. We provide an up-to-date outlook on the diversity and taxonomic distribution of all major types of DNA transposons in eukaryotes, including Helitrons and Mavericks. We discuss some of the evolutionary forces that influence their maintenance and diversification in various genomic environments. Finally, we highlight how the distinctive biological features of DNA transposons have contributed to shape genome architecture and led to the emergence of genetic innovations in different eukaryotic lineages. PMID:18076328

  2. The Sex Chromosomes of Frogs: Variability and Tolerance Offer Clues to Genome Evolution and Function

    PubMed Central

    Malcom, Jacob W.; Kudra, Randal S.; Malone, John H.

    2014-01-01

    Frog sex chromosomes offer an ideal system for advancing our understanding of genome evolution and function because of the variety of sex determination systems in the group, the diversity of sex chromosome maturation states, the ease of experimental manipulation during early development. After briefly reviewing sex chromosome biology generally, we focus on what is known about frog sex determination, sex chromosome evolution, and recent, genomics-facilitated advances in the field. In closing we highlight gaps in our current knowledge of frog sex chromosomes, and suggest priorities for future research that can advance broad knowledge of gene dose and sex chromosome evolution. PMID:25031658

  3. Genome sequence of the brown Norway rat yields insights into mammalian evolution

    SciTech Connect

    Gibbs, Richard A.; Weinstock, George M.; Metzker, Michael L.; Muzny, Donna M.; Sodergren, Erica J.; Scherer, Steven; Scott, Graham; Steffen, David; Worley, Kim C.; Burch, Paula E.; Okwuonu, Geoffrey; Hines, Sandra; Lewis, Lora; DeRamo, Christine; Delgado, Oliver; Dugan-Rocha, Shannon; Miner, George; Morgan, Margaret; Hawes, Alicia; Gill, Rachel; Holt, Robert A.; Adams, Mark D.; Amanatides, Peter G.; Baden-Tillson, Holly; Barnstead, Mary; Chin, Soo; Evans, Cheryl A.; Ferriera, Steven; Fosler, Carl; Glodek, Anna; Gu, Zhiping; Jennings, Don; Kraft, Cheryl L.; Nguyen, Trixie; Pfannkoch, Cynthia M.; Sitter, Cynthia; Sutton, Granger G.; Venter, J. Craig; Woodage, Trevor; Smith, Douglas; Lee, Hong-Maei; Gustafson, Erik; Cahill, Patrick; Kana, Arnold; Doucette-Stamm, Lynn; Weinstock, Keith; Fechtel, Kim; Weiss, Robert B.; Dunn, Diane M.; Green, Eric D.; Blakesley, Robert W.; Bouffard, Gerard G.; de Jong, Pieter J.; Osoegawa, Kazutoyo; Zhu, Baoli; Marra, Marco; Schein, Jacqueline; Bosdet, Ian; Fjell, Chris; Jones, Steven; Krzywinski, Martin; Mathewson, Carrie; Siddiqui, Asim; Wye, Natasja; McPherson, John; Zhao, Shaying; Fraser, Claire M.; Shetty, Jyoti; Shatsman, Sofiya; Geer, Keita; Chen, Yixin; Abramzon, Sofyia; Nierman, William C.; Havlak, Paul H.; Chen, Rui; Durbin, K. James; Egan, Amy; Ren, Yanru; Song, Xing-Zhi; Li, Bingshan; Liu, Yue; Qin, Xiang; Cawley, Simon; Cooney, A.J.; D'Souza, Lisa M.; Martin, Kirt; Wu, Jia Qian; Gonzalez-Garay, Manuel L.; Jackson, Andrew R.; Kalafus, Kenneth J.; McLeod, Michael P.; Milosavljevic, Aleksandar; Virk, Davinder; Volkov, Andrei; Wheeler, David A.; Zhang, Zhengdong; Bailey, Jeffrey A.; Eichler, Evan E.; Tuzun, Eray; Birney, Ewan; Mongin, Emmanuel; Ureta-Vidal, Abel; Woodwark, Cara; Zdobnov, Evgeny; Bork, Peer; Suyama, Mikita; Torrents, David; Alexandersson, Marina; Trask, Barbara J.; Young, Janet M.; et al.

    2004-02-02

    The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90 percent of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

  4. Neutrophil adhesion molecules in experimental rhinovirus infection in COPD

    PubMed Central

    2013-01-01

    Background COPD exacerbations are associated with neutrophilic airway inflammation. Adhesion molecules on the surface of neutrophils may play a key role in their movement from blood to the airways. We analysed adhesion molecule expression on blood and sputum neutrophils from COPD subjects and non-obstructed smokers during experimental rhinovirus infections. Methods Blood and sputum were collected from 9 COPD subjects and 10 smoking and age-matched control subjects at baseline, and neutrophil expression of the adhesion molecules and activation markers measured using flow cytometry. The markers examined were CD62L and CD162 (mediating initial steps of neutrophil rolling and capture), CD11a and CD11b (required for firm neutrophil adhesion), CD31 and CD54 (involved in neutrophil transmigration through the endothelial monolayer) and CD63 and CD66b (neutrophil activation markers). Subjects were then experimentally infected with rhinovirus-16 and repeat samples collected for neutrophil analysis at post-infection time points. Results At baseline there were no differences in adhesion molecule expression between the COPD and non-COPD subjects. Expression of CD11a, CD31, CD62L and CD162 was reduced on sputum neutrophils compared to blood neutrophils. Following rhinovirus infection expression of CD11a expression on blood neutrophils was significantly reduced in both subject groups. CD11b, CD62L and CD162 expression was significantly reduced only in the COPD subjects. Blood neutrophil CD11b expression correlated inversely with inflammatory markers and symptom scores in COPD subjects. Conclusion Following rhinovirus infection neutrophils with higher surface expression of adhesion molecules are likely preferentially recruited to the lungs. CD11b may be a key molecule involved in neutrophil trafficking in COPD exacerbations. PMID:23834268

  5. Reductive Evolution of Bacterial Genome in Insect Gut Environment

    PubMed Central

    Nikoh, Naruo; Hosokawa, Takahiro; Oshima, Kenshiro; Hattori, Masahira; Fukatsu, Takema

    2011-01-01

    Obligate endocellular symbiotic bacteria of insects and other organisms generally exhibit drastic genome reduction. Recently, it was shown that symbiotic gut bacteria of some stinkbugs also have remarkably reduced genomes. Here, we report the complete genome sequence of such a gut bacterium Ishikawaella capsulata of the plataspid stinkbug Megacopta punctatissima. Gene repertoire and evolutionary patterns, including AT richness and elevated evolutionary rate, of the 745,590 bp genome were strikingly similar to those of obligate γ-proteobacterial endocellular insect symbionts like Buchnera in aphids and Wigglesworthia in tsetse flies. Ishikawaella was suggested to supply essential amino acids for the plant-sucking stinkbug as Buchnera does for the host aphid. Although Buchnera is phylogenetically closer to Wigglesworthia than to Ishikawaella, in terms of gene repertoire Buchnera was similar to Ishikawaella rather than to Wigglesworthia, providing a possible case of genome-level convergence of gene content. Meanwhile, several notable differences were identified between the genomes of Ishikawaella and Buchnera, including retention of TCA cycle genes and lack of flagellum-related genes in Ishikawaella, which may reflect their adaptation to distinct symbiotic habitats. Unexpectedly, Ishikawaella retained fewer genes related to cell wall synthesis and lipid metabolism than many endocellular insect symbionts. The plasmid of Ishikawaella encoded genes for arginine metabolism and oxalate detoxification, suggesting the possibility of additional Ishikawaella roles similar to those of human gut bacteria. Our data highlight strikingly similar evolutionary patterns that are shared between the extracellular and endocellular insect symbiont genomes. PMID:21737395

  6. Reductive evolution of bacterial genome in insect gut environment.

    PubMed

    Nikoh, Naruo; Hosokawa, Takahiro; Oshima, Kenshiro; Hattori, Masahira; Fukatsu, Takema

    2011-01-01

    Obligate endocellular symbiotic bacteria of insects and other organisms generally exhibit drastic genome reduction. Recently, it was shown that symbiotic gut bacteria of some stinkbugs also have remarkably reduced genomes. Here, we report the complete genome sequence of such a gut bacterium Ishikawaella capsulata of the plataspid stinkbug Megacopta punctatissima. Gene repertoire and evolutionary patterns, including AT richness and elevated evolutionary rate, of the 745,590 bp genome were strikingly similar to those of obligate ?-proteobacterial endocellular insect symbionts like Buchnera in aphids and Wigglesworthia in tsetse flies. Ishikawaella was suggested to supply essential amino acids for the plant-sucking stinkbug as Buchnera does for the host aphid. Although Buchnera is phylogenetically closer to Wigglesworthia than to Ishikawaella, in terms of gene repertoire Buchnera was similar to Ishikawaella rather than to Wigglesworthia, providing a possible case of genome-level convergence of gene content. Meanwhile, several notable differences were identified between the genomes of Ishikawaella and Buchnera, including retention of TCA cycle genes and lack of flagellum-related genes in Ishikawaella, which may reflect their adaptation to distinct symbiotic habitats. Unexpectedly, Ishikawaella retained fewer genes related to cell wall synthesis and lipid metabolism than many endocellular insect symbionts. The plasmid of Ishikawaella encoded genes for arginine metabolism and oxalate detoxification, suggesting the possibility of additional Ishikawaella roles similar to those of human gut bacteria. Our data highlight strikingly similar evolutionary patterns that are shared between the extracellular and endocellular insect symbiont genomes. PMID:21737395

  7. How does rhinovirus cause the common cold cough?

    PubMed

    Atkinson, Samantha K; Sadofsky, Laura R; Morice, Alyn H

    2016-01-01

    Cough is a protective reflex to prevent aspiration and can be triggered by a multitude of stimuli. The commonest form of cough is caused by upper respiratory tract infection and has no benefit to the host. The virus hijacks this natural defence mechanism in order to propagate itself through the population. Despite the resolution of the majority of cold symptoms within 2?weeks, cough can persist for some time thereafter. Unfortunately, the mechanism of infectious cough brought on by pathogenic viruses, such as human rhinovirus, during colds, remains elusive despite the extensive work that has been undertaken. For socioeconomic reasons, it is imperative we identify the mechanism of cough. There are several theories which have been proposed as the causative mechanism of cough in rhinovirus infection, encompassing a range of different processes. Those of which hold most promise are physical disruption of the epithelial lining, excess mucus production and an inflammatory response to rhinovirus infection which may be excessive. And finally, neuronal modulation, the most convincing hypothesis, is thought to potentiate cough long after the original stimulus has been cleared. All these hypotheses will be briefly covered in the following sections. PMID:26835135

  8. How does rhinovirus cause the common cold cough?

    PubMed Central

    Atkinson, Samantha K; Sadofsky, Laura R; Morice, Alyn H

    2016-01-01

    Cough is a protective reflex to prevent aspiration and can be triggered by a multitude of stimuli. The commonest form of cough is caused by upper respiratory tract infection and has no benefit to the host. The virus hijacks this natural defence mechanism in order to propagate itself through the population. Despite the resolution of the majority of cold symptoms within 2 weeks, cough can persist for some time thereafter. Unfortunately, the mechanism of infectious cough brought on by pathogenic viruses, such as human rhinovirus, during colds, remains elusive despite the extensive work that has been undertaken. For socioeconomic reasons, it is imperative we identify the mechanism of cough. There are several theories which have been proposed as the causative mechanism of cough in rhinovirus infection, encompassing a range of different processes. Those of which hold most promise are physical disruption of the epithelial lining, excess mucus production and an inflammatory response to rhinovirus infection which may be excessive. And finally, neuronal modulation, the most convincing hypothesis, is thought to potentiate cough long after the original stimulus has been cleared. All these hypotheses will be briefly covered in the following sections. PMID:26835135

  9. Rhinovirus 39 infection in allergic and nonallergic subjects.

    PubMed

    Doyle, W J; Skoner, D P; Fireman, P; Seroky, J T; Green, I; Ruben, F; Kardatzke, D R; Gwaltney, J M

    1992-05-01

    To determine if individuals with allergic rhinitis are hyperresponsive to upper respiratory tract viral infections, 20 allergic and 18 nonallergic, susceptible, adult volunteers were challenged and infected with rhinovirus type 39 before the pollen seasons. Before challenge and on each of 6 days of cloister, all volunteers were interviewed for symptoms and completed a test battery consisting of evaluations of secretion production by weighed tissues, nasal patency by active posterior rhinomanometry, nasal clearance by the dyed saccharin technique, pulmonary function by spirometry, eustachian tube function by sonotubometry, and middle ear status by tympanometry. The symptomatology and pathophysiology resulting from the rhinovirus infection were consistent with those reported in previous studies with this challenge system. Between-group comparisons revealed no differences in symptom presentation, nasal secretion production, or overall pathophysiologic response. However, for decreased mucociliary clearance rate, increased nasal congestion, eustachian tube dysfunction, and symptoms of sneezing, the allergic group demonstrated an earlier onset compared with that of the nonallergic group. The biologic significance of the differences in onset of dysfunction is tempered by the observation that the temporal pattern of responses in the allergic group was similar with that of nonallergic subjects in previous studies. The results of the present study do not support the hypothesis of a physiologic hyperresponsiveness to rhinovirus type 39 infection in allergic subjects during nonallergy seasons. PMID:1316390

  10. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic and genomic analyses of Upland cotton (Gossypium hirsutum) are difficult because it has a complex allotetraploid (AADD; 2n = 4x = 52) genome. Here we sequenced, assembled and analyzed the world's most important cultivated cotton genome with 246.2 gigabase (Gb) clean data obtained using whol...

  11. Genomics on a phylogeny: Evolution of genes and genomes in the genus Drosophila

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of inferences in evolutionary genomics. The genomes of 12 Drosophila species, nine of which are presented here for the first time (sechellia, yakuba, erecta, ananassae, persimili...

  12. [From random mutagenesis to precise genome editing: the development and evolution of genome editing techniques in Drosophila].

    PubMed

    Su, Fang; Huang, Zongliang; Guo, Yawen; Jiao, Renjie; Zi, Li; Chen, Jianming; Liu, Jiyong

    2016-01-01

    Drosophila melanogaster, an important model organism for studying life science, has contributed more to the research of genetics, developmental biology and biomedicine with the development of genome editing techniques. Drosophila genome-editing techniques have evolved from random mutagenesis to precise genome editing and from simple mutant construction to diverse genome editing methods since the 20th century. Chemical mutagenesis, using Ethyl methanesulfonate (EMS), is an important technique to study gene function in forward genetics, however, the precise knockout of Drosophila genes could not be achieved. The gene targeting technology, based on homologous recombination, has accomplished the precise editing of Drosophila genome for the first time, but with low efficiency. The CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein)-mediated precise genome editing is simple, fast and highly efficient compared with the gene targeting technology in Drosophila. In this review, we focus on Drosophila gene knockout, and summarize the evolution of genome editing techniques in Drosophila, emphasizing the development and applications of gene targeting, zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and CRISPR/Cas9 techniques. PMID:26787520

  13. Phenotypic Responses of Differentiated Asthmatic Human Airway Epithelial Cultures to Rhinovirus

    PubMed Central

    Bai, Jianwu; Smock, Steven L.; Jackson, George R.; MacIsaac, Kenzie D.; Huang, Yongsheng; Mankus, Courtney; Oldach, Jonathan; Roberts, Brian; Ma, Yu-Lu; Klappenbach, Joel A.; Crackower, Michael A.; Alves, Stephen E.; Hayden, Patrick J.

    2015-01-01

    Objectives Human airway epithelial cells are the principal target of human rhinovirus (HRV), a common cold pathogen that triggers the majority of asthma exacerbations. The objectives of this study were 1) to evaluate an in vitro air liquid interface cultured human airway epithelial cell model for HRV infection, and 2) to identify gene expression patterns associated with asthma intrinsically and/or after HRV infection using this model. Methods Air-liquid interface (ALI) human airway epithelial cell cultures were prepared from 6 asthmatic and 6 non-asthmatic donors. The effects of rhinovirus RV-A16 on ALI cultures were compared. Genome-wide gene expression changes in ALI cultures following HRV infection at 24 hours post exposure were further analyzed using RNA-seq technology. Cellular gene expression and cytokine/chemokine secretion were further evaluated by qPCR and a Luminex-based protein assay, respectively. Main Results ALI cultures were readily infected by HRV. RNA-seq analysis of HRV infected ALI cultures identified sets of genes associated with asthma specific viral responses. These genes are related to inflammatory pathways, epithelial structure and remodeling and cilium assembly and function, including those described previously (e.g. CCL5, CXCL10 and CX3CL1, MUC5AC, CDHR3), and novel ones that were identified for the first time in this study (e.g. CCRL1). Conclusions ALI-cultured human airway epithelial cells challenged with HRV are a useful translational model for the study of HRV-induced responses in airway epithelial cells, given that gene expression profile using this model largely recapitulates some important patterns of gene responses in patients during clinical HRV infection. Furthermore, our data emphasize that both abnormal airway epithelial structure and inflammatory signaling are two important asthma signatures, which can be further exacerbated by HRV infection. PMID:25706956

  14. What's in a genome? The C-value enigma and the evolution of eukaryotic genome content.

    PubMed

    Elliott, Tyler A; Gregory, T Ryan

    2015-09-26

    Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60,000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of 'complete' genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future. PMID:26323762

  15. Universal genome in the origin of metazoa: thoughts about evolution.

    PubMed

    Sherman, Michael

    2007-08-01

    Recent advances in paleontology, genome analysis, genetics and embryology raise a number of questions about the origin of Animal Kingdom. These questions include:(1) seemingly simultaneous appearance of diverse Metazoan phyla in Cambrian period, (2) similarities of genomes among Metazoan phyla of diverse complexity, (3) seemingly excessive complexity of genomes of lower taxons and (4) similar genetic switches of functionally similar but non-homologous developmental programs. Here I propose an experimentally testable hypothesis of Universal Genome that addresses these questions. According to this model, (a) the Universal Genome that encodes all major developmental programs essential for various phyla of Metazoa emerged in a unicellular or a primitive multicellular organism shortly before the Cambrian period; (b) The Metazoan phyla, all having similar genomes, are nonetheless so distinct because they utilize specific combinations of developmental programs. This model has two major predictions, first that a significant fraction of genetic information in lower taxons must be functionally useless but becomes useful in higher taxons, and second that one should be able to turn on in lower taxons some of the complex latent developmental programs, e.g., a program of eye development or antibody synthesis in sea urchin. An example of natural turning on of a complex latent program in a lower taxon is discussed. PMID:17660714

  16. Endosymbiont evolution: predictions from theory and surprises from genomes.

    PubMed

    Wernegreen, Jennifer J

    2015-12-01

    Genome data have created new opportunities to untangle evolutionary processes shaping microbial variation. Among bacteria, long-term mutualists of insects represent the smallest and (typically) most AT-rich genomes. Evolutionary theory provides a context to predict how an endosymbiotic lifestyle may alter fundamental evolutionary processes-mutation, selection, genetic drift, and recombination-and thus contribute to extreme genomic outcomes. These predictions can then be explored by comparing evolutionary rates, genome size and stability, and base compositional biases across endosymbiotic and free-living bacteria. Recent surprises from such comparisons include genome reduction among uncultured, free-living species. Some studies suggest that selection generally drives this streamlining, while drift drives genome reduction in endosymbionts; however, this remains an hypothesis requiring additional data. Unexpected evidence of selection acting on endosymbiont GC content hints that even weak selection may be effective in some long-term mutualists. Moving forward, intraspecific analysis offers a promising approach to distinguish underlying mechanisms, by testing the null hypothesis of neutrality and by quantifying mutational spectra. Such analyses may clarify whether endosymbionts and free-living bacteria occupy distinct evolutionary trajectories or, alternatively, represent varied outcomes of similar underlying forces. PMID:25866055

  17. Role of transposable elements in genomic rearrangement, evolution, gene regulation and epigenetics in primates.

    PubMed

    Lee, Hee-Eun; Ayarpadikannan, Selvam; Kim, Heui-Soo

    2016-03-23

    The Human Genome Project revealed that almost half of the human genome consists of transposable elements (TEs), which are also abundant in non-human primates. Various studies have confirmed the roles of different TE families in primate evolution. TEs such as endogenous retroviruses (ERVs), long terminal repeats (LTRs), long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) all have numerous effects on the primate genome, including genomic rearrangement, regulatory functions and epigenetic mechanisms. This review offers an overview of research on TEs, including our current understanding of their presence in modern primate lineages, their evolutionary origins, and their regulatory and modifying effects on primate as well as human genomes. The information provided here should be useful for the study of primate genomics. PMID:26781081

  18. Distribution and evolution of cotton fiber development genes in the fibreless Gossypium raimondii genome.

    PubMed

    Xu, Zhanyou; Yu, Jing; Kohel, Russell J; Percy, Richard G; Beavis, William D; Main, Dorrie; Yu, John Z

    2015-07-01

    Cotton fiber represents the largest single cell in plants and they serve as models to study cell development. This study investigated the distribution and evolution of fiber Unigenes anchored to recombination hotspots between tetraploid cotton (Gossypium hirsutum) At and Dt subgenomes, and within a parental diploid cotton (Gossypium raimondii) D genome. Comparative analysis of At vs D and Dt vs D showed that 1) the D genome provides many fiber genes after its merger with another parental diploid cotton (Gossypium arboreum) A genome although the D genome itself does not produce any spinnable fiber; 2) similarity of fiber genes is higher between At vs D than between Dt vs D genomic hotspots. This is the first report that fiber genes have higher similarity between At and D than between Dt and D. The finding provides new insights into cotton genomic regions that would facilitate genetic improvement of natural fiber properties. PMID:25796538

  19. Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.

    PubMed

    Linkeviciute, Viktorija; Rackham, Owen J L; Gough, Julian; Oates, Matt E; Fang, Hai

    2015-12-01

    To help evaluate how protein function impacts on genome evolution, we introduce a new concept of 'architecture plasticity potential' - the capacity to form distinct domain architectures - both for an individual domain, or more generally for a set of domains grouped by shared function. We devise a scoring metric to measure the plasticity potential for these domain sets, and evaluate how function has changed over time for different species. Applying this metric to a phylogenetic tree of eukaryotic genomes, we find that the involvement of each function is not random but highly selective. For certain lineages there is strong bias for evolution to involve domains related to certain functions. In general eukaryotic genomes, particularly animals, expand complex functional activities such as signalling and regulation, but at the cost of reducing metabolic processes. We also observe differential evolution of transcriptional regulation and a unique evolutionary role of channel regulators; crucially this is only observable in terms of the architecture plasticity potential. Our findings provide a new layer of information to understand the significance of function in eukaryotic genome evolution. A web search tool, available at http://supfam.org/Pevo, offers a wide spectrum of options for exploring functional importance in eukaryotic genome evolution. PMID:25980317

  20. Function-selective domain architecture plasticity potentials in eukaryotic genome evolution

    PubMed Central

    Linkeviciute, Viktorija; Rackham, Owen J.L.; Gough, Julian; Oates, Matt E.; Fang, Hai

    2015-01-01

    To help evaluate how protein function impacts on genome evolution, we introduce a new concept of ‘architecture plasticity potential’ – the capacity to form distinct domain architectures – both for an individual domain, or more generally for a set of domains grouped by shared function. We devise a scoring metric to measure the plasticity potential for these domain sets, and evaluate how function has changed over time for different species. Applying this metric to a phylogenetic tree of eukaryotic genomes, we find that the involvement of each function is not random but highly selective. For certain lineages there is strong bias for evolution to involve domains related to certain functions. In general eukaryotic genomes, particularly animals, expand complex functional activities such as signalling and regulation, but at the cost of reducing metabolic processes. We also observe differential evolution of transcriptional regulation and a unique evolutionary role of channel regulators; crucially this is only observable in terms of the architecture plasticity potential. Our findings provide a new layer of information to understand the significance of function in eukaryotic genome evolution. A web search tool, available at http://supfam.org/Pevo, offers a wide spectrum of options for exploring functional importance in eukaryotic genome evolution. PMID:25980317

  1. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

    PubMed

    Kapheim, Karen M; Pan, Hailin; Li, Cai; Salzberg, Steven L; Puiu, Daniela; Magoc, Tanja; Robertson, Hugh M; Hudson, Matthew E; Venkat, Aarti; Fischman, Brielle J; Hernandez, Alvaro; Yandell, Mark; Ence, Daniel; Holt, Carson; Yocum, George D; Kemp, William P; Bosch, Jordi; Waterhouse, Robert M; Zdobnov, Evgeny M; Stolle, Eckart; Kraus, F Bernhard; Helbing, Sophie; Moritz, Robin F A; Glastad, Karl M; Hunt, Brendan G; Goodisman, Michael A D; Hauser, Frank; Grimmelikhuijzen, Cornelis J P; Pinheiro, Daniel Guariz; Nunes, Francis Morais Franco; Soares, Michelle Prioli Miranda; Tanaka, rica Donato; Simes, Zil Luz Paulino; Hartfelder, Klaus; Evans, Jay D; Barribeau, Seth M; Johnson, Reed M; Massey, Jonathan H; Southey, Bruce R; Hasselmann, Martin; Hamacher, Daniel; Biewer, Matthias; Kent, Clement F; Zayed, Amro; Blatti, Charles; Sinha, Saurabh; Johnston, J Spencer; Hanrahan, Shawn J; Kocher, Sarah D; Wang, Jun; Robinson, Gene E; Zhang, Guojie

    2015-06-01

    The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks. PMID:25977371

  2. RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering.

    PubMed

    Si, Tong; Luo, Yunzi; Bao, Zehua; Zhao, Huimin

    2015-03-20

    A fundamental challenge in basic and applied biology is to reprogram cells with improved or novel traits on a genomic scale. However, the current ability to reprogram a cell on the genome scale is limited to bacterial cells. Here, we report RNA interference (RNAi)-assisted genome evolution (RAGE) as a generally applicable method for genome-scale engineering in the yeast Saccharomyces cerevisiae. Through iterative cycles of creating a library of RNAi induced reduction-of-function mutants coupled with high throughput screening or selection, RAGE can continuously improve target trait(s) by accumulating multiplex beneficial genetic modifications in an evolving yeast genome. To validate the RNAi library constructed with yeast genomic DNA and convergent-promoter expression cassette, we demonstrated RNAi screening in Saccharomyces cerevisiae for the first time by identifying two known and three novel suppressors of a telomerase-deficient mutation yku70?. We then showed the application of RAGE for improved acetic acid tolerance, a key trait for microbial production of chemicals and fuels. Three rounds of iterative RNAi screening led to the identification of three gene knockdown targets that acted synergistically to confer an engineered yeast strain with substantially improved acetic acid tolerance. RAGE should greatly accelerate the design and evolution of organisms with desired traits and provide new insights on genome structure, function, and evolution. PMID:24758359

  3. Project 1: Microbial Genomes: A Genomic Approach to Understanding the Evolution of Virulence. Project 2: From Genomes to Life: Drosophilia Development in Space and Time

    SciTech Connect

    Robert DeSalle

    2004-09-10

    This project seeks to use the genomes of two close relatives, A. actinomycetemcomitans and H. aphrophilus, to understand the evolutionary changes that take place in a genome to make it more or less virulent. Our primary specific aim of this project was to sequence, annotate, and analyze the genomes of Actinobacillus actinomycetemcomitans (CU1000, serotype f) and Haemophilus aphrophilus. With these genome sequences we have then compared the whole genome sequences to each other and to the current Aa (HK1651 www.genome.ou.edu) genome project sequence along with other fully sequenced Pasteurellaceae to determine inter and intra species differences that may account for the differences and similarities in disease. We also propose to create and curate a comprehensive database where sequence information and analysis for the Pasteurellaceae (family that includes the genera Actinobacillus and Haemophilus) are readily accessible. And finally we have proposed to develop phylogenetic techniques that can be used to efficiently and accurately examine the evolution of genomes. Below we report on progress we have made on these major specific aims. Progress on the specific aims is reported below under two major headings--experimental approaches and bioinformatics and systematic biology approaches.

  4. Rhinovirus Infection Induces Degradation of Antimicrobial Peptides and Secondary Bacterial Infection in Chronic Obstructive Pulmonary Disease

    PubMed Central

    Mallia, Patrick; Footitt, Joseph; Sotero, Rosa; Jepson, Annette; Contoli, Marco; Trujillo-Torralbo, Maria-Belen; Kebadze, Tatiana; Aniscenko, Julia; Oleszkiewicz, Gregory; Gray, Katrina; Message, Simon D.; Ito, Kazuhiro; Barnes, Peter J.; Adcock, Ian M.; Papi, Alberto; Stanciu, Luminita A.; Elkin, Sarah L.; Kon, Onn M.; Johnson, Malcolm

    2012-01-01

    Rationale: Chronic obstructive pulmonary disease (COPD) exacerbations are associated with virus (mostly rhinovirus) and bacterial infections, but it is not known whether rhinovirus infections precipitate secondary bacterial infections. Objectives: To investigate relationships between rhinovirus infection and bacterial infection and the role of antimicrobial peptides in COPD exacerbations. Methods: We infected subjects with moderate COPD and smokers and nonsmokers with normal lung function with rhinovirus. Induced sputum was collected before and repeatedly after rhinovirus infection and virus and bacterial loads measured with quantitative polymerase chain reaction and culture. The antimicrobial peptides secretory leukoprotease inhibitor (SLPI), elafin, pentraxin, LL-37, α-defensins and β-defensin-2, and the protease neutrophil elastase were measured in sputum supernatants. Measurements and Main Results: After rhinovirus infection, secondary bacterial infection was detected in 60% of subjects with COPD, 9.5% of smokers, and 10% of nonsmokers (P < 0.001). Sputum virus load peaked on Days 5–9 and bacterial load on Day 15. Sputum neutrophil elastase was significantly increased and SLPI and elafin significantly reduced after rhinovirus infection exclusively in subjects with COPD with secondary bacterial infections, and SLPI and elafin levels correlated inversely with bacterial load. Conclusions: Rhinovirus infections are frequently followed by secondary bacterial infections in COPD and cleavage of the antimicrobial peptides SLPI and elafin by virus-induced neutrophil elastase may precipitate these secondary bacterial infections. Therapy targeting neutrophil elastase or enhancing innate immunity may be useful novel therapies for prevention of secondary bacterial infections in virus-induced COPD exacerbations. PMID:23024024

  5. Role of Rhinovirus C in Apparently Life-Threatening Events in Infants, Spain

    PubMed Central

    Garca, M. Luz; Pozo, Francisco; Reyes, Noelia; Prez-Brea, Pilar; Casas, Inmaculada

    2009-01-01

    To assess whether infants hospitalized after an apparently life-threatening event had an associated respiratory virus infection, we analyzed nasopharyngeal aspirates from 16 patients. Nine of 11 infants with positive virus results were infected by rhinoviruses. We detected the new genogroup of rhinovirus C in 6 aspirates. PMID:19788827

  6. Evidence of nosocomial transmission of human rhinovirus in a neonatal intensive care unit.

    PubMed

    Reese, Sara M; Thompson, Meredyth; Price, Connie S; Young, Heather L

    2016-03-01

    Nosocomial respiratory infections cause significant morbidity and mortality, especially among the extremely susceptible neonatal population. Human rhinovirus C is a common viral respiratory illness that causes significant complications in children <2 years old. We describe a nosocomial outbreak of human rhinovirus C in a level II-III neonatal intensive care unit in an urban public safety net hospital. PMID:26775935

  7. When parasitic wasps hijacked viruses: genomic and functional evolution of polydnaviruses.

    PubMed

    Herniou, Elisabeth A; Huguet, Elisabeth; Thz, Julien; Bzier, Annie; Periquet, Georges; Drezen, Jean-Michel

    2013-09-19

    The Polydnaviridae (PDV), including the Bracovirus (BV) and Ichnovirus genera, originated from the integration of unrelated viruses in the genomes of two parasitoid wasp lineages, in a remarkable example of convergent evolution. Functionally active PDVs represent the most compelling evolutionary success among endogenous viral elements (EVEs). BV evolved from the domestication by braconid wasps of a nudivirus 100 Ma. The nudivirus genome has become an EVE involved in BV particle production but is not encapsidated. Instead, BV genomes have co-opted virulence genes, used by the wasps to control the immunity and development of their hosts. Gene transfers and duplications have shaped BV genomes, now encoding hundreds of genes. Phylogenomic studies suggest that BVs contribute largely to wasp diversification and adaptation to their hosts. A genome evolution model explains how multidirectional wasp adaptation to different host species could have fostered PDV genome extension. Integrative studies linking ecological data on the wasp to genomic analyses should provide new insights into the adaptive role of particular BV genes. Forthcoming genomic advances should also indicate if the associations between endoparasitoid wasps and symbiotic viruses evolved because of their particularly intimate interactions with their hosts, or if similar domesticated EVEs could be uncovered in other parasites. PMID:23938758

  8. Association of Intron Loss with High Mutation Rate in Arabidopsis: Implications for Genome Size Evolution

    PubMed Central

    Yang, Yu-Fei; Zhu, Tao; Niu, Deng-Ke

    2013-01-01

    Despite the prevalence of intron losses during eukaryotic evolution, the selective forces acting on them have not been extensively explored. Arabidopsis thaliana lost half of its genome and experienced an elevated rate of intron loss after diverging from A. lyrata. The selective force for genome reduction was suggested to have driven the intron loss. However, the evolutionary mechanism of genome reduction is still a matter of debate. In this study, we found that intron-lost genes have high synonymous substitution rates. Assuming that differences in mutability among different introns are conserved among closely related species, we used the nucleotide substitution rate between orthologous introns in other species as the proxy of the mutation rate of Arabidopsis introns, either lost or extant. The lost introns were found to have higher mutation rates than extant introns. At the genome-wide level, A. thaliana has a higher mutation rate than A. lyrata, which correlates with the higher rate of intron loss and rapid genome reduction of A. thaliana. Our results indicate that selection to minimize mutational hazards might be the selective force for intron loss, and possibly also for genome reduction, in the evolution of A. thaliana. Small genome size and lower genome-wide intron density were widely reported to be correlated with phenotypic features, such as high metabolic rates and rapid growth. We argue that the mutational-hazard hypothesis is compatible with these correlations, by suggesting that selection for rapid growth might indirectly increase mutational hazards. PMID:23516254

  9. Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates

    PubMed Central

    Spring-Pearson, Senanu M.; Stone, Joshua K.; Doyle, Adina; Allender, Christopher J.; Okinaka, Richard T.; Mayo, Mark; Broomall, Stacey M.; Hill, Jessica M.; Karavis, Mark A.; Hubbard, Kyle S.; Insalaco, Joseph M.; McNew, Lauren A.; Rosenzweig, C. Nicole; Gibbons, Henry S.; Currie, Bart J.; Wagner, David M.; Keim, Paul; Tuanyok, Apichai

    2015-01-01

    The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is ‘open’, with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order. PMID:26484663

  10. Dynamics of genome evolution in facultative symbionts of aphids

    PubMed Central

    Degnan, Patrick H; Leonardo, Teresa E; Cass, Bodil N; Hurwitz, Bonnie; Stern, David; Gibbs, Richard A; Richards, Stephen; Moran, Nancy A

    2010-01-01

    Aphids are sap-feeding insects that host a range of bacterial endosymbionts including the obligate, nutritional mutualist Buchnera plus several bacteria that are not required for host survival. Among the latter, Candidatus Regiella insecticola and Candidatus Hamiltonella defensa are found in pea aphids and other hosts and have been shown to protect aphids from natural enemies. We have sequenced almost the entire genome of R. insecticola (2.07 Mbp) and compared it with the recently published genome of H. defensa (2.11 Mbp). Despite being sister species the two genomes are highly rearranged and the genomes only have ?55% of genes in common. The functions encoded by the shared genes imply that the bacteria have similar metabolic capabilities, including only two essential amino acid biosynthetic pathways and active uptake mechanisms for the remaining eight, and similar capacities for host cell toxicity and invasion (type 3 secretion systems and RTX toxins). These observations, combined with high sequence divergence of orthologues, strongly suggest an ancient divergence after establishment of a symbiotic lifestyle. The divergence in gene sets and in genome architecture implies a history of rampant recombination and gene inactivation and the ongoing integration of mobile DNA (insertion sequence elements, prophage and plasmids). PMID:21966902

  11. The pineapple genome and the evolution of CAM photosynthesis.

    PubMed

    Ming, Ray; VanBuren, Robert; Wai, Ching Man; Tang, Haibao; Schatz, Michael C; Bowers, John E; Lyons, Eric; Wang, Ming-Li; Chen, Jung; Biggers, Eric; Zhang, Jisen; Huang, Lixian; Zhang, Lingmao; Miao, Wenjing; Zhang, Jian; Ye, Zhangyao; Miao, Chenyong; Lin, Zhicong; Wang, Hao; Zhou, Hongye; Yim, Won C; Priest, Henry D; Zheng, Chunfang; Woodhouse, Margaret; Edger, Patrick P; Guyot, Romain; Guo, Hao-Bo; Guo, Hong; Zheng, Guangyong; Singh, Ratnesh; Sharma, Anupma; Min, Xiangjia; Zheng, Yun; Lee, Hayan; Gurtowski, James; Sedlazeck, Fritz J; Harkess, Alex; McKain, Michael R; Liao, Zhenyang; Fang, Jingping; Liu, Juan; Zhang, Xiaodan; Zhang, Qing; Hu, Weichang; Qin, Yuan; Wang, Kai; Chen, Li-Yu; Shirley, Neil; Lin, Yann-Rong; Liu, Li-Yu; Hernandez, Alvaro G; Wright, Chris L; Bulone, Vincent; Tuskan, Gerald A; Heath, Katy; Zee, Francis; Moore, Paul H; Sunkar, Ramanjulu; Leebens-Mack, James H; Mockler, Todd; Bennetzen, Jeffrey L; Freeling, Michael; Sankoff, David; Paterson, Andrew H; Zhu, Xinguang; Yang, Xiaohan; Smith, J Andrew C; Cushman, John C; Paull, Robert E; Yu, Qingyi

    2015-12-01

    Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication. PMID:26523774

  12. Evolution and Diversity in Human Herpes Simplex Virus Genomes

    PubMed Central

    Gatherer, Derek; Ochoa, Alejandro; Greenbaum, Benjamin; Dolan, Aidan; Bowden, Rory J.; Enquist, Lynn W.; Legendre, Matthieu; Davison, Andrew J.

    2014-01-01

    Herpes simplex virus 1 (HSV-1) causes a chronic, lifelong infection in >60% of adults. Multiple recent vaccine trials have failed, with viral diversity likely contributing to these failures. To understand HSV-1 diversity better, we comprehensively compared 20 newly sequenced viral genomes from China, Japan, Kenya, and South Korea with six previously sequenced genomes from the United States, Europe, and Japan. In this diverse collection of passaged strains, we found that one-fifth of the newly sequenced members share a gene deletion and one-third exhibit homopolymeric frameshift mutations (HFMs). Individual strains exhibit genotypic and potential phenotypic variation via HFMs, deletions, short sequence repeats, and single-nucleotide polymorphisms, although the protein sequence identity between strains exceeds 90% on average. In the first genome-scale analysis of positive selection in HSV-1, we found signs of selection in specific proteins and residues, including the fusion protein glycoprotein H. We also confirmed previous results suggesting that recombination has occurred with high frequency throughout the HSV-1 genome. Despite this, the HSV-1 strains analyzed clustered by geographic origin during whole-genome distance analysis. These data shed light on likely routes of HSV-1 adaptation to changing environments and will aid in the selection of vaccine antigens that are invariant worldwide. PMID:24227835

  13. Genome analysis of the platypus reveals unique signatures of evolution

    PubMed Central

    Warren, Wesley C.; Hillier, LaDeana W.; Marshall Graves, Jennifer A.; Birney, Ewan; Ponting, Chris P.; Grtzner, Frank; Belov, Katherine; Miller, Webb; Clarke, Laura; Chinwalla, Asif T.; Yang, Shiaw-Pyng; Heger, Andreas; Locke, Devin P.; Miethke, Pat; Waters, Paul D.; Veyrunes, Frdric; Fulton, Lucinda; Fulton, Bob; Graves, Tina; Wallis, John; Puente, Xose S.; Lpez-Otn, Carlos; Ordez, Gonzalo R.; Eichler, Evan E.; Chen, Lin; Cheng, Ze; Deakin, Janine E.; Alsop, Amber; Thompson, Katherine; Kirby, Patrick; Papenfuss, Anthony T.; Wakefield, Matthew J.; Olender, Tsviya; Lancet, Doron; Huttley, Gavin A.; Smit, Arian F. A.; Pask, Andrew; Temple-Smith, Peter; Batzer, Mark A.; Walker, Jerilyn A.; Konkel, Miriam K.; Harris, Robert S.; Whittington, Camilla M.; Wong, Emily S. W.; Gemmell, Neil J.; Buschiazzo, Emmanuel; Vargas Jentzsch, Iris M.; Merkel, Angelika; Schmitz, Juergen; Zemann, Anja; Churakov, Gennady; Kriegs, Jan Ole; Brosius, Juergen; Murchison, Elizabeth P.; Sachidanandam, Ravi; Smith, Carly; Hannon, Gregory J.; Tsend-Ayush, Enkhjargal; McMillan, Daniel; Attenborough, Rosalind; Rens, Willem; Ferguson-Smith, Malcolm; Lefvre, Christophe M.; Sharp, Julie A.; Nicholas, Kevin R.; Ray, David A.; Kube, Michael; Reinhardt, Richard; Pringle, Thomas H.; Taylor, James; Jones, Russell C.; Nixon, Brett; Dacheux, Jean-Louis; Niwa, Hitoshi; Sekita, Yoko; Huang, Xiaoqiu; Stark, Alexander; Kheradpour, Pouya; Kellis, Manolis; Flicek, Paul; Chen, Yuan; Webber, Caleb; Hardison, Ross; Nelson, Joanne; Hallsworth-Pepin, Kym; Delehaunty, Kim; Markovic, Chris; Minx, Pat; Feng, Yucheng; Kremitzki, Colin; Mitreva, Makedonka; Glasscock, Jarret; Wylie, Todd; Wohldmann, Patricia; Thiru, Prathapan; Nhan, Michael N.; Pohl, Craig S.; Smith, Scott M.; Hou, Shunfeng; Renfree, Marilyn B.; Mardis, Elaine R.; Wilson, Richard K.

    2009-01-01

    We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation. PMID:18464734

  14. Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration

    PubMed Central

    Liu, Yan; Zhou, Qian; Wang, Yongjun; Luo, Longhai; Yang, Jian; Yang, Linfeng; Liu, Mei; Li, Yingrui; Qian, Tianmei; Zheng, Yuan; Li, Meiyuan; Li, Jiang; Gu, Yun; Han, Zujing; Xu, Man; Wang, Yingjie; Zhu, Changlai; Yu, Bin; Yang, Yumin; Ding, Fei; Jiang, Jianping; Yang, Huanming; Gu, Xiaosong

    2015-01-01

    Reptiles are the most morphologically and physiologically diverse tetrapods, and have undergone 300 million years of adaptive evolution. Within the reptilian tetrapods, geckos possess several interesting features, including the ability to regenerate autotomized tails and to climb on smooth surfaces. Here we sequence the genome of Gekko japonicus (Schlegel's Japanese Gecko) and investigate genetic elements related to its physiology. We obtain a draft G. japonicus genome sequence of 2.55 Gb and annotated 22,487 genes. Comparative genomic analysis reveals specific gene family expansions or reductions that are associated with the formation of adhesive setae, nocturnal vision and tail regeneration, as well as the diversification of olfactory sensation. The obtained genomic data provide robust genetic evidence of adaptive evolution in reptiles. PMID:26598231

  15. The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization.

    PubMed

    Luo, Yi-Jyun; Takeuchi, Takeshi; Koyanagi, Ryo; Yamada, Lixy; Kanda, Miyuki; Khalturina, Mariia; Fujie, Manabu; Yamasaki, Shin-ichi; Endo, Kazuyoshi; Satoh, Noriyuki

    2015-01-01

    The evolutionary origins of lingulid brachiopods and their calcium phosphate shells have been obscure. Here we decode the 425-Mb genome of Lingula anatina to gain insights into brachiopod evolution. Comprehensive phylogenomic analyses place Lingula close to molluscs, but distant from annelids. The Lingula gene number has increased to ?34,000 by extensive expansion of gene families. Although Lingula and vertebrates have superficially similar hard tissue components, our genomic, transcriptomic and proteomic analyses show that Lingula lacks genes involved in bone formation, indicating an independent origin of their phosphate biominerals. Several genes involved in Lingula shell formation are shared by molluscs. However, Lingula has independently undergone domain combinations to produce shell matrix collagens with EGF domains and carries lineage-specific shell matrix proteins. Gene family expansion, domain shuffling and co-option of genes appear to be the genomic background of Lingula's unique biomineralization. This Lingula genome provides resources for further studies of lophotrochozoan evolution. PMID:26383154

  16. The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution

    PubMed Central

    Elsik, Christine G.; Tellam, Ross L.; Worley, Kim C.

    2010-01-01

    To understand the biology and evolution of ruminants, the cattle genome was sequenced to ∼7× coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1,217 are absent or undetected in non-eutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides an enabling resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production. PMID:19390049

  17. The genome sequence of taurine cattle: a window to ruminant biology and evolution.

    PubMed

    Elsik, Christine G; Tellam, Ross L; Worley, Kim C; Gibbs, Richard A; Muzny, Donna M; Weinstock, George M; Adelson, David L; Eichler, Evan E; Elnitski, Laura; Guig, Roderic; Hamernik, Debora L; Kappes, Steve M; Lewin, Harris A; Lynn, David J; Nicholas, Frank W; Reymond, Alexandre; Rijnkels, Monique; Skow, Loren C; Zdobnov, Evgeny M; Schook, Lawrence; Womack, James; Alioto, Tyler; Antonarakis, Stylianos E; Astashyn, Alex; Chapple, Charles E; Chen, Hsiu-Chuan; Chrast, Jacqueline; Cmara, Francisco; Ermolaeva, Olga; Henrichsen, Charlotte N; Hlavina, Wratko; Kapustin, Yuri; Kiryutin, Boris; Kitts, Paul; Kokocinski, Felix; Landrum, Melissa; Maglott, Donna; Pruitt, Kim; Sapojnikov, Victor; Searle, Stephen M; Solovyev, Victor; Souvorov, Alexandre; Ucla, Catherine; Wyss, Carine; Anzola, Juan M; Gerlach, Daniel; Elhaik, Eran; Graur, Dan; Reese, Justin T; Edgar, Robert C; McEwan, John C; Payne, Gemma M; Raison, Joy M; Junier, Thomas; Kriventseva, Evgenia V; Eyras, Eduardo; Plass, Mireya; Donthu, Ravikiran; Larkin, Denis M; Reecy, James; Yang, Mary Q; Chen, Lin; Cheng, Ze; Chitko-McKown, Carol G; Liu, George E; Matukumalli, Lakshmi K; Song, Jiuzhou; Zhu, Bin; Bradley, Daniel G; Brinkman, Fiona S L; Lau, Lilian P L; Whiteside, Matthew D; Walker, Angela; Wheeler, Thomas T; Casey, Theresa; German, J Bruce; Lemay, Danielle G; Maqbool, Nauman J; Molenaar, Adrian J; Seo, Seongwon; Stothard, Paul; Baldwin, Cynthia L; Baxter, Rebecca; Brinkmeyer-Langford, Candice L; Brown, Wendy C; Childers, Christopher P; Connelley, Timothy; Ellis, Shirley A; Fritz, Krista; Glass, Elizabeth J; Herzig, Carolyn T A; Iivanainen, Antti; Lahmers, Kevin K; Bennett, Anna K; Dickens, C Michael; Gilbert, James G R; Hagen, Darren E; Salih, Hanni; Aerts, Jan; Caetano, Alexandre R; Dalrymple, Brian; Garcia, Jose Fernando; Gill, Clare A; Hiendleder, Stefan G; Memili, Erdogan; Spurlock, Diane; Williams, John L; Alexander, Lee; Brownstein, Michael J; Guan, Leluo; Holt, Robert A; Jones, Steven J M; Marra, Marco A; Moore, Richard; Moore, Stephen S; Roberts, Andy; Taniguchi, Masaaki; Waterman, Richard C; Chacko, Joseph; Chandrabose, Mimi M; Cree, Andy; Dao, Marvin Diep; Dinh, Huyen H; Gabisi, Ramatu Ayiesha; Hines, Sandra; Hume, Jennifer; Jhangiani, Shalini N; Joshi, Vandita; Kovar, Christie L; Lewis, Lora R; Liu, Yih-Shin; Lopez, John; Morgan, Margaret B; Nguyen, Ngoc Bich; Okwuonu, Geoffrey O; Ruiz, San Juana; Santibanez, Jireh; Wright, Rita A; Buhay, Christian; Ding, Yan; Dugan-Rocha, Shannon; Herdandez, Judith; Holder, Michael; Sabo, Aniko; Egan, Amy; Goodell, Jason; Wilczek-Boney, Katarzyna; Fowler, Gerald R; Hitchens, Matthew Edward; Lozado, Ryan J; Moen, Charles; Steffen, David; Warren, James T; Zhang, Jingkun; Chiu, Readman; Schein, Jacqueline E; Durbin, K James; Havlak, Paul; Jiang, Huaiyang; Liu, Yue; Qin, Xiang; Ren, Yanru; Shen, Yufeng; Song, Henry; Bell, Stephanie Nicole; Davis, Clay; Johnson, Angela Jolivet; Lee, Sandra; Nazareth, Lynne V; Patel, Bella Mayurkumar; Pu, Ling-Ling; Vattathil, Selina; Williams, Rex Lee; Curry, Stacey; Hamilton, Cerissa; Sodergren, Erica; Wheeler, David A; Barris, Wes; Bennett, Gary L; Eggen, Andr; Green, Ronnie D; Harhay, Gregory P; Hobbs, Matthew; Jann, Oliver; Keele, John W; Kent, Matthew P; Lien, Sigbjrn; McKay, Stephanie D; McWilliam, Sean; Ratnakumar, Abhirami; Schnabel, Robert D; Smith, Timothy; Snelling, Warren M; Sonstegard, Tad S; Stone, Roger T; Sugimoto, Yoshikazu; Takasuga, Akiko; Taylor, Jeremy F; Van Tassell, Curtis P; Macneil, Michael D; Abatepaulo, Antonio R R; Abbey, Colette A; Ahola, Virpi; Almeida, Iassudara G; Amadio, Ariel F; Anatriello, Elen; Bahadue, Suria M; Biase, Fernando H; Boldt, Clayton R; Carroll, Jeffery A; Carvalho, Wanessa A; Cervelatti, Eliane P; Chacko, Elsa; Chapin, Jennifer E; Cheng, Ye; Choi, Jungwoo; Colley, Adam J; de Campos, Tatiana A; De Donato, Marcos; Santos, Isabel K F de Miranda; de Oliveira, Carlo J F; Deobald, Heather; Devinoy, Eve; Donohue, Kaitlin E; Dovc, Peter; Eberlein, Annett; Fitzsimmons, Carolyn J; Franzin, Alessandra M; Garcia, Gustavo R; Genini, Sem; Gladney, Cody J; Grant, Jason R; Greaser, Marion L; Green, Jonathan A; Hadsell, Darryl L; Hakimov, Hatam A; Halgren, Rob; Harrow, Jennifer L; Hart, Elizabeth A; Hastings, Nicola; Hernandez, Marta; Hu, Zhi-Liang; Ingham, Aaron; Iso-Touru, Terhi; Jamis, Catherine; Jensen, Kirsty; Kapetis, Dimos; Kerr, Tovah; Khalil, Sari S; Khatib, Hasan; Kolbehdari, Davood; Kumar, Charu G; Kumar, Dinesh; Leach, Richard; Lee, Justin C-M; Li, Changxi; Logan, Krystin M; Malinverni, Roberto; Marques, Elisa; Martin, William F; Martins, Natalia F; Maruyama, Sandra R; Mazza, Raffaele; McLean, Kim L; Medrano, Juan F; Moreno, Barbara T; Mor, Daniela D; Muntean, Carl T; Nandakumar, Hari P; Nogueira, Marcelo F G; Olsaker, Ingrid; Pant, Sameer D; Panzitta, Francesca; Pastor, Rosemeire C P; Poli, Mario A; Poslusny, Nathan; Rachagani, Satyanarayana; Ranganathan, Shoba; Razpet, Andrej; Riggs, Penny K; Rincon, Gonzalo; Rodriguez-Osorio, Nelida; Rodriguez-Zas, Sandra L; Romero, Natasha E; Rosenwald, Anne; Sando, Lillian; Schmutz, Sheila M; Shen, Libing; Sherman, Laura; Southey, Bruce R; Lutzow, Ylva Strandberg; Sweedler, Jonathan V; Tammen, Imke; Telugu, Bhanu Prakash V L; Urbanski, Jennifer M; Utsunomiya, Yuri T; Verschoor, Chris P; Waardenberg, Ashley J; Wang, Zhiquan; Ward, Robert; Weikard, Rosemarie; Welsh, Thomas H; White, Stephen N; Wilming, Laurens G; Wunderlich, Kris R; Yang, Jianqi; Zhao, Feng-Qi

    2009-04-24

    To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production. PMID:19390049

  18. Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration.

    PubMed

    Liu, Yan; Zhou, Qian; Wang, Yongjun; Luo, Longhai; Yang, Jian; Yang, Linfeng; Liu, Mei; Li, Yingrui; Qian, Tianmei; Zheng, Yuan; Li, Meiyuan; Li, Jiang; Gu, Yun; Han, Zujing; Xu, Man; Wang, Yingjie; Zhu, Changlai; Yu, Bin; Yang, Yumin; Ding, Fei; Jiang, Jianping; Yang, Huanming; Gu, Xiaosong

    2015-01-01

    Reptiles are the most morphologically and physiologically diverse tetrapods, and have undergone 300 million years of adaptive evolution. Within the reptilian tetrapods, geckos possess several interesting features, including the ability to regenerate autotomized tails and to climb on smooth surfaces. Here we sequence the genome of Gekko japonicus (Schlegel's Japanese Gecko) and investigate genetic elements related to its physiology. We obtain a draft G. japonicus genome sequence of 2.55 Gb and annotated 22,487 genes. Comparative genomic analysis reveals specific gene family expansions or reductions that are associated with the formation of adhesive setae, nocturnal vision and tail regeneration, as well as the diversification of olfactory sensation. The obtained genomic data provide robust genetic evidence of adaptive evolution in reptiles. PMID:26598231

  19. The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization

    PubMed Central

    Luo, Yi-Jyun; Takeuchi, Takeshi; Koyanagi, Ryo; Yamada, Lixy; Kanda, Miyuki; Khalturina, Mariia; Fujie, Manabu; Yamasaki, Shin-ichi; Endo, Kazuyoshi; Satoh, Noriyuki

    2015-01-01

    The evolutionary origins of lingulid brachiopods and their calcium phosphate shells have been obscure. Here we decode the 425-Mb genome of Lingula anatina to gain insights into brachiopod evolution. Comprehensive phylogenomic analyses place Lingula close to molluscs, but distant from annelids. The Lingula gene number has increased to ∼34,000 by extensive expansion of gene families. Although Lingula and vertebrates have superficially similar hard tissue components, our genomic, transcriptomic and proteomic analyses show that Lingula lacks genes involved in bone formation, indicating an independent origin of their phosphate biominerals. Several genes involved in Lingula shell formation are shared by molluscs. However, Lingula has independently undergone domain combinations to produce shell matrix collagens with EGF domains and carries lineage-specific shell matrix proteins. Gene family expansion, domain shuffling and co-option of genes appear to be the genomic background of Lingula's unique biomineralization. This Lingula genome provides resources for further studies of lophotrochozoan evolution. PMID:26383154

  20. Host imprints on bacterial genomes--rapid, divergent evolution in individual patients.

    PubMed

    Zdziarski, Jaroslaw; Brzuszkiewicz, Elzbieta; Wullt, Björn; Liesegang, Heiko; Biran, Dvora; Voigt, Birgit; Grönberg-Hernandez, Jenny; Ragnarsdottir, Bryndis; Hecker, Michael; Ron, Eliora Z; Daniel, Rolf; Gottschalk, Gerhard; Hacker, Jörg; Svanborg, Catharina; Dobrindt, Ulrich

    2010-01-01

    Bacteria lose or gain genetic material and through selection, new variants become fixed in the population. Here we provide the first, genome-wide example of a single bacterial strain's evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora. By first obtaining the complete genome sequence of the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its descendants after therapeutic bladder colonization of different patients, we identified 34 mutations, which affected metabolic and virulence-related genes. Further transcriptome and proteome analysis proved that these genome changes altered bacterial gene expression resulting in unique adaptation patterns in each patient. Our results provide evidence that, in addition to stochastic events, adaptive bacterial evolution is driven by individual host environments. Ongoing loss of gene function supports the hypothesis that evolution towards commensalism rather than virulence is favored during asymptomatic bladder colonization. PMID:20865122

  1. A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments

    PubMed Central

    Bentkowski, Piotr; Van Oosterhout, Cock; Mock, Thomas

    2015-01-01

    Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand how organisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results show that a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt. PMID:26242601

  2. Genome size reduction can trigger rapid phenotypic evolution in invasive plants

    PubMed Central

    Lavergne, Sbastien; Muenke, Nikolas J.; Molofsky, Jane

    2010-01-01

    Background and Aims The study of rapid evolution in invasive species has highlighted the fundamental role played by founder events, emergence of genetic novelties through recombination and rapid response to new selective pressures. However, whether rapid adaptation of introduced species can be driven by punctual changes in genome organization has received little attention. In plants, variation in genome size, i.e. variation in the amount of DNA per monoploid set of chromosomes through loss or gain of repeated DNA sequences, is known to influence a number of physiological, phenological and life-history features. The present study investigated whether change in genome size has contributed to the evolution of greater potential of vegetative growth in invasive populations of an introduced grass. Methods The study was based on the recent demonstration that invasive genotypes of reed canarygrass (Phalaris arundinacea) occurring in North America have emerged from recombination between introduced European strains. The genome sizes of more than 200 invasive and native genotypes were measured and their genome size was related to their phenotypic traits measured in a common glasshouse environment. Population genetics data were used to infer phylogeographical relationships between study populations, and the evolutionary history of genome size within the study species was inferred. Key Results Invasive genotypes had a smaller genome than European native genotypes from which they are derived. This smaller genome size had phenotypic effects that increased the species' invasive potential, including a higher early growth rate, due to a negative relationship between genome size and rate of stem elongation. Based on inferred phylogeographical relationships of invasive and native populations, evolutionary models were consistent with a scenario of genome reduction by natural selection during the invasion process, rather than a scenario of stochastic change. Conclusions Punctual reduction in genome size could cause rapid changes in key phenotypic traits that enhance invasive ability. Although the generality of genome size variation leading to phenotypic evolution and the specific genomic mechanisms involved are not known, change in genome size may constitute an important but previously under-appreciated mechanism of rapid evolutionary change that may promote evolutionary novelties over short time scales. PMID:19887472

  3. The tomato genome sequence provides insights into fleshy fruit evolution.

    PubMed

    2012-05-31

    Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness. PMID:22660326

  4. Biology, genome organization and evolution of parvoviruses in marine shrimp

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A number of parvoviruses are now know to infect marine shrimp, and these viruses alone or in combination with other viruses have the potential to cause major losses in shrimp aquaculture globally. This review provides a comprehensive overview of the biology, genome organization, gene expression, and...

  5. Phylogenomics of the Zygomycete lineages: Exploring phylogeny and genome evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Zygomycete lineages mark the major transition from zoosporic life histories of the common ancestors of Fungi and the earliest diverging chytrid lineages (Chytridiomycota and Blastocladiomycota). Genome comparisons from these lineages may reveal gene content changes that reflect the transition to...

  6. Elephant shark genome provides unique insights into gnathostome evolution.

    PubMed

    Venkatesh, Byrappa; Lee, Alison P; Ravi, Vydianathan; Maurya, Ashish K; Lian, Michelle M; Swann, Jeremy B; Ohta, Yuko; Flajnik, Martin F; Sutoh, Yoichi; Kasahara, Masanori; Hoon, Shawn; Gangu, Vamshidhar; Roy, Scott W; Irimia, Manuel; Korzh, Vladimir; Kondrychyn, Igor; Lim, Zhi Wei; Tay, Boon-Hui; Tohari, Sumanty; Kong, Kiat Whye; Ho, Shufen; Lorente-Galdos, Belen; Quilez, Javier; Marques-Bonet, Tomas; Raney, Brian J; Ingham, Philip W; Tay, Alice; Hillier, LaDeana W; Minx, Patrick; Boehm, Thomas; Wilson, Richard K; Brenner, Sydney; Warren, Wesley C

    2014-01-01

    The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C.?milii genome is the slowest evolving of all known vertebrates, including the 'living fossil' coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class?II molecules. It thus presents a new model for understanding the origin of adaptive immunity. PMID:24402279

  7. The medicago genome provides insight into evolution of rhizobial symbiosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Medicago truncatula is an excellent model for the study of legume-specific biology, especially endosymbiotic interactions with bacteria and fungi. This paper describes the sequence of the euchromatic portion of the M. truncatula genome based on a recently completed BAC-based assembly supplemented by...

  8. Elephant shark genome provides unique insights into gnathostome evolution

    PubMed Central

    Venkatesh, Byrappa; Lee, Alison P.; Ravi, Vydianathan; Maurya, Ashish K.; Lian, Michelle M.; Swann, Jeremy B.; Ohta, Yuko; Flajnik, Martin F.; Sutoh, Yoichi; Kasahara, Masanori; Hoon, Shawn; Gangu, Vamshidhar; Roy, Scott W.; Irimia, Manuel; Korzh, Vladimir; Kondrychyn, Igor; Lim, Zhi Wei; Tay, Boon-Hui; Tohari, Sumanty; Kong, Kiat Whye; Ho, Shufen; Lorente-Galdos, Belen; Quilez, Javier; Marques-Bonet, Tomas; Raney, Brian J.; Ingham, Philip W.; Tay, Alice; Hillier, LaDeana W.; Minx, Patrick; Boehm, Thomas; Wilson, Richard K.; Brenner, Sydney; Warren, Wesley C.

    2014-01-01

    The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the ‘living fossil’ coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity. PMID:24402279

  9. Evolution: a genomic guide to bird population history.

    PubMed

    Toews, David P L

    2015-06-01

    How species responded to the climatic oscillations during the past few million years is debated. A new study analyzing the genomes of 38 bird species finds variable patterns of population growth and declines that broadly correlate with global environmental change. PMID:26035791

  10. EXAMPLES OF GENOME EVOLUTION IN POLYPLIODS WHERE BIGGER IS BETTER

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Polyploids created by different methods exhibit a range of phenotypic changes and highlight the impact of genetic diversity on ornamental plant breeding. The effects of genome doubling are typically highly visible and include larger flowers, short internodes, stronger stems, thicker leaves, and larg...

  11. Down the slippery slope: plastid genome evolution in Convolvulaceae.

    PubMed

    Stefanović, Sasa; Olmstead, Richard G

    2005-09-01

    Cuscuta (dodder) is the only parasitic genus found in Convolvulaceae (morning-glory family). We used long PCR approach to obtain large portions of plastid genome sequence from Cuscuta sandwichiana in order to determine the size, structure, gene content, and synteny in the plastid genome of this Cuscuta species belonging to the poorly investigated holoparasitic subgenus Grammica. These new sequences are compared with the tobacco chloroplast genome, and, where data are available, with corresponding regions from taxa in the other Cuscuta subgenera. When all known plastid genome structural rearrangements in parasitic and nonparasitic Convolvulaceae are considered in a molecular phylogenetic framework, three categories of rearrangements in Cuscuta are revealed: plesiomorphic, autapomorphic, and synapomorphic. Many of the changes in Cuscuta, previously attributed to its parasitic mode of life, are better explained either as plesiomorphic conditions within the family, i.e., conditions shared with the rest of the Convolvulaceae, or, in most cases, autapomorphies of particular Cuscuta taxa, not shared with the rest of the species in the genus. The synapomorphic rearrangements are most likely to correlate with the parasitic lifestyle, because they represent changes found in Cuscuta exclusively. However, it appears that most of the affected regions, belonging to all of these three categories, have probably no function (e.g., introns) or are of unknown function (a number of open reading frames, the function of which, if any, has yet to be discovered). PMID:15999247

  12. Evolution: ctenophore genomes and the origin of neurons.

    PubMed

    Marlow, Heather; Arendt, Detlev

    2014-08-18

    Recent sequencing of ctenophore genomes opens a new era in the study of this unique and phylogenetically distant group. The presence of neurodevelopmental genes, pre- and postsynaptic modules, and transmitter molecules is consistent with a single origin of neurons. PMID:25137591

  13. Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution

    PubMed Central

    Pace, John K.; Sen, Shurjo K.; Batzer, Mark A.; Feschotte, Cdric

    2009-01-01

    DNA double-strand breaks (DSBs) are a common form of cellular damage that can lead to cell death if not repaired promptly. Experimental systems have shown that DSB repair in eukaryotic cells is often imperfect and may result in the insertion of extra chromosomal DNA or the duplication of existing DNA at the breakpoint. These events are thought to be a source of genomic instability and human diseases, but it is unclear whether they have contributed significantly to genome evolution. Here we developed an innovative computational pipeline that takes advantage of the repetitive structure of genomes to detect repair-mediated duplication events (RDs) that occurred in the germline and created insertions of at least 50 bp of genomic DNA. Using this pipeline we identified over 1,000 probable RDs in the human genome. Of these, 824 were intra-chromosomal, closely linked duplications of up to 619 bp bearing the hallmarks of the synthesis-dependent strand-annealing repair pathway. This mechanism has duplicated hundreds of sequences predicted to be functional in the human genome, including exons, UTRs, intron splice sites and transcription factor binding sites. Dating of the duplication events using comparative genomics and experimental validation revealed that the mechanism has operated continuously but with decreasing intensity throughout primate evolution. The mechanism has produced species-specific duplications in all primate species surveyed and is contributing to genomic variation among humans. Finally, we show that RDs have also occurred, albeit at a lower frequency, in non-primate mammals and other vertebrates, indicating that this mechanism has been an important force shaping vertebrate genome evolution. PMID:19424419

  14. Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution.

    PubMed

    Pace, John K; Sen, Shurjo K; Batzer, Mark A; Feschotte, Cdric

    2009-05-01

    DNA double-strand breaks (DSBs) are a common form of cellular damage that can lead to cell death if not repaired promptly. Experimental systems have shown that DSB repair in eukaryotic cells is often imperfect and may result in the insertion of extra chromosomal DNA or the duplication of existing DNA at the breakpoint. These events are thought to be a source of genomic instability and human diseases, but it is unclear whether they have contributed significantly to genome evolution. Here we developed an innovative computational pipeline that takes advantage of the repetitive structure of genomes to detect repair-mediated duplication events (RDs) that occurred in the germline and created insertions of at least 50 bp of genomic DNA. Using this pipeline we identified over 1,000 probable RDs in the human genome. Of these, 824 were intra-chromosomal, closely linked duplications of up to 619 bp bearing the hallmarks of the synthesis-dependent strand-annealing repair pathway. This mechanism has duplicated hundreds of sequences predicted to be functional in the human genome, including exons, UTRs, intron splice sites and transcription factor binding sites. Dating of the duplication events using comparative genomics and experimental validation revealed that the mechanism has operated continuously but with decreasing intensity throughout primate evolution. The mechanism has produced species-specific duplications in all primate species surveyed and is contributing to genomic variation among humans. Finally, we show that RDs have also occurred, albeit at a lower frequency, in non-primate mammals and other vertebrates, indicating that this mechanism has been an important force shaping vertebrate genome evolution. PMID:19424419

  15. Complete Genome Viral Phylogenies Suggests the Concerted Evolution of Regulatory Cores and Accessory Satellites

    PubMed Central

    de Andrade Zanotto, Paolo Marinho; Krakauer, David C.

    2008-01-01

    We consider the concerted evolution of viral genomes in four families of DNA viruses. Given the high rate of horizontal gene transfer among viruses and their hosts, it is an open question as to how representative particular genes are of the evolutionary history of the complete genome. To address the concerted evolution of viral genes, we compared genomic evolution across four distinct, extant viral families. For all four viral families we constructed DNA-dependent DNA polymerase-based (DdDp) phylogenies and in addition, whole genome sequence, as quantitative descriptions of inter-genome relationships. We found that the history of the polymerase gene was highly predictive of the history of the genome as a whole, which we explain in terms of repeated, co-divergence events of the core DdDp gene accompanied by a number of satellite, accessory genetic loci. We also found that the rate of gene gain in baculovirus and poxviruses proceeds significantly more quickly than the rate of gene loss and that there is convergent acquisition of satellite functions promoting contextual adaptation when distinct viral families infect related hosts. The congruence of the genome and polymerase trees suggests that a large set of viral genes, including polymerase, derive from a phylogenetically conserved core of genes of host origin, secondarily reinforced by gene acquisition from common hosts or co-infecting viruses within the host. A single viral genome can be thought of as a mutualistic network, with the core genes acting as an effective host and the satellite genes as effective symbionts. Larger virus genomes show a greater departure from linkage equilibrium between core and satellites functions. PMID:18941535

  16. Distribution and Evolution of Repeated Sequences in Genomes of Triatominae (Hemiptera-Reduviidae) Inferred from Genomic In Situ Hybridization

    PubMed Central

    Pita, Sebastian; Panzera, Francisco; Snchez, Antonio; Panzera, Yanina; Palomeque, Teresa; Lorite, Pedro

    2014-01-01

    The subfamily Triatominae, vectors of Chagas disease, comprises 140 species characterized by a highly homogeneous chromosome number. We analyzed the chromosomal distribution and evolution of repeated sequences in Triatominae genomes by Genomic in situ Hybridization using Triatoma delpontei and Triatoma infestans genomic DNAs as probes. Hybridizations were performed on their own chromosomes and on nine species included in six genera from the two main tribes: Triatomini and Rhodniini. Genomic probes clearly generate two different hybridization patterns, dispersed or accumulated in specific regions or chromosomes. The three used probes generate the same hybridization pattern in each species. However, these patterns are species-specific. In closely related species, the probes strongly hybridized in the autosomal heterochromatic regions, resembling C-banding and DAPI patterns. However, in more distant species these co-localizations are not observed. The heterochromatic Y chromosome is constituted by highly repeated sequences, which is conserved among 10 species of Triatomini tribe suggesting be an ancestral character for this group. However, the Y chromosome in Rhodniini tribe is markedly different, supporting the early evolutionary dichotomy between both tribes. In some species, sex chromosomes and autosomes shared repeated sequences, suggesting meiotic chromatin exchanges among these heterologous chromosomes. Our GISH analyses enabled us to acquire not only reliable information about autosomal repeated sequences distribution but also an insight into sex chromosome evolution in Triatominae. Furthermore, the differentiation obtained by GISH might be a valuable marker to establish phylogenetic relationships and to test the controversial origin of the Triatominae subfamily. PMID:25478792

  17. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes

    PubMed Central

    Cannon, Steven B.; Sterck, Lieven; Rombauts, Stephane; Sato, Shusei; Cheung, Foo; Gouzy, Jérôme; Wang, Xiaohong; Mudge, Joann; Vasdewani, Jayprakash; Schiex, Thomas; Spannagl, Manuel; Monaghan, Erin; Nicholson, Christine; Humphray, Sean J.; Schoof, Heiko; Mayer, Klaus F. X.; Rogers, Jane; Quétier, Francis; Oldroyd, Giles E.; Debellé, Frédéric; Cook, Douglas R.; Retzel, Ernest F.; Roe, Bruce A.; Town, Christopher D.; Tabata, Satoshi; Van de Peer, Yves; Young, Nevin D.

    2006-01-01

    Genome sequencing of the model legumes, Medicago truncatula and Lotus japonicus, provides an opportunity for large-scale sequence-based comparison of two genomes in the same plant family. Here we report synteny comparisons between these species, including details about chromosome relationships, large-scale synteny blocks, microsynteny within blocks, and genome regions lacking clear correspondence. The Lotus and Medicago genomes share a minimum of 10 large-scale synteny blocks, each with substantial collinearity and frequently extending the length of whole chromosome arms. The proportion of genes syntenic and collinear within each synteny block is relatively homogeneous. Medicago–Lotus comparisons also indicate similar and largely homogeneous gene densities, although gene-containing regions in Mt occupy 20–30% more space than Lj counterparts, primarily because of larger numbers of Mt retrotransposons. Because the interpretation of genome comparisons is complicated by large-scale genome duplications, we describe synteny, synonymous substitutions and phylogenetic analyses to identify and date a probable whole-genome duplication event. There is no direct evidence for any recent large-scale genome duplication in either Medicago or Lotus but instead a duplication predating speciation. Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar). PMID:17003129

  18. TALENs-Assisted Multiplex Editing for Accelerated Genome Evolution To Improve Yeast Phenotypes.

    PubMed

    Zhang, Guoqiang; Lin, Yuping; Qi, Xianni; Li, Lin; Wang, Qinhong; Ma, Yanhe

    2015-10-16

    Genome editing is an important tool for building novel genotypes with a desired phenotype. However, the fundamental challenge is to rapidly generate desired alterations on a genome-wide scale. Here, we report TALENs (transcription activator-like effector nucleases)-assisted multiplex editing (TAME), based on the interaction of designed TALENs with the DNA sequences between the critical TATA and GC boxes, for generating multiple targeted genomic modifications. Through iterative cycles of TAME to induce abundant semirational indels coupled with efficient screening using a reporter, the targeted fluorescent trait can be continuously and rapidly improved by accumulating multiplex beneficial genetic modifications in the evolving yeast genome. To further evaluate its efficiency, we also demonstrate the application of TAME for significantly improving ethanol tolerance of yeast in a short amount of time. Therefore, TAME is a broadly generalizable platform for accelerated genome evolution to rapidly improve yeast phenotypes. PMID:26011297

  19. Large-scale trends in the evolution of gene structures within 11 animal genomes.

    PubMed

    Yandell, Mark; Mungall, Chris J; Smith, Chris; Prochnik, Simon; Kaminker, Joshua; Hartzell, George; Lewis, Suzanna; Rubin, Gerald M

    2006-03-01

    We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences of five unannotated Drosophila genomes to survey changes in protein sequence and gene structure over a variety of timescales--from the less than 5 million years since the divergence of D. simulans and D. melanogaster to the more than 500 million years that have elapsed since the Cambrian explosion. To do so, we have developed a new open-source software library called CGL (for "Comparative Genomics Library"). Our results demonstrate that change in intron-exon structure is gradual, clock-like, and largely independent of coding-sequence evolution. This means that genome annotations can be used in new ways to inform, corroborate, and test conclusions drawn from comparative genomics analyses that are based upon protein and nucleotide sequence similarities. PMID:16518452

  20. The genomic impact of 100 million years of social evolution in seven ant species

    PubMed Central

    Gadau, Jürgen; Helmkampf, Martin; Nygaard, Sanne; Roux, Julien; Simola, Daniel F.; Smith, Chris R.; Suen, Garret; Wurm, Yannick; Smith, Christopher D.

    2011-01-01

    Ants (Hymenoptera, Formicidae) represent one of the most successful eusocial taxa in terms of both their geographic distribution and species number. The publication of seven ant genomes within the past year was a quantum leap for socio- and ant genomics. The diversity of social organization in ants makes them excellent model organisms to study the evolution of social systems. Comparing the ant genomes with those of the honeybee, a lineage that evolved eusociality independently from ants, and solitary insects suggests that there are significant differences in key aspects of genome organization between social and solitary insects, as well as among ant species. Altogether, these seven ant genomes open exciting new research avenues and opportunities for understanding the genetic basis and regulation of social species, and adaptive complex systems in general. PMID:21982512

  1. The genomic impact of 100 million years of social evolution in seven ant species.

    PubMed

    Gadau, Jrgen; Helmkampf, Martin; Nygaard, Sanne; Roux, Julien; Simola, Daniel F; Smith, Chris R; Suen, Garret; Wurm, Yannick; Smith, Christopher D

    2012-01-01

    Ants (Hymenoptera, Formicidae) represent one of the most successful eusocial taxa in terms of both their geographic distribution and species number. The publication of seven ant genomes within the past year was a quantum leap for socio- and ant genomics. The diversity of social organization in ants makes them excellent model organisms to study the evolution of social systems. Comparing the ant genomes with those of the honeybee, a lineage that evolved eusociality independently from ants, and solitary insects suggests that there are significant differences in key aspects of genome organization between social and solitary insects, as well as among ant species. Altogether, these seven ant genomes open exciting new research avenues and opportunities for understanding the genetic basis and regulation of social species, and adaptive complex systems in general. PMID:21982512

  2. Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes

    PubMed Central

    Yandell, Mark; Mungall, Chris J; Smith, Chris; Prochnik, Simon; Kaminker, Joshua; Hartzell, George; Lewis, Suzanna; Rubin, Gerald M

    2006-01-01

    We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences of five unannotated Drosophila genomes to survey changes in protein sequence and gene structure over a variety of timescalesfrom the less than 5 million years since the divergence of D. simulans and D. melanogaster to the more than 500 million years that have elapsed since the Cambrian explosion. To do so, we have developed a new open-source software library called CGL (for Comparative Genomics Library). Our results demonstrate that change in intronexon structure is gradual, clock-like, and largely independent of coding-sequence evolution. This means that genome annotations can be used in new ways to inform, corroborate, and test conclusions drawn from comparative genomics analyses that are based upon protein and nucleotide sequence similarities. PMID:16518452

  3. Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution

    PubMed Central

    Yap, Jia-Yee S.; Rohner, Thore; Greenfield, Abigail; Van Der Merwe, Marlien; McPherson, Hannah; Glenn, Wendy; Kornfeld, Geoff; Marendy, Elessa; Pan, Annie Y. H.; Wilkins, Marc R.; Rossetto, Maurizio; Delaney, Sven K.

    2015-01-01

    The Wollemi pine (Wollemia nobilis) is a rare Southern conifer with striking morphological similarity to fossil pines. A small population of W. nobilis was discovered in 1994 in a remote canyon system in the Wollemi National Park (near Sydney, Australia). This population contains fewer than 100 individuals and is critically endangered. Previous genetic studies of the Wollemi pine have investigated its evolutionary relationship with other pines in the family Araucariaceae, and have suggested that the Wollemi pine genome contains little or no variation. However, these studies were performed prior to the widespread use of genome sequencing, and their conclusions were based on a limited fraction of the Wollemi pine genome. In this study, we address this problem by determining the entire sequence of the W. nobilis chloroplast genome. A detailed analysis of the structure of the genome is presented, and the evolution of the genome is inferred by comparison with the chloroplast sequences of other members of the Araucariaceae and the related family Podocarpaceae. Pairwise alignments of whole genome sequences, and the presence of unique pseudogenes, gene duplications and insertions in W. nobilis and Araucariaceae, indicate that the W. nobilis chloroplast genome is most similar to that of its sister taxon Agathis. However, the W. nobilis genome contains an unusually high number of repetitive sequences, and these could be used in future studies to investigate and conserve any remnant genetic diversity in the Wollemi pine. PMID:26061691

  4. Genomic Science in Understanding Cholera Outbreaks and Evolution of Vibrio cholerae as a Human Pathogen

    PubMed Central

    Mekalanos, John J.

    2014-01-01

    Modern genomic and bioinformatic approaches have been applied to interrogate the V. cholerae genome, the role of genomic elements in cholera disease, and the origin, relatedness, and dissemination of epidemic strains. A universal attribute of choleragenic strains includes a repertoire of pathogenicity islands and virulence genes, namely the CTX? prophage and Toxin Co-regulated Pilus (TCP) in addition to other virulent genetic elements including those referred to as Seventh Pandemic Islands. During the last decade, the advent of Next Generation Sequencing (NGS) has provided highly resolved and often complete genomic sequences of epidemic isolates in addition to both clinical and environmental strains isolated from geographically unconnected regions. Genomic comparisons of these strains, as was completed during and following the Haitian outbreak in 2010, reveals that most epidemic strains appear closely related, regardless of region of origin. Non-O1 clinical or environmental strains may also possess some virulence islands, but phylogenic analysis of the core genome suggests they are more diverse and distantly related than those isolated during epidemics. Like Haiti, genomic studies that examine both the Vibrio core- and pan-genome in addition to Single Nucleotide Polymorphisms (SNPs) conclude that a number of epidemics are caused by strains that closely resemble those in Asia, and often appear to originate there and then spread globally. The accumulation of SNPs in the epidemic strains over time can then be applied to better understand the evolution of the V. cholerae genome as an etiological agent. PMID:24590676

  5. Genome Evolution by Matrix Algorithms: Cellular Automata Approach to Population Genetics

    PubMed Central

    Qiu, Shuhao; McSweeny, Andrew; Choulet, Samuel; Saha-Mandal, Arnab; Fedorova, Larisa; Fedorov, Alexei

    2014-01-01

    Mammalian genomes are replete with millions of polymorphic sites, among which those genetic variants that are colocated on the same chromosome and exist close to one another form blocks of closely linked mutations known as haplotypes. The linkage within haplotypes is constantly disrupted due to meiotic recombination events. Whole ensembles of such numerous haplotypes are subjected to evolutionary pressure, where mutations influence each other and should be considered as a whole entitya gigantic matrix, unique for each individual genome. This idea was implemented into a computational approach, named Genome Evolution by Matrix Algorithms (GEMA) to model genomic changes taking into account all mutations in a population. GEMA has been tested for modeling of entire human chromosomes. The program can precisely mimic real biological processes that have influence on genome evolution such as: 1) Authentic arrangements of genes and functional genomic elements, 2) frequencies of various types of mutations in different nucleotide contexts, and 3) nonrandom distribution of meiotic recombination events along chromosomes. Computer modeling with GEMA has demonstrated that the number of meiotic recombination events per gamete is among the most crucial factors influencing population fitness. In humans, these recombinations create a gamete genome consisting on an average of 48 pieces of corresponding parental chromosomes. Such highly mosaic gamete structure allows preserving fitness of population under the intense influx of novel mutations (40 per individual) even when the number of mutations with deleterious effects is up to ten times more abundant than those with beneficial effects. PMID:24723728

  6. Universal features in the genome-level evolution of protein domains

    PubMed Central

    Cosentino Lagomarsino, Marco; Sellerio, Alessandro L; Heijning, Philip D; Bassetti, Bruno

    2009-01-01

    Background Protein domains can be used to study proteome evolution at a coarse scale. In particular, they are found on genomes with notable statistical distributions. It is known that the distribution of domains with a given topology follows a power law. We focus on a further aspect: these distributions, and the number of distinct topologies, follow collective trends, or scaling laws, depending on the total number of domains only, and not on genome-specific features. Results We present a stochastic duplication/innovation model, in the class of the so-called 'Chinese restaurant processes', that explains this observation with two universal parameters, representing a minimal number of domains and the relative weight of innovation to duplication. Furthermore, we study a model variant where new topologies are related to occurrence in genomic data, accounting for fold specificity. Conclusions Both models have general quantitative agreement with data from hundreds of genomes, which indicates that the domains of a genome are built with a combination of specificity and robust self-organizing phenomena. The latter are related to the basic evolutionary 'moves' of duplication and innovation, and give rise to the observed scaling laws, a priori of the specific evolutionary history of a genome. We interpret this as the concurrent effect of neutral and selective drives, which increase duplication and decrease innovation in larger and more complex genomes. The validity of our model would imply that the empirical observation of a small number of folds in nature may be a consequence of their evolution. PMID:19183449

  7. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

    PubMed

    Braasch, Ingo; Gehrke, Andrew R; Smith, Jeramiah J; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M; Campbell, Michael S; Barrell, Daniel; Martin, Kyle J; Mulley, John F; Ravi, Vydianathan; Lee, Alison P; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E G; Sun, Yi; Hertel, Jana; Beam, Michael J; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H; Litman, Gary W; Litman, Ronda T; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F; Wang, Han; Taylor, John S; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M J; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T; Venkatesh, Byrappa; Holland, Peter W H; Guiguen, Yann; Bobe, Julien; Shubin, Neil H; Di Palma, Federica; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H

    2016-04-01

    To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences. PMID:26950095

  8. Insights into Minor Group Rhinovirus Uncoating: The X-ray Structure of the HRV2 Empty Capsid

    PubMed Central

    Garriga, Damià; Pickl-Herk, Angela; Luque, Daniel; Wruss, Jürgen; Castón, José R.; Blaas, Dieter; Verdaguer, Núria

    2012-01-01

    Upon attachment to their respective receptor, human rhinoviruses (HRVs) are internalized into the host cell via different pathways but undergo similar structural changes. This ultimately results in the delivery of the viral RNA into the cytoplasm for replication. To improve our understanding of the conformational modifications associated with the release of the viral genome, we have determined the X-ray structure at 3.0 Å resolution of the end-stage of HRV2 uncoating, the empty capsid. The structure shows important conformational changes in the capsid protomer. In particular, a hinge movement around the hydrophobic pocket of VP1 allows a coordinated shift of VP2 and VP3. This overall displacement forces a reorganization of the inter-protomer interfaces, resulting in a particle expansion and in the opening of new channels in the capsid core. These new breaches in the capsid, opening one at the base of the canyon and the second at the particle two-fold axes, might act as gates for the externalization of the VP1 N-terminus and the extrusion of the viral RNA, respectively. The structural comparison between native and empty HRV2 particles unveils a number of pH-sensitive amino acid residues, conserved in rhinoviruses, which participate in the structural rearrangements involved in the uncoating process. PMID:22241997

  9. Evolution Along the Mutation Gradient in the Dynamic Mitochondrial Genome of Salamanders

    PubMed Central

    Chong, Rebecca A.; Mueller, Rachel Lockridge

    2013-01-01

    Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes. PMID:23918809

  10. Transposable elements play an important role during cotton genome evolution and fiber cell development.

    PubMed

    Wang, Kun; Huang, Gai; Zhu, Yuxian

    2016-02-01

    Transposable elements (TEs) usually occupy largest fractions of plant genome and are also the most variable part of the structure. Although traditionally it is hallmarked as "junk and selfish DNA", today more and more evidence points out TE's participation in gene regulations including gene mutation, duplication, movement and novel gene creation via genetic and epigenetic mechanisms. The recently sequenced genomes of diploid cottons Gossypium arboreum (AA) and Gossypium raimondii (DD) together with their allotetraploid progeny Gossypium hirsutum (AtAtDtDt) provides a unique opportunity to compare genome variations in the Gossypium genus and to analyze the functions of TEs during its evolution. TEs accounted for 57%, 68.5% and 67.2%, respectively in DD, AA and AtAtDtDt genomes. The 1,694 Mb A-genome was found to harbor more LTR(long terminal repeat)-type retrotransposons that made cardinal contributions to the twofold increase in its genome size after evolution from the 775.2 Mb D-genome. Although the 2,173 Mb AtAtDtDt genome showed similar TE content to the A-genome, the total numbers of LTR-gypsy and LTR-copia type TEs varied significantly between these two genomes. Considering their roles on rewiring gene regulatory networks, we believe that TEs may somehow be involved in cotton fiber cell development. Indeed, the insertion or deletion of different TEs in the upstream region of two important transcription factor genes in At or Dt subgenomes resulted in qualitative differences in target gene expression. We suggest that our findings may open a window for improving cotton agronomic traits by editing TE activities. PMID:26687725

  11. Gibbon genome and the fast karyotype evolution of small apes

    PubMed Central

    Carbone, Lucia; Harris, R. Alan; Gnerre, Sante; Veeramah, Krishna R.; Lorente-Galdos, Belen; Huddleston, John; Meyer, Thomas J.; Herrero, Javier; Roos, Christian; Aken, Bronwen; Anaclerio, Fabio; Archidiacono, Nicoletta; Baker, Carl; Barrell, Daniel; Batzer, Mark A.; Beal, Kathryn; Blancher, Antoine; Bohrson, Craig L.; Brameier, Markus; Campbell, Michael S.; Capozzi, Oronzo; Casola, Claudio; Chiatante, Giorgia; Cree, Andrew; Damert, Annette; de Jong, Pieter J.; Dumas, Laura; Fernandez-Callejo, Marcos; Flicek, Paul; Fuchs, Nina V.; Gut, Marta; Gut, Ivo; Hahn, Matthew W.; Hernandez-Rodriguez, Jessica; Hillier, LaDeana W.; Hubley, Robert; Ianc, Bianca; Izsvák, Zsuzsanna; Jablonski, Nina G.; Johnstone, Laurel M.; Karimpour-Fard, Anis; Konkel, Miriam K.; Kostka, Dennis; Lazar, Nathan H.; Lee, Sandra L.; Lewis, Lora R.; Liu, Yue; Locke, Devin P.; Mallick, Swapan; Mendez, Fernando L.; Muffato, Matthieu; Nazareth, Lynne V.; Nevonen, Kimberly A.; O,Bleness, Majesta; Ochis, Cornelia; Odom, Duncan T.; Pollard, Katherine S.; Quilez, Javier; Reich, David; Rocchi, Mariano; Schumann, Gerald G.; Searle, Stephen; Sikela, James M.; Skollar, Gabriella; Smit, Arian; Sonmez, Kemal; Hallers, Boudewijn ten; Terhune, Elizabeth; Thomas, Gregg W.C.; Ullmer, Brygg; Ventura, Mario; Walker, Jerilyn A.; Wall, Jeffrey D.; Walter, Lutz; Ward, Michelle C.; Wheelan, Sarah J.; Whelan, Christopher W.; White, Simon; Wilhelm, Larry J.; Woerner, August E.; Yandell, Mark; Zhu, Baoli; Hammer, Michael F.; Marques-Bonet, Tomas; Eichler, Evan E.; Fulton, Lucinda; Fronick, Catrina; Muzny, Donna M.; Warren, Wesley C.; Worley, Kim C.; Rogers, Jeffrey; Wilson, Richard K.; Gibbs, Richard A.

    2014-01-01

    Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation ~5 million years ago, coincident with major geographical changes in Southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat. PMID:25209798

  12. Gibbon genome and the fast karyotype evolution of small apes.

    PubMed

    Carbone, Lucia; Harris, R Alan; Gnerre, Sante; Veeramah, Krishna R; Lorente-Galdos, Belen; Huddleston, John; Meyer, Thomas J; Herrero, Javier; Roos, Christian; Aken, Bronwen; Anaclerio, Fabio; Archidiacono, Nicoletta; Baker, Carl; Barrell, Daniel; Batzer, Mark A; Beal, Kathryn; Blancher, Antoine; Bohrson, Craig L; Brameier, Markus; Campbell, Michael S; Capozzi, Oronzo; Casola, Claudio; Chiatante, Giorgia; Cree, Andrew; Damert, Annette; de Jong, Pieter J; Dumas, Laura; Fernandez-Callejo, Marcos; Flicek, Paul; Fuchs, Nina V; Gut, Ivo; Gut, Marta; Hahn, Matthew W; Hernandez-Rodriguez, Jessica; Hillier, LaDeana W; Hubley, Robert; Ianc, Bianca; Izsvk, Zsuzsanna; Jablonski, Nina G; Johnstone, Laurel M; Karimpour-Fard, Anis; Konkel, Miriam K; Kostka, Dennis; Lazar, Nathan H; Lee, Sandra L; Lewis, Lora R; Liu, Yue; Locke, Devin P; Mallick, Swapan; Mendez, Fernando L; Muffato, Matthieu; Nazareth, Lynne V; Nevonen, Kimberly A; O'Bleness, Majesta; Ochis, Cornelia; Odom, Duncan T; Pollard, Katherine S; Quilez, Javier; Reich, David; Rocchi, Mariano; Schumann, Gerald G; Searle, Stephen; Sikela, James M; Skollar, Gabriella; Smit, Arian; Sonmez, Kemal; ten Hallers, Boudewijn; Terhune, Elizabeth; Thomas, Gregg W C; Ullmer, Brygg; Ventura, Mario; Walker, Jerilyn A; Wall, Jeffrey D; Walter, Lutz; Ward, Michelle C; Wheelan, Sarah J; Whelan, Christopher W; White, Simon; Wilhelm, Larry J; Woerner, August E; Yandell, Mark; Zhu, Baoli; Hammer, Michael F; Marques-Bonet, Tomas; Eichler, Evan E; Fulton, Lucinda; Fronick, Catrina; Muzny, Donna M; Warren, Wesley C; Worley, Kim C; Rogers, Jeffrey; Wilson, Richard K; Gibbs, Richard A

    2014-09-11

    Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation ?5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat. PMID:25209798

  13. Evolution of pathogenicity and sexual reproduction in eight Candida genomes

    PubMed Central

    Butler, Geraldine; Rasmussen, Matthew D.; Lin, Michael F.; Santos, Manuel A.S.; Sakthikumar, Sharadha; Munro, Carol A.; Rheinbay, Esther; Grabherr, Manfred; Forche, Anja; Reedy, Jennifer L.; Agrafioti, Ino; Arnaud, Martha B.; Bates, Steven; Brown, Alistair J.P.; Brunke, Sascha; Costanzo, Maria C.; Fitzpatrick, David A.; de Groot, Piet W. J.; Harris, David; Hoyer, Lois L.; Hube, Bernhard; Klis, Frans M.; Kodira, Chinnappa; Lennard, Nicola; Logue, Mary E.; Martin, Ronny; Neiman, Aaron M.; Nikolaou, Elissavet; Quail, Michael A.; Quinn, Janet; Santos, Maria C.; Schmitzberger, Florian F.; Sherlock, Gavin; Shah, Prachi; Silverstein, Kevin; Skrzypek, Marek S.; Soll, David; Staggs, Rodney; Stansfield, Ian; Stumpf, Michael P H; Sudbery, Peter E.; Thyagarajan, Srikantha; Zeng, Qiandong; Berman, Judith; Berriman, Matthew; Heitman, Joseph; Gow, Neil A. R.; Lorenz, Michael C.; Birren, Bruce W.; Kellis, Manolis; Cuomo, Christina A.

    2009-01-01

    Candida species are the most common cause of opportunistic fungal infection worldwide. We report the genome sequences of six Candida species and compare these and related pathogens and nonpathogens. There are significant expansions of cell wall, secreted, and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the Mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/alpha2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine to serine genetic code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the C. albicans gene catalog, identifying many new genes. PMID:19465905

  14. Decoding the molecular evolution of human cognition using comparative genomics

    PubMed Central

    Usui, Noriyoshi; Co, Marissa; Konopka, Genevieve

    2014-01-01

    Identification of genetic and molecular factors responsible for the specialized cognitive abilities of humans is expected to provide important insights into the mechanisms responsible for disorders of cognition such as autism, schizophrenia, and Alzheimer’s disease. Here, we discuss the use of comparative genomics for identifying salient genes and gene networks that may underlie cognition. We focus on the comparison of human and non-human primate brain gene expression and the utility of building gene co-expression networks for prioritizing hundreds of genes that differ in expression among the species queried. We also discuss the importance and methods for functional studies of individual genes identified. Together, this integration of comparative genomics with cellular and animal models should provide improved systems for developing effective therapeutics for disorders of cognition. PMID:25247723

  15. Genome increase as a clock for the origin and evolution of life

    PubMed Central

    Sharov, Alexei A

    2006-01-01

    Background The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. Several positive feedback mechanisms including gene cooperation and duplication with subsequent specialization may result in the exponential growth of biological complexity in macro-evolution. Results I propose a hypothesis that biological complexity increased exponentially during evolution. Regression of the logarithm of functional non-redundant genome size versus time of origin in major groups of organisms showed a 7.8-fold increase per 1 billion years, and hence the increase of complexity can be viewed as a clock of macro-evolution. A strong version of the exponential hypothesis is that the rate of complexity increase in early (pre-prokaryotic) evolution of life was at most the same (or even slower) than observed in the evolution of prokaryotes and eukaryotes. Conclusion The increase of functional non-redundant genome size in macro-evolution was consistent with the exponential hypothesis. If the strong exponential hypothesis is true, then the origin of life should be dated 10 billion years ago. Thus, the possibility of panspermia as a source of life on earth should be discussed on equal basis with alternative hypotheses of de-novo life origin. Panspermia may be proven if bacteria similar to terrestrial ones are found on other planets or satellites in the solar system. Reviewers This article was reviewed by Eugene V. Koonin, Chris Adami and Arcady Mushegian. PMID:16768805

  16. The evolution of genomic imprinting: theories, predictions and empirical tests

    PubMed Central

    Patten, M M; Ross, L; Curley, J P; Queller, D C; Bonduriansky, R; Wolf, J B

    2014-01-01

    The epigenetic phenomenon of genomic imprinting has motivated the development of numerous theories for its evolutionary origins and genomic distribution. In this review, we examine the three theories that have best withstood theoretical and empirical scrutiny. These are: Haig and colleagues' kinship theory; Day and Bonduriansky's sexual antagonism theory; and Wolf and Hager's maternaloffspring coadaptation theory. These theories have fundamentally different perspectives on the adaptive significance of imprinting. The kinship theory views imprinting as a mechanism to change gene dosage, with imprinting evolving because of the differential effect that gene dosage has on the fitness of matrilineal and patrilineal relatives. The sexual antagonism and maternaloffspring coadaptation theories view genomic imprinting as a mechanism to modify the resemblance of an individual to its two parents, with imprinting evolving to increase the probability of expressing the fitter of the two alleles at a locus. In an effort to stimulate further empirical work on the topic, we carefully detail the logic and assumptions of all three theories, clarify the specific predictions of each and suggest tests to discriminate between these alternative theories for why particular genes are imprinted. PMID:24755983

  17. Reflections on ancestral haplotypes: medical genomics, evolution, and human individuality.

    PubMed

    Steele, Edward J

    2014-01-01

    The major histocompatibility complex (MHC), once labelled the "sphinx of immunology" by Jan Klein, provides powerful challenges to evolutionary thinking. This essay highlights the main discoveries that established the block ancestral haplotype structure of the MHC and the wider genome, focusing on the work by the Perth (Australia) group, led by Roger Dawkins, and the Boston group, led by Chester Alper and Edmond Yunis. Their achievements have been overlooked in the rush to sequence the first and subsequent drafts of the human genome. In Caucasoids, where most of the detailed work has been done, about 70% of all known allelic MHC diversity can be accounted for by 30 or so ancestral haplotypes (AHs), or conserved sequences of many mega-bases, and their recombinants. The block haplotype structure of the genome, as shown for the MHC (and other genetic regions), is a story that needs to be understood in its own right, particularly given the promotion of the "HapMap" project and single nucleotide polymorphism (SNP) linkage disequilibrium (LD) analysis, which has been wrongly touted as the only way to pinpoint those genes that are important in genetic disorders or other desired (qualitative) characteristics. PMID:25544323

  18. Human rhinovirus VPg uridylylation AlphaScreen for high-throughput screening.

    PubMed

    Gingras, Rock; Mekhssian, Kevork; Fenwick, Craig; White, Peter W; Thibeault, Diane

    2014-02-01

    As an obligate step for picornaviruses to replicate their genome, the small viral peptide VPg must first be specifically conjugated with uridine nucleotides at a conserved tyrosine hydroxyl group. The resulting VPg-pUpU serves as the primer for genome replication. The uridylylation reaction requires the coordinated activity of many components, including the viral polymerase, a conserved internal RNA stem loop structure, and additional viral proteins. Formation of this complex and the resulting conjugation reaction catalyzed by the polymerase, offers a number of biochemical targets for inhibition of an essential process in the viral life cycle. Therefore, an assay recapitulating uridylylation would provide multiple opportunities for discovering potential antiviral agents. Our goal was to identify inhibitors of human rhinovirus (HRV) VPg uridylylation, which might ultimately be useful to reduce or prevent HRV-induced lower airway immunologic inflammatory responses, a major cause of asthma and chronic obstructive pulmonary disease exacerbations. We have reconstituted the complex uridylylation reaction in an AlphaScreen suitable for high-throughput screening, in which a rabbit polyclonal antiserum specific for uridylylated VPg serves as a key reagent. Assay results were validated by quantitative mass spectrometric detection of uridylylation. PMID:23813021

  19. Extreme Recombination Frequencies Shape Genome Variation and Evolution in the Honeybee, Apis mellifera

    PubMed Central

    Wallberg, Andreas; Glémin, Sylvain; Webster, Matthew T.

    2015-01-01

    Meiotic recombination is a fundamental cellular process, with important consequences for evolution and genome integrity. However, we know little about how recombination rates vary across the genomes of most species and the molecular and evolutionary determinants of this variation. The honeybee, Apis mellifera, has extremely high rates of meiotic recombination, although the evolutionary causes and consequences of this are unclear. Here we use patterns of linkage disequilibrium in whole genome resequencing data from 30 diploid honeybees to construct a fine-scale map of rates of crossing over in the genome. We find that, in contrast to vertebrate genomes, the recombination landscape is not strongly punctate. Crossover rates strongly correlate with levels of genetic variation, but not divergence, which indicates a pervasive impact of selection on the genome. Germ-line methylated genes have reduced crossover rate, which could indicate a role of methylation in suppressing recombination. Controlling for the effects of methylation, we do not infer a strong association between gene expression patterns and recombination. The site frequency spectrum is strongly skewed from neutral expectations in honeybees: rare variants are dominated by AT-biased mutations, whereas GC-biased mutations are found at higher frequencies, indicative of a major influence of GC-biased gene conversion (gBGC), which we infer to generate an allele fixation bias 5 – 50 times the genomic average estimated in humans. We uncover further evidence that this repair bias specifically affects transitions and favours fixation of CpG sites. Recombination, via gBGC, therefore appears to have profound consequences on genome evolution in honeybees and interferes with the process of natural selection. These findings have important implications for our understanding of the forces driving molecular evolution. PMID:25902173

  20. Extreme recombination frequencies shape genome variation and evolution in the honeybee, Apis mellifera.

    PubMed

    Wallberg, Andreas; Glmin, Sylvain; Webster, Matthew T

    2015-04-01

    Meiotic recombination is a fundamental cellular process, with important consequences for evolution and genome integrity. However, we know little about how recombination rates vary across the genomes of most species and the molecular and evolutionary determinants of this variation. The honeybee, Apis mellifera, has extremely high rates of meiotic recombination, although the evolutionary causes and consequences of this are unclear. Here we use patterns of linkage disequilibrium in whole genome resequencing data from 30 diploid honeybees to construct a fine-scale map of rates of crossing over in the genome. We find that, in contrast to vertebrate genomes, the recombination landscape is not strongly punctate. Crossover rates strongly correlate with levels of genetic variation, but not divergence, which indicates a pervasive impact of selection on the genome. Germ-line methylated genes have reduced crossover rate, which could indicate a role of methylation in suppressing recombination. Controlling for the effects of methylation, we do not infer a strong association between gene expression patterns and recombination. The site frequency spectrum is strongly skewed from neutral expectations in honeybees: rare variants are dominated by AT-biased mutations, whereas GC-biased mutations are found at higher frequencies, indicative of a major influence of GC-biased gene conversion (gBGC), which we infer to generate an allele fixation bias 5 - 50 times the genomic average estimated in humans. We uncover further evidence that this repair bias specifically affects transitions and favours fixation of CpG sites. Recombination, via gBGC, therefore appears to have profound consequences on genome evolution in honeybees and interferes with the process of natural selection. These findings have important implications for our understanding of the forces driving molecular evolution. PMID:25902173

  1. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

    PubMed Central

    Andersson, Jan O; Sjgren, sa M; Horner, David S; Murphy, Colleen A; Dyal, Patricia L; Svrd, Staffan G; Logsdon, John M; Ragan, Mark A; Hirt, Robert P; Roger, Andrew J

    2007-01-01

    Background Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus). Results The analyses revealed a compact genome with few, if any, introns and very short 3' untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes mostly encoding metabolic proteins that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals. Conclusion Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution. PMID:17298675

  2. Optimality models in the age of experimental evolution and genomics

    PubMed Central

    Bull, J. J.; Wang, I.-N.

    2010-01-01

    Optimality models have been used to predict evolution of many properties of organisms. They typically neglect genetic details, whether by necessity or design. This omission is a common source of criticism, and although this limitation of optimality is widely acknowledged, it has mostly been defended rather than evaluated for its impact. Experimental adaptation of model organisms provides a new arena for testing optimality models and for simultaneously integrating genetics. First, an experimental context with a well-researched organism allows dissection of the evolutionary process to identify causes of model failure – whether the model is wrong about genetics or selection. Second, optimality models provide a meaningful context for the process and mechanics of evolution, and thus may be used to elicit realistic genetic bases of adaptation – an especially useful augmentation to well-researched genetic systems. A few studies of microbes have begun to pioneer this new direction. Incompatibility between the assumed and actual genetics has been demonstrated to be the cause of model failure in some cases. More interestingly, evolution at the phenotypic level has sometimes matched prediction even though the adaptive mutations defy mechanisms established by decades of classic genetic studies. Integration of experimental evolutionary tests with genetics heralds a new wave for optimality models and their extensions that does not merely emphasize the forces driving evolution. PMID:20646132

  3. Complete Chloroplast Genome Sequence of Aquilaria sinensis (Lour.) Gilg and Evolution Analysis within the Malvales Order

    PubMed Central

    Wang, Ying; Zhan, Di-Feng; Jia, Xian; Mei, Wen-Li; Dai, Hao-Fu; Chen, Xiong-Ting; Peng, Shi-Qing

    2016-01-01

    Aquilaria sinensis (Lour.) Gilg is an important medicinal woody plant producing agarwood, which is widely used in traditional Chinese medicine. High-throughput sequencing of chloroplast (cp) genomes enhanced the understanding about evolutionary relationships within plant families. In this study, we determined the complete cp genome sequences for A. sinensis. The size of the A. sinensis cp genome was 159,565 bp. This genome included a large single-copy region of 87,482 bp, a small single-copy region of 19,857 bp, and a pair of inverted repeats (IRa and IRb) of 26,113 bp each. The GC content of the genome was 37.11%. The A. sinensis cp genome encoded 113 functional genes, including 82 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. A total of 45 polymorphic simple-sequence repeat loci and 60 pairs of large repeats were identified. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited high A/T content. Moreover, 33 pairs of large repeat sequences were located in the protein-coding genes, whereas 27 pairs were located in the intergenic regions. Aquilaria sinensis cp genome bias ended with A/T on the basis of codon usage. The distribution of codon usage in A. sinensis cp genome was most similar to that in the Gonystylus bancanus cp genome. Comparative results of 82 protein-coding genes from 29 species of cp genomes demonstrated that A. sinensis was a sister species to G. bancanus within the Malvales order. Aquilaria sinensis cp genome presented the highest sequence similarity of >90% with the G. bancanus cp genome by using CGView Comparison Tool. This finding strongly supports the placement of A. sinensis as a sister to G. bancanus within the Malvales order. The complete A. sinensis cp genome information will be highly beneficial for further studies on this traditional medicinal plant. Moreover, the results will enhance our understanding about the evolution of cp genomes of the Malvales order, particularly with regard to the role of A. sinensis in plant systematics and evolution. PMID:27014304

  4. Genome mapping in capsicum and the evolution of genome structure in the solanaceae.

    PubMed Central

    Livingstone, K D; Lackney, V K; Blauth, J R; van Wijk, R; Jahn, M K

    1999-01-01

    We have created a genetic map of Capsicum (pepper) from an interspecific F2 population consisting of 11 large (76.2-192.3 cM) and 2 small (19.1 and 12.5 cM) linkage groups that cover a total of 1245.7 cM. Many of the markers are tomato probes that were chosen to cover the tomato genome, allowing comparison of this pepper map to the genetic map of tomato. Hybridization of all tomato-derived probes included in this study to positions throughout the pepper map suggests that no major losses have occurred during the divergence of these genomes. Comparison of the pepper and tomato genetic maps showed that 18 homeologous linkage blocks cover 98.1% of the tomato genome and 95.0% of the pepper genome. Through these maps and the potato map, we determined the number and types of rearrangements that differentiate these species and reconstructed a hypothetical progenitor genome. We conclude there have been 30 breaks as part of 5 translocations, 10 paracentric inversions, 2 pericentric inversions, and 4 disassociations or associations of genomic regions that differentiate tomato, potato, and pepper, as well as an additional reciprocal translocation, nonreciprocal translocation, and a duplication or deletion that differentiate the two pepper mapping parents. PMID:10388833

  5. Genomics of Rapid Adaptation to Antibiotics: Convergent Evolution and Scalable Sequence Amplification

    PubMed Central

    Laehnemann, David; Pea-Miller, Rafael; Rosenstiel, Philip; Beardmore, Robert; Jansen, Gunther; Schulenburg, Hinrich

    2014-01-01

    Evolutionary adaptation can be extremely fast, especially in response to high selection intensities. A prime example is the surge of antibiotic resistance in bacteria. The genomic underpinnings of such rapid changes may provide information on the genetic processes that enhance fast responses and the particular trait functions under selection. Here, we use experimentally evolved Escherichia coli for a detailed dissection of the genomics of rapid antibiotic resistance evolution. Our new analyses demonstrate that amplification of a sequence region containing several known antibiotic resistance genes represents a fast genomic response mechanism under high antibiotic stress, here exerted by drug combination. In particular, higher dosage of such antibiotic combinations coincided with higher copy number of the sequence region. The amplification appears to be evolutionarily costly, because amplification levels rapidly dropped after removal of the drugs. Our results suggest that amplification is a scalable process, as copy number rapidly changes in response to the selective pressure encountered. Moreover, repeated patterns of convergent evolution were found across the experimentally evolved bacterial populations, including those with lower antibiotic selection intensities. Intriguingly, convergent evolution was identified on different organizational levels, ranging from the above sequence amplification, high variant frequencies in specific genes, prevalence of individual nonsynonymous mutations to the unusual repeated occurrence of a particular synonymous mutation in Glycine codons. We conclude that constrained evolutionary trajectories underlie rapid adaptation to antibiotics. Of the identified genomic changes, sequence amplification seems to represent the most potent, albeit costly genomic response mechanism to high antibiotic stress. PMID:24850796

  6. Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges.

    PubMed

    Lavrov, Dennis V; Maikova, Olga O; Pett, Walker; Belikov, Sergey I

    2012-08-15

    Demosponges, the largest and most diverse class in the phylum Porifera, possess mitochondrial DNA (mtDNA) markedly different from that in other animals. Although several studies investigated evolution of demosponge mtDNA among major lineages of the group, the changes within these groups remain largely unexplored. Recently we determined mitochondrial genomic sequence of the Lake Baikal sponge Lubomirskia baicalensis and described proliferation of small inverted repeats (hairpins) that occurred in it since the divergence between L. baicalensis and the most closely related cosmopolitan freshwater sponge Ephydatia muelleri. Here we report mitochondrial genomes of three additional species of Lake Baikal sponges: Swartschewskia papyracea, Rezinkovia echinata and Baikalospongia intermedia morpha profundalis (Demospongiae, Haplosclerida, Lubomirskiidae) and from a more distantly related freshwater sponge Corvomeyenia sp. (Demospongiae, Haplosclerida, Metaniidae). We use these additional sequences to explore mtDNA evolution in Baikalian sponges, paying particular attention to the variation in the rates of nucleotide substitutions and the distribution of hairpins, abundant in these genomes. We show that most of the changes in Lubomirskiidae mitochondrial genomes are due to insertion/deletion/duplication of these elements rather than single nucleotide substitutions. Thus inverted repeats can act as an important force in evolution of mitochondrial genome architecture and be a valuable marker for population- and species-level studies in this group. In addition, we infer (((Rezinkovia+Lubomirskia)+Swartschewskia)+Baikalospongia) phylogeny for the family Lubomirskiidae based on the analysis of mitochondrial coding sequences from freshwater sponges. PMID:22669046

  7. Nitrogen limitation as a driver of genome size evolution in a group of karst plants.

    PubMed

    Kang, Ming; Wang, Jing; Huang, Hongwen

    2015-01-01

    Genome size is of fundamental biological importance with significance in predicting structural and functional attributes of organisms. Although abundant evidence has shown that the genome size can be largely explained by differential proliferation and removal of non-coding DNA of the genome, the evolutionary and ecological basis of genome size variation remains poorly understood. Nitrogen (N) and phosphorus (P) are essential elements of DNA and protein building blocks, yet often subject to environmental limitation in natural ecosystems. Using phylogenetic comparative methods, we test this hypothesis by determining whether leaf N and P availability affects genome sizes in 99 species of Primulina (Gesneriaceae), a group of soil specialists adapted to limestone karst environment in south China. We find that genome sizes in Primulina are strongly positively correlated with plant N content, but the correlation with plant P content is not significant when phylogeny history was taken into account. This study shows for the first time that N limitation might have been a plausible driver of genome size variation in a group of plants. We propose that competition for nitrogen nutrient between DNA synthesis and cellular functions is a possible mechanism for genome size evolution in Primulina under N-limitation. PMID:26109237

  8. Genomic evolution of porcine reproductive and respiratory syndrome virus (PRRSV) isolates revealed by deep sequencing.

    PubMed

    Brar, Manreetpal Singh; Shi, Mang; Hui, Raymond Kin-Hi; Leung, Frederick Chi-Ching

    2014-01-01

    Most studies on PRRSV evolution have been limited to a particular region of the viral genome. A thorough genome-wide understanding of the impact of different mechanisms on shaping PRRSV genetic diversity is still lacking. To this end, deep sequencing was used to obtain genomic sequences of a diverse set of 16 isolates from a region of Hong Kong with a complex PRRSV epidemiological record. Genome assemblies and phylogenetic typing indicated the co-circulation of strains of both genotypes (type 1 and type 2) with varying Nsp2 deletion patterns and distinct evolutionary lineages ("High Fever"-like and local endemic type). Recombination analyses revealed genomic breakpoints in structural and non-structural regions of genomes of both genotypes with evidence of many recombination events originating from common ancestors. Additionally, the high fold of coverage per nucleotide allowed the characterization of minor variants arising from the quasispecies of each strain. Overall, 0.56-2.83% of sites were found to be polymorphic with respect to cognate consensus genomes. The distribution of minor variants across each genome was not uniform indicating the influence of selective forces. Proportion of variants capable of causing an amino acid change in their respective codons ranged between 25-67% with many predicted to be non-deleterious. Low frequency deletion variants were also detected providing one possible mechanism for their sudden emergence as cited in previous reports. PMID:24698958

  9. Genomic Evolution of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Isolates Revealed by Deep Sequencing

    PubMed Central

    Brar, Manreetpal Singh; Shi, Mang; Hui, Raymond Kin-Hi; Leung, Frederick Chi-Ching

    2014-01-01

    Most studies on PRRSV evolution have been limited to a particular region of the viral genome. A thorough genome-wide understanding of the impact of different mechanisms on shaping PRRSV genetic diversity is still lacking. To this end, deep sequencing was used to obtain genomic sequences of a diverse set of 16 isolates from a region of Hong Kong with a complex PRRSV epidemiological record. Genome assemblies and phylogenetic typing indicated the co-circulation of strains of both genotypes (type 1and type 2) with varying Nsp2 deletion patterns and distinct evolutionary lineages (High Fever-like and local endemic type). Recombination analyses revealed genomic breakpoints in structural and non-structural regions of genomes of both genotypes with evidence of many recombination events originating from common ancestors. Additionally, the high fold of coverage per nucleotide allowed the characterization of minor variants arising from the quasispecies of each strain. Overall, 0.562.83% of sites were found to be polymorphic with respect to cognate consensus genomes. The distribution of minor variants across each genome was not uniform indicating the influence of selective forces. Proportion of variants capable of causing an amino acid change in their respective codons ranged between 2567% with many predicted to be non-deleterious. Low frequency deletion variants were also detected providing one possible mechanism for their sudden emergence as cited in previous reports. PMID:24698958

  10. Nitrogen limitation as a driver of genome size evolution in a group of karst plants

    NASA Astrophysics Data System (ADS)

    Kang, Ming; Wang, Jing; Huang, Hongwen

    2015-06-01

    Genome size is of fundamental biological importance with significance in predicting structural and functional attributes of organisms. Although abundant evidence has shown that the genome size can be largely explained by differential proliferation and removal of non-coding DNA of the genome, the evolutionary and ecological basis of genome size variation remains poorly understood. Nitrogen (N) and phosphorus (P) are essential elements of DNA and protein building blocks, yet often subject to environmental limitation in natural ecosystems. Using phylogenetic comparative methods, we test this hypothesis by determining whether leaf N and P availability affects genome sizes in 99 species of Primulina (Gesneriaceae), a group of soil specialists adapted to limestone karst environment in south China. We find that genome sizes in Primulina are strongly positively correlated with plant N content, but the correlation with plant P content is not significant when phylogeny history was taken into account. This study shows for the first time that N limitation might have been a plausible driver of genome size variation in a group of plants. We propose that competition for nitrogen nutrient between DNA synthesis and cellular functions is a possible mechanism for genome size evolution in Primulina under N-limitation.

  11. Nitrogen limitation as a driver of genome size evolution in a group of karst plants

    PubMed Central

    Kang, Ming; Wang, Jing; Huang, Hongwen

    2015-01-01

    Genome size is of fundamental biological importance with significance in predicting structural and functional attributes of organisms. Although abundant evidence has shown that the genome size can be largely explained by differential proliferation and removal of non-coding DNA of the genome, the evolutionary and ecological basis of genome size variation remains poorly understood. Nitrogen (N) and phosphorus (P) are essential elements of DNA and protein building blocks, yet often subject to environmental limitation in natural ecosystems. Using phylogenetic comparative methods, we test this hypothesis by determining whether leaf N and P availability affects genome sizes in 99 species of Primulina (Gesneriaceae), a group of soil specialists adapted to limestone karst environment in south China. We find that genome sizes in Primulina are strongly positively correlated with plant N content, but the correlation with plant P content is not significant when phylogeny history was taken into account. This study shows for the first time that N limitation might have been a plausible driver of genome size variation in a group of plants. We propose that competition for nitrogen nutrient between DNA synthesis and cellular functions is a possible mechanism for genome size evolution in Primulina under N-limitation. PMID:26109237

  12. Retrotransposons Within Syntenic Regions Between Soybean and Medicago Truncatula and Their Contribution to Local Genome Evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparative genome analyses have described the extent of gene level macro and microsynteny among closely related legume species. Yet the organization of the intergenic regions within syntenic blocks and the involvement of retrotransposons in the evolution of these regions have not been studied in d...

  13. Recent Advances in Understanding the Role of Nutrition in Human Genome Evolution12

    PubMed Central

    Ye, Kaixiong; Gu, Zhenglong

    2011-01-01

    Dietary transitions in human history have been suggested to play important roles in the evolution of mankind. Genetic variations caused by adaptation to diet during human evolution could have important health consequences in current society. The advance of sequencing technologies and the rapid accumulation of genome information provide an unprecedented opportunity to comprehensively characterize genetic variations in human populations and unravel the genetic basis of human evolution. Series of selection detection methods, based on various theoretical models and exploiting different aspects of selection signatures, have been developed. Their applications at the species and population levels have respectively led to the identification of human specific selection events that distinguish human from nonhuman primates and local adaptation events that contribute to human diversity. Scrutiny of candidate genes has revealed paradigms of adaptations to specific nutritional components and genome-wide selection scans have verified the prevalence of diet-related selection events and provided many more candidates awaiting further investigation. Understanding the role of diet in human evolution is fundamental for the development of evidence-based, genome-informed nutritional practices in the era of personal genomics. PMID:22332091

  14. Evolution of an endofungal Lifestyle: Deductions from the Burkholderia rhizoxinica Genome

    PubMed Central

    2011-01-01

    Background Burkholderia rhizoxinica is an intracellular symbiont of the phytopathogenic zygomycete Rhizopus microsporus, the causative agent of rice seedling blight. The endosymbiont produces the antimitotic macrolide rhizoxin for its host. It is vertically transmitted within vegetative spores and is essential for spore formation of the fungus. To shed light on the evolution and genetic potential of this model organism, we analysed the whole genome of B. rhizoxinica HKI 0454 - a type strain of endofungal Burkholderia species. Results The genome consists of a structurally conserved chromosome and two plasmids. Compared to free-living Burkholderia species, the genome is smaller in size and harbors less transcriptional regulator genes. Instead, we observed accumulation of transposons over the genome. Prediction of primary metabolic pathways and transporters suggests that endosymbionts consume host metabolites like citrate, but might deliver some amino acids and cofactors to the host. The rhizoxin biosynthesis gene cluster shows evolutionary traces of horizontal gene transfer. Furthermore, we analysed gene clusters coding for nonribosomal peptide synthetases (NRPS). Notably, B. rhizoxinica lacks common genes which are dedicated to quorum sensing systems, but is equipped with a large number of virulence-related factors and putative type III effectors. Conclusions B. rhizoxinica is the first endofungal bacterium, whose genome has been sequenced. Here, we present models of evolution, metabolism and tools for host-symbiont interaction of the endofungal bacterium deduced from whole genome analyses. Genome size and structure suggest that B. rhizoxinica is in an early phase of adaptation to the intracellular lifestyle (genome in transition). By analysis of tranporters and metabolic pathways we predict how metabolites might be exchanged between the symbiont and its host. Gene clusters for biosynthesis of secondary metabolites represent novel targets for genomic mining of cryptic natural products. In silico analyses of virulence-associated genes, secreted proteins and effectors might inspire future studies on molecular mechanisms underlying bacterial-fungal interaction. PMID:21539752

  15. Gene interactions in the evolution of genomic imprinting

    PubMed Central

    Wolf, J B; Brandvain, Y

    2014-01-01

    Numerous evolutionary theories have been developed to explain the epigenetic phenomenon of genomic imprinting. Here, we explore a subset of theories wherein non-additive genetic interactions can favour imprinting. In the simplest genic interactionthe case of underdominanceimprinting can be favoured to hide effectively low-fitness heterozygous genotypes; however, as there is no asymmetry between maternally and paternally inherited alleles in this model, other means of enforcing monoallelic expression may be more plausible evolutionary outcomes than genomic imprinting. By contrast, more successful interaction models of imprinting rely on an asymmetry between the maternally and paternally inherited alleles at a locus that favours the silencing of one allele as a means of coordinating the expression of high-fitness allelic combinations. For example, with interactions between autosomal loci, imprinting functionally preserves high-fitness genotypes that were favoured by selection in the previous generation. In this scenario, once a focal locus becomes imprinted, selection at interacting loci favours a matching imprint. Uniparental transmission generates similar asymmetries for sex chromosomes and cytoplasmic factors interacting with autosomal loci, with selection favouring the expression of either maternal or paternally derived autosomal alleles depending on the pattern of transmission of the uniparentally inherited factor. In a final class of models, asymmetries arise when genes expressed in offspring interact with genes expressed in one of its parents. Under such a scenario, a locus evolves to have imprinted expression in offspring to coordinate the interaction with its parent's genome. We illustrate these models and explore key links and differences using a unified framework. PMID:24619179

  16. A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

    PubMed Central

    Lin, Chen-Ching; Zhao, Junfei; Jia, Peilin; Li, Wen-Hsiung; Zhao, Zhongming

    2015-01-01

    Cancer development and progression result from somatic evolution by an accumulation of genomic alterations. The effects of those alterations on the fitness of somatic cells lead to evolutionary adaptations such as increased cell proliferation, angiogenesis, and altered anticancer drug responses. However, there are few general mathematical models to quantitatively examine how perturbations of a single gene shape subsequent evolution of the cancer genome. In this study, we proposed the gene gravity model to study the evolution of cancer genomes by incorporating the genome-wide transcription and somatic mutation profiles of ~3,000 tumors across 9 cancer types from The Cancer Genome Atlas into a broad gene network. We found that somatic mutations of a cancer driver gene may drive cancer genome evolution by inducing mutations in other genes. This functional consequence is often generated by the combined effect of genetic and epigenetic (e.g., chromatin regulation) alterations. By quantifying cancer genome evolution using the gene gravity model, we identified six putative cancer genes (AHNAK, COL11A1, DDX3X, FAT4, STAG2, and SYNE1). The tumor genomes harboring the nonsynonymous somatic mutations in these genes had a higher mutation density at the genome level compared to the wild-type groups. Furthermore, we provided statistical evidence that hypermutation of cancer driver genes on inactive X chromosomes is a general feature in female cancer genomes. In summary, this study sheds light on the functional consequences and evolutionary characteristics of somatic mutations during tumorigenesis by propelling adaptive cancer genome evolution, which would provide new perspectives for cancer research and therapeutics. PMID:26352260

  17. A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.

    PubMed

    Cheng, Feixiong; Liu, Chuang; Lin, Chen-Ching; Zhao, Junfei; Jia, Peilin; Li, Wen-Hsiung; Zhao, Zhongming

    2015-09-01

    Cancer development and progression result from somatic evolution by an accumulation of genomic alterations. The effects of those alterations on the fitness of somatic cells lead to evolutionary adaptations such as increased cell proliferation, angiogenesis, and altered anticancer drug responses. However, there are few general mathematical models to quantitatively examine how perturbations of a single gene shape subsequent evolution of the cancer genome. In this study, we proposed the gene gravity model to study the evolution of cancer genomes by incorporating the genome-wide transcription and somatic mutation profiles of ~3,000 tumors across 9 cancer types from The Cancer Genome Atlas into a broad gene network. We found that somatic mutations of a cancer driver gene may drive cancer genome evolution by inducing mutations in other genes. This functional consequence is often generated by the combined effect of genetic and epigenetic (e.g., chromatin regulation) alterations. By quantifying cancer genome evolution using the gene gravity model, we identified six putative cancer genes (AHNAK, COL11A1, DDX3X, FAT4, STAG2, and SYNE1). The tumor genomes harboring the nonsynonymous somatic mutations in these genes had a higher mutation density at the genome level compared to the wild-type groups. Furthermore, we provided statistical evidence that hypermutation of cancer driver genes on inactive X chromosomes is a general feature in female cancer genomes. In summary, this study sheds light on the functional consequences and evolutionary characteristics of somatic mutations during tumorigenesis by propelling adaptive cancer genome evolution, which would provide new perspectives for cancer research and therapeutics. PMID:26352260

  18. The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan.

    PubMed

    Valenzano, Dario Riccardo; Benayoun, Brnice A; Singh, Param Priya; Zhang, Elisa; Etter, Paul D; Hu, Chi-Kuo; Clment-Ziza, Mathieu; Willemsen, David; Cui, Rongfeng; Harel, Itamar; Machado, Ben E; Yee, Muh-Ching; Sharp, Sabrina C; Bustamante, Carlos D; Beyer, Andreas; Johnson, Eric A; Brunet, Anne

    2015-12-01

    Lifespan is a remarkably diverse trait ranging from a few days to several hundred years in nature, but the mechanisms underlying the evolution of lifespan differences remain elusive. Here we de novo assemble a reference genome for the naturally short-lived African turquoise killifish, providing a unique resource for comparative and experimental genomics. The identification of genes under positive selection in this fish reveals potential candidates to explain its compressed lifespan. Several aging genes are under positive selection in this short-lived fish and long-lived species, raising the intriguing possibility that the same gene could underlie evolution of both compressed and extended lifespans. Comparative genomics and linkage analysis identify candidate genes associated with lifespan differences between various turquoise killifish strains. Remarkably, these genes are clustered on the sex chromosome, suggesting that short lifespan might have co-evolved with sex determination. Our study provides insights into the evolutionary forces that shape lifespan in nature. PMID:26638078

  19. Genomic Organization and Evolution of Alternative Exons in a Drosophila Calcium Channel Gene

    PubMed Central

    Peixoto, A. A.; Smith, L. A.; Hall, J. C.

    1997-01-01

    The genomic organization of a gene coding for an ?1 subunit of a voltage-gated calcium channel of Drosophila melanogaster (Dmca1A) was determined. Thirty-four exons, distributed over 45 kb of genomic sequence, have been identified and mapped, including exons in three regions involved in alternative splicing and new sites potentially involved in RNA editing. The comparison of the intron/exon boundaries of this channel with a mammalian counterpart shows that the genomic structure of these two genes has remained fairly similar during evolution, with more than half of the Drosophila intron positions being perfectly conserved compared to the human channel. Phylogenetic analysis of the mutually exclusive alternative exons revealed that they have diverged considerably. It is suggested that this divergence, rather than reflecting evolutionary age, is the likely result of accelerated rates of evolution following duplication. PMID:9093853

  20. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

    PubMed Central

    de Bruin, Elza C.; McGranahan, Nicholas; Mitter, Richard; Salm, Max; Wedge, David C.; Yates, Lucy; Jamal-Hanjani, Mariam; Shafi, Seema; Murugaesu, Nirupa; Rowan, Andrew J.; Grnroos, Eva; Muhammad, Madiha A.; Horswell, Stuart; Gerlinger, Marco; Varela, Ignacio; Jones, David; Marshall, John; Voet, Thierry; Van Loo, Peter; Rassl, Doris M.; Rintoul, Robert C.; Janes, Sam M.; Lee, Siow-Ming; Forster, Martin; Ahmad, Tanya; Lawrence, David; Falzon, Mary; Capitanio, Arrigo; Harkins, Timothy T.; Lee, Clarence C.; Tom, Warren; Teefe, Enock; Chen, Shann-Ching; Begum, Sharmin; Rabinowitz, Adam; Phillimore, Benjamin; Spencer-Dene, Bradley; Stamp, Gordon; Szallasi, Zoltan; Matthews, Nik; Stewart, Aengus; Campbell, Peter; Swanton, Charles

    2015-01-01

    Spatial and temporal dissection of the genomic changes occurring during the evolution of human nonsmall cell lung cancer (NSCLC) may help elucidate the basis for its dismal prognosis. We sequenced 25 spatially distinct regions from seven operable NSCLCs and found evidence of branched evolution, with driver mutations arising before and after subclonal diversification. There was pronounced intratumor heterogeneity in copy number alterations, translocations, and mutations associated with APOBEC cytidine deaminase activity. Despite maintained carcinogen exposure, tumors from smokers showed a relative decrease in smoking-related mutations over time, accompanied by an increase in APOBEC-associated mutations. In tumors from former smokers, genome-doubling occurred within a smoking-signature context before subclonal diversification, which suggested that a long period of tumor latency had preceded clinical detection. The regionally separated driver mutations, coupled with the relentless and heterogeneous nature of the genome instability processes, are likely to confound treatment success in NSCLC. PMID:25301630

  1. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution.

    PubMed

    de Bruin, Elza C; McGranahan, Nicholas; Mitter, Richard; Salm, Max; Wedge, David C; Yates, Lucy; Jamal-Hanjani, Mariam; Shafi, Seema; Murugaesu, Nirupa; Rowan, Andrew J; Grnroos, Eva; Muhammad, Madiha A; Horswell, Stuart; Gerlinger, Marco; Varela, Ignacio; Jones, David; Marshall, John; Voet, Thierry; Van Loo, Peter; Rassl, Doris M; Rintoul, Robert C; Janes, Sam M; Lee, Siow-Ming; Forster, Martin; Ahmad, Tanya; Lawrence, David; Falzon, Mary; Capitanio, Arrigo; Harkins, Timothy T; Lee, Clarence C; Tom, Warren; Teefe, Enock; Chen, Shann-Ching; Begum, Sharmin; Rabinowitz, Adam; Phillimore, Benjamin; Spencer-Dene, Bradley; Stamp, Gordon; Szallasi, Zoltan; Matthews, Nik; Stewart, Aengus; Campbell, Peter; Swanton, Charles

    2014-10-10

    Spatial and temporal dissection of the genomic changes occurring during the evolution of human non-small cell lung cancer (NSCLC) may help elucidate the basis for its dismal prognosis. We sequenced 25 spatially distinct regions from seven operable NSCLCs and found evidence of branched evolution, with driver mutations arising before and after subclonal diversification. There was pronounced intratumor heterogeneity in copy number alterations, translocations, and mutations associated with APOBEC cytidine deaminase activity. Despite maintained carcinogen exposure, tumors from smokers showed a relative decrease in smoking-related mutations over time, accompanied by an increase in APOBEC-associated mutations. In tumors from former smokers, genome-doubling occurred within a smoking-signature context before subclonal diversification, which suggested that a long period of tumor latency had preceded clinical detection. The regionally separated driver mutations, coupled with the relentless and heterogeneous nature of the genome instability processes, are likely to confound treatment success in NSCLC. PMID:25301630

  2. Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes

    PubMed Central

    Fierst, Janna L.; Willis, John H.; Thomas, Cristel G.; Wang, Wei; Reynolds, Rose M.; Ahearne, Timothy E.; Cutter, Asher D.; Phillips, Patrick C.

    2015-01-01

    The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se. PMID:26114425

  3. Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes.

    PubMed

    Fierst, Janna L; Willis, John H; Thomas, Cristel G; Wang, Wei; Reynolds, Rose M; Ahearne, Timothy E; Cutter, Asher D; Phillips, Patrick C

    2015-06-01

    The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se. PMID:26114425

  4. Short-term genome evolution of Listeria monocytogenes in a non-controlled environment

    PubMed Central

    Orsi, Renato H; Borowsky, Mark L; Lauer, Peter; Young, Sarah K; Nusbaum, Chad; Galagan, James E; Birren, Bruce W; Ivy, Reid A; Sun, Qi; Graves, Lewis M; Swaminathan, Bala; Wiedmann, Martin

    2008-01-01

    Background While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus performed full genome analyses on four Listeria monocytogenes, including human and food isolates from both a 1988 case of sporadic listeriosis and a 2000 listeriosis outbreak, which had been linked to contaminated food from a single processing facility. All four isolates had been shown to have identical subtypes, suggesting that a specific L. monocytogenes strain persisted in this processing plant over at least 12 years. While a genome sequence for the 1988 food isolate has been reported, we sequenced the genomes of the 1988 human isolate as well as a human and a food isolate from the 2000 outbreak to allow for comparative genome analyses. Results The two L. monocytogenes isolates from 1988 and the two isolates from 2000 had highly similar genome backbone sequences with very few single nucleotide (nt) polymorphisms (1 – 8 SNPs/isolate; confirmed by re-sequencing). While no genome rearrangements were identified in the backbone genome of the four isolates, a 42 kb prophage inserted in the chromosomal comK gene showed evidence for major genome rearrangements. The human-food isolate pair from each 1988 and 2000 had identical prophage sequence; however, there were significant differences in the prophage sequences between the 1988 and 2000 isolates. Diversification of this prophage appears to have been caused by multiple homologous recombination events or possibly prophage replacement. In addition, only the 2000 human isolate contained a plasmid, suggesting plasmid loss or acquisition events. Surprisingly, besides the polymorphisms found in the comK prophage, a single SNP in the tRNA Thr-4 prophage represents the only SNP that differentiates the 1988 isolates from the 2000 isolates. Conclusion Our data support the hypothesis that the 2000 human listeriosis outbreak was caused by a L. monocytogenes strain that persisted in a food processing facility over 12 years and show that genome sequencing is a valuable and feasible tool for retrospective epidemiological analyses. Short-term evolution of L. monocytogenes in non-controlled environments appears to involve limited diversification beyond plasmid gain or loss and prophage diversification, highlighting the importance of phages in bacterial evolution. PMID:19014550

  5. IL-33Dependent Type 2 Inflammation during Rhinovirus-induced Asthma Exacerbations In Vivo

    PubMed Central

    Jackson, David J.; Makrinioti, Heidi; Rana, Batika M. J.; Shamji, Betty W. H.; Trujillo-Torralbo, Maria-Belen; Footitt, Joseph; Jerico del-Rosario; Telcian, Aurica G.; Nikonova, Alexandra; Zhu, Jie; Aniscenko, Julia; Gogsadze, Leila; Bakhsoliani, Eteri; Traub, Stephanie; Dhariwal, Jaideep; Porter, James; Hunt, Duncan; Hunt, Toby; Hunt, Trevor; Stanciu, Luminita A.; Khaitov, Musa; Bartlett, Nathan W.; Edwards, Michael R.; Kon, Onn Min; Mallia, Patrick; Papadopoulos, Nikolaos G.; Akdis, Cezmi A.; Westwick, John; Edwards, Matthew J.; Cousins, David J.; Walton, Ross P.

    2014-01-01

    Rationale: Rhinoviruses are the major cause of asthma exacerbations; however, its underlying mechanisms are poorly understood. We hypothesized that the epithelial cellderived cytokine IL-33 plays a central role in exacerbation pathogenesis through augmentation of type 2 inflammation. Objectives: To assess whether rhinovirus induces a type 2 inflammatory response in asthma in vivo and to define a role for IL-33 in this pathway. Methods: We used a human experimental model of rhinovirus infection and novel airway sampling techniques to measure IL-4, IL-5, IL-13, and IL-33 levels in the asthmatic and healthy airways during a rhinovirus infection. Additionally, we cultured human T cells and type 2 innate lymphoid cells (ILC2s) with the supernatants of rhinovirus-infected bronchial epithelial cells (BECs) to assess type 2 cytokine production in the presence or absence of IL-33 receptor blockade. Measurements and Main Results: IL-4, IL-5, IL-13, and IL-33 are all induced by rhinovirus in the asthmatic airway in vivo and relate to exacerbation severity. Further, induction of IL-33 correlates with viral load and IL-5 and IL-13 levels. Rhinovirus infection of human primary BECs induced IL-33, and culture of human T cells and ILC2s with supernatants of rhinovirus-infected BECs strongly induced type 2 cytokines. This induction was entirely dependent on IL-33. Conclusions: IL-33 and type 2 cytokines are induced during a rhinovirus-induced asthma exacerbation in vivo. Virus-induced IL-33 and IL-33responsive T cells and ILC2s are key mechanistic links between viral infection and exacerbation of asthma. IL-33 inhibition is a novel therapeutic approach for asthma exacerbations. PMID:25350863

  6. Genomic mutation rates that neutralize adaptive evolution and natural selection

    PubMed Central

    Gerrish, Philip J.; Colato, Alexandre; Sniegowski, Paul D.

    2013-01-01

    When mutation rates are low, natural selection remains effective, and increasing the mutation rate can give rise to an increase in adaptation rate. When mutation rates are high to begin with, however, increasing the mutation rate may have a detrimental effect because of the overwhelming presence of deleterious mutations. Indeed, if mutation rates are high enough: (i) adaptive evolution may be neutralized, resulting in a zero (or negative) adaptation rate despite the continued availability of adaptive and/or compensatory mutations, or (ii) natural selection may be neutralized, because the fitness of lineages bearing adaptive and/or compensatory mutationswhether established or newly arisingis eroded by excessive mutation, causing such lineages to decline in frequency. We apply these two criteria to a standard model of asexual adaptive evolution and derive mathematical expressionssome new, some old in new guisedelineating the mutation rates under which either adaptive evolution or natural selection is neutralized. The expressions are simple and require no a priori knowledge of organism- and/or environment-specific parameters. Our discussion connects these results to each other and to previous theory, showing convergence or equivalence of the different results in most cases. PMID:23720539

  7. Major transitions in evolution by genome fusions: from prokaryotes to eukaryotes, metazoans, bilaterians and vertebrates.

    PubMed

    Spring, Jürg

    2003-01-01

    The major transitions in human evolution from prokaryotes to eukaryotes, from protozoans to metazoans, from the first animals to bilaterians and finally from a primitive chordate to vertebrates were all accompanied by increases in genome complexity. Rare fusion of divergent genomes rather than continuous single gene duplications could explain these jumps in evolution. The origin of eukaryotes was proposed to be due to a symbiosis of Archaea and Bacteria. Symbiosis is clearly seen as the source for mitochondria. A fundamental difference of higher eukaryotes is the cycle from haploidy to diploidy, a well-regulated genome duplication. Of course, self-fertilization exists, but the potential of sex increases with the difference of the haploid stages, such as the sperm and the egg. What should be the advantage of having two identical copies of a gene? Still, genes duplicate all the time and even genomes duplicate rather often. In plants, polyploidy is well recognized, but seems to be abundant in fungi and even in animals, too. However, hybridization, rather than autopolyploidy, seems to be the potential mechanism for creating something new. The problem with chimaeric, symbiotic or reticulate evolution events is that they blur phylogenetic lineages. Unrecognized paralogous genes or random loss of one of the paralogs in different lineages can lead to false conclusions. Horizontal genome transfer, genome fusion or hybridization might be only truly innovative combined with rare geological transitions such as change to an oxygen atmosphere, snowball Earth events or the Cambrian explosion, but correlates well with the major transitions in evolution. PMID:12836681

  8. Recombination is associated with the evolution of genome structure and worker behavior in honey bees

    PubMed Central

    Kent, Clement F.; Minaei, Shermineh; Harpur, Brock A.; Zayed, Amro

    2012-01-01

    The rise of insect societies, marked by the formation of reproductive and sterile castes, represents a major unsolved mystery in evolution. Across several independent origins of sociality, the genomes of social hymenopterans share two peculiar attributes: high recombination and low but heterogeneous GC content. For example, the genome of the honey bee, Apis mellifera, represents a mosaic of GC-poor and GC-rich regions with rates of recombination an order of magnitude higher than in humans. However, it is unclear how heterogeneity in GC content arises, and how it relates to the expression and evolution of worker traits. Using population genetic analyses, we demonstrate a bias in the allele frequency and fixation rate of derived C or G mutations in high-recombination regions, consistent with recombinations causal influence on GC-content evolution via biased gene conversion. We also show that recombination and biased gene conversion actively maintain the heterogeneous GC content of the honey bee genome despite an overall A/T mutation bias. Further, we found that GC-rich genes and intergenic regions have higher levels of genetic diversity and divergence relative to GC-poor regions, also consistent with recombinations causal influence on the rate of molecular evolution. Finally, we found that genes associated with behavior and those with worker-biased expression are found in GC-rich regions of the bee genome and also experience high rates of molecular evolution. Taken together, these findings suggest that recombination acts to maintain a genetically diverse and dynamic part of the genome where genes underlying worker behavior evolve more quickly. PMID:23071321

  9. The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

    PubMed Central

    Traeger, Stefanie; Altegoer, Florian; Freitag, Michael; Gabaldon, Toni; Kempken, Frank; Kumar, Abhishek; Marcet-Houben, Marina; Pöggeler, Stefanie; Stajich, Jason E.; Nowrousian, Minou

    2013-01-01

    Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ∼13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator. PMID:24068976

  10. The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

    PubMed

    Traeger, Stefanie; Altegoer, Florian; Freitag, Michael; Gabaldon, Toni; Kempken, Frank; Kumar, Abhishek; Marcet-Houben, Marina; Pggeler, Stefanie; Stajich, Jason E; Nowrousian, Minou

    2013-01-01

    Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ~13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator. PMID:24068976

  11. Spider genomes provide insight into composition and evolution of venom and silk

    PubMed Central

    Sanggaard, Kristian W.; Bechsgaard, Jesper S.; Fang, Xiaodong; Duan, Jinjie; Dyrlund, Thomas F.; Gupta, Vikas; Jiang, Xuanting; Cheng, Ling; Fan, Dingding; Feng, Yue; Han, Lijuan; Huang, Zhiyong; Wu, Zongze; Liao, Li; Settepani, Virginia; Thøgersen, Ida B.; Vanthournout, Bram; Wang, Tobias; Zhu, Yabing; Funch, Peter; Enghild, Jan J.; Schauser, Leif; Andersen, Stig U.; Villesen, Palle; Schierup, Mikkel H; Bilde, Trine; Wang, Jun

    2014-01-01

    Spiders are ecologically important predators with complex venom and extraordinarily tough silk that enables capture of large prey. Here we present the assembled genome of the social velvet spider and a draft assembly of the tarantula genome that represent two major taxonomic groups of spiders. The spider genomes are large with short exons and long introns, reminiscent of mammalian genomes. Phylogenetic analyses place spiders and ticks as sister groups supporting polyphyly of the Acari. Complex sets of venom and silk genes/proteins are identified. We find that venom genes evolved by sequential duplication, and that the toxic effect of venom is most likely activated by proteases present in the venom. The set of silk genes reveals a highly dynamic gene evolution, new types of silk genes and proteins, and a novel use of aciniform silk. These insights create new opportunities for pharmacological applications of venom and biomaterial applications of silk. PMID:24801114

  12. The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism

    PubMed Central

    Waters, Elizabeth; Hohn, Michael J.; Ahel, Ivan; Graham, David E.; Adams, Mark D.; Barnstead, Mary; Beeson, Karen Y.; Bibbs, Lisa; Bolanos, Randall; Keller, Martin; Kretz, Keith; Lin, Xiaoying; Mathur, Eric; Ni, Jingwei; Podar, Mircea; Richardson, Toby; Sutton, Granger G.; Simon, Melvin; Sll, Dieter; Stetter, Karl O.; Short, Jay M.; Noordewier, Michiel

    2003-01-01

    The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in coculture with the crenarchaeon Ignicoccus. Ribosomal protein and rRNA-based phylogenies place its branching point early in the archaeal lineage, representing the new archaeal kingdom Nanoarchaeota. The N. equitans genome (490,885 base pairs) encodes the machinery for information processing and repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide biosyntheses. It is the smallest microbial genome sequenced to date, and also one of the most compact, with 95% of the DNA predicted to encode proteins or stable RNAs. Its limited biosynthetic and catabolic capacity indicates that N. equitans' symbiotic relationship to Ignicoccus is parasitic, making it the only known archaeal parasite. Unlike the small genomes of bacterial parasites that are undergoing reductive evolution, N. equitans has few pseudogenes or extensive regions of noncoding DNA. This organism represents a basal archaeal lineage and has a highly reduced genome. PMID:14566062

  13. The Common Marmoset Genome Provides Insight into Primate Biology and Evolution

    PubMed Central

    2014-01-01

    A first analysis of the genome sequence of the common marmoset (Callithrix jacchus), assembled using traditional Sanger methods and Ensembl annotation, has permitted genomic comparison with apes and old world monkeys and the identification of specific molecular features that may contribute to the unique biology of this diminutive primate. The common marmoset has a rapid reproductive capacity partly due to prevalence of dizygotic twins. Remarkably, these twins share placental circulation and exchange hematopoietic stem cells in utero, resulting in adults that are hematopoietic chimeras. We observed positive selection or non-synonymous substitutions for genes encoding growth hormone/insulin-like growth factor (growth pathways), respiratory complex I (metabolic pathways), immunobiology, and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibit rapid sequence evolution. This New World monkey genome sequence enables significantly increased power for comparative analyses among available primate genomes and facilitates biomedical research application. PMID:25038751

  14. Spider genomes provide insight into composition and evolution of venom and silk.

    PubMed

    Sanggaard, Kristian W; Bechsgaard, Jesper S; Fang, Xiaodong; Duan, Jinjie; Dyrlund, Thomas F; Gupta, Vikas; Jiang, Xuanting; Cheng, Ling; Fan, Dingding; Feng, Yue; Han, Lijuan; Huang, Zhiyong; Wu, Zongze; Liao, Li; Settepani, Virginia; Thgersen, Ida B; Vanthournout, Bram; Wang, Tobias; Zhu, Yabing; Funch, Peter; Enghild, Jan J; Schauser, Leif; Andersen, Stig U; Villesen, Palle; Schierup, Mikkel H; Bilde, Trine; Wang, Jun

    2014-01-01

    Spiders are ecologically important predators with complex venom and extraordinarily tough silk that enables capture of large prey. Here we present the assembled genome of the social velvet spider and a draft assembly of the tarantula genome that represent two major taxonomic groups of spiders. The spider genomes are large with short exons and long introns, reminiscent of mammalian genomes. Phylogenetic analyses place spiders and ticks as sister groups supporting polyphyly of the Acari. Complex sets of venom and silk genes/proteins are identified. We find that venom genes evolved by sequential duplication, and that the toxic effect of venom is most likely activated by proteases present in the venom. The set of silk genes reveals a highly dynamic gene evolution, new types of silk genes and proteins, and a novel use of aciniform silk. These insights create new opportunities for pharmacological applications of venom and biomaterial applications of silk. PMID:24801114

  15. Genome sequence of mungbean and insights into evolution within Vigna species

    PubMed Central

    Kang, Yang Jae; Kim, Sue K.; Kim, Moon Young; Lestari, Puji; Kim, Kil Hyun; Ha, Bo-Keun; Jun, Tae Hwan; Hwang, Won Joo; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Yoon, Min Young; Jang, Young Eun; Han, Kwang Soo; Taeprayoon, Puntaree; Yoon, Na; Somta, Prakit; Tanya, Patcharin; Kim, Kwang Soo; Gwag, Jae-Gyun; Moon, Jung-Kyung; Lee, Yeong-Ho; Park, Beom-Seok; Bombarely, Aureliano; Doyle, Jeffrey J.; Jackson, Scott A.; Schafleitner, Roland; Srinives, Peerasak; Varshney, Rajeev K.; Lee, Suk-Ha

    2014-01-01

    Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis. PMID:25384727

  16. What can whole genome expression data tell us about the ecology and evolution of personality?

    PubMed Central

    Bell, Alison M.; Aubin-Horth, Nadia

    2010-01-01

    Consistent individual differences in behaviour, aka personality, pose several evolutionary questions. For example, it is difficult to explain within-individual consistency in behaviour because behavioural plasticity is often advantageous. In addition, selection erodes heritable behavioural variation that is related to fitness, therefore we wish to know the mechanisms that can maintain between-individual variation in behaviour. In this paper, we argue that whole genome expression data can reveal new insights into the proximate mechanisms underlying personality, as well as its evolutionary consequences. After introducing the basics of whole genome expression analysis, we show how whole genome expression data can be used to understand whether behaviours in different contexts are affected by the same molecular mechanisms. We suggest strategies for using the power of genomics to understand what maintains behavioural variation, to study the evolution of behavioural correlations and to compare personality traits across diverse organisms. PMID:21078652

  17. Stochastic dynamics modeling of the protein sequence length distribution in genomes: Implications for microbial evolution

    NASA Astrophysics Data System (ADS)

    Jain, Rinku; Ramakumar, S.

    1999-12-01

    In this paper, we report an analysis of the protein sequence length distribution for 13 bacteria, four archaea and one eukaryote whose genomes have been completely sequenced. The frequency distribution of protein sequence length for all the 18 organisms are remarkably similar, independent of genome size and can be described in terms of a lognormal probability distribution function. A simple stochastic model based on multiplicative processes has been proposed to explain the sequence length distribution. The stochastic model supports the random-origin hypothesis of protein sequences in genomes. Distributions of large proteins deviate from the overall lognormal behavior. Their cumulative distribution follows a power-law analogous to Pareto's law used to describe the income distribution of the wealthy. The protein sequence length distribution in genomes of organisms has important implications for microbial evolution and applications.

  18. The origin and evolution of genomic imprinting and viviparity in mammals

    PubMed Central

    Renfree, Marilyn B.; Suzuki, Shunsuke; Kaneko-Ishino, Tomoko

    2013-01-01

    Genomic imprinting is widespread in eutherian mammals. Marsupial mammals also have genomic imprinting, but in fewer loci. It has long been thought that genomic imprinting is somehow related to placentation and/or viviparity in mammals, although neither is restricted to mammals. Most imprinted genes are expressed in the placenta. There is no evidence for genomic imprinting in the egg-laying monotreme mammals, despite their short-lived placenta that transfers nutrients from mother to embryo. Post natal genomic imprinting also occurs, especially in the brain. However, little attention has been paid to the primary source of nutrition in the neonate in all mammals, the mammary gland. Differentially methylated regions (DMRs) play an important role as imprinting control centres in each imprinted region which usually comprises both paternally and maternally expressed genes (PEGs and MEGs). The DMR is established in the male or female germline (the gDMR). Comprehensive comparative genome studies demonstrated that two imprinted regions, PEG10 and IGF2-H19, are conserved in both marsupials and eutherians and that PEG10 and H19 DMRs emerged in the therian ancestor at least 160 Ma, indicating the ancestral origin of genomic imprinting during therian mammal evolution. Importantly, these regions are known to be deeply involved in placental and embryonic growth. It appears that most maternal gDMRs are always associated with imprinting in eutherian mammals, but emerged at differing times during mammalian evolution. Thus, genomic imprinting could evolve from a defence mechanism against transposable elements that depended on DNA methylation established in germ cells. PMID:23166401

  19. Parental Origin and Genome Evolution in the Allopolyploid Iris versicolor

    PubMed Central

    Lim, K. Yoong; Matyasek, Roman; Kovarik, Ales; Leitch, Andrew

    2007-01-01

    Background Aims One of the classic examples of an allopolyploid is Iris versicolor, ‘Blue Flag’ (2n = 108), first studied by Edgar Anderson and later popularized by George Ledyard Stebbins in cytogenetics and evolutionary text-books. It is revisited here using modern molecular and cytogenetic tools to investigate its putative allopolyploid origin involving progenitors of I. virginica (2n = 70) and I. setosa (2n = 38). Methods Genomic in situ hybridization (GISH), fluorescent in situ hybridization (FISH) and Southern hybridization with 5S and 18–26S ribosomal DNA (rDNA) probes were used to identify the parental origin of chromosomes, and to study the unit structure, relative abundance and chromosomal location of rDNA sequences. Key Results GISH shows that I. versicolor has inherited the sum of the chromosome complement from the two progenitor species. In I. versicolor all the 18–26S rDNA units and loci are inherited from the progenitor of I. virginica, those loci from the I. setosa progenitor are absent. In contrast 5S rDNA loci and units from both progenitors are found, although one of the two 5S loci expected from the I. setosa progenitor is absent. Conclusions These data confirm Anderson's hypothesis that I. versicolor is an allopolyploid involving progenitors of I. virginica and I. setosa. The number of 18–26S rDNA loci in I. versicolor is similar to that of progenitor I. virginica, suggestive of a first stage in genome diploidization. The locus loss is targeted at the I. setosa-origin subgenome, and this is discussed in relation to other polyploidy systems. PMID:17591610

  20. The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae

    PubMed Central

    2009-01-01

    Background The Xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, Xanthomonas albilineans and Xylella fastidiosa. X. fastidiosa was the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possess hrp genes which encode a Type III secretion system found in most plant pathogenic bacteria. X. fastidiosa was excluded from the Xanthomonas group based on phylogenetic analyses with rRNA sequences. Results The complete genome of X. albilineans was sequenced and annotated. X. albilineans, which is not known to be insect-vectored, also has a reduced genome and does not possess hrp genes. Phylogenetic analysis using X. albilineans genomic sequences showed that X. fastidiosa belongs to the Xanthomonas group. Order of divergence of the Xanthomonadaceae revealed that X. albilineans and X. fastidiosa experienced a convergent reductive genome evolution during their descent from the progenitor of the Xanthomonas genus. Reductive genome evolutions of the two xylem-limited Xanthomonadaceae were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens. Conclusion The two xylem-limited Xanthomonadaceae, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. Adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. However, genome characteristics of X. albilineans differ from those of X. fastidiosa and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. The possible role in genome reduction of the unique toxin albicidin, produced by X. albilineans, is discussed. PMID:20017926

  1. The Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes

    PubMed Central

    Lin, Yen-Lung; Pavlidis, Pavlos; Karakoc, Emre; Ajay, Jerry; Gokcumen, Omer

    2015-01-01

    Allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-African introgression from archaic hominins. However, evolution of polymorphic human deletions that are shared with archaic hominin genomes has yet to be studied. We identified 427 polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the HumanNeandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed). Recurrence, incomplete lineage sorting between human and chimp lineages, and hominid-specific insertions constitute the remaining approximately 4% of allele sharing between humans and archaic hominins. We observed that ancient deletions correspond to more than 13% of all common (>5% allele frequency) deletion variation among modern humans. Our analyses indicate that the genomic landscapes of both ancient and introgressed deletion variants were primarily shaped by purifying selection, eliminating large and exonic variants. We found 17 exonic deletions that are shared with archaic hominin genomes, including those leading to three fusion transcripts. The affected genes are involved in metabolism of external and internal compounds, growth and sperm formation, as well as susceptibility to psoriasis and Crohns disease. Our analyses suggest that these exonic deletion variants have evolved through different adaptive forces, including balancing and population-specific positive selection. Our findings reveal that genomic structural variants that are shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionarily important phenotypes. PMID:25556237

  2. The evolution and functional impact of human deletion variants shared with archaic hominin genomes.

    PubMed

    Lin, Yen-Lung; Pavlidis, Pavlos; Karakoc, Emre; Ajay, Jerry; Gokcumen, Omer

    2015-04-01

    Allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-African introgression from archaic hominins. However, evolution of polymorphic human deletions that are shared with archaic hominin genomes has yet to be studied. We identified 427 polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the Human-Neandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed). Recurrence, incomplete lineage sorting between human and chimp lineages, and hominid-specific insertions constitute the remaining approximately 4% of allele sharing between humans and archaic hominins. We observed that ancient deletions correspond to more than 13% of all common (>5% allele frequency) deletion variation among modern humans. Our analyses indicate that the genomic landscapes of both ancient and introgressed deletion variants were primarily shaped by purifying selection, eliminating large and exonic variants. We found 17 exonic deletions that are shared with archaic hominin genomes, including those leading to three fusion transcripts. The affected genes are involved in metabolism of external and internal compounds, growth and sperm formation, as well as susceptibility to psoriasis and Crohn's disease. Our analyses suggest that these "exonic" deletion variants have evolved through different adaptive forces, including balancing and population-specific positive selection. Our findings reveal that genomic structural variants that are shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionarily important phenotypes. PMID:25556237

  3. Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome

    PubMed Central

    Amemiya, Chris T.; Powers, Thomas P.; Prohaska, Sonja J.; Grimwood, Jane; Schmutz, Jeremy; Dickson, Mark; Miyake, Tsutomu; Schoenborn, Michael A.; Myers, Richard M.; Ruddle, Francis H.; Stadler, Peter F.

    2010-01-01

    The living coelacanth is a lobe-finned fish that represents an early evolutionary departure from the lineage that led to land vertebrates, and is of extreme interest scientifically. It has changed very little in appearance from fossilized coelacanths of the Cretaceous (150 to 65 million years ago), and is often referred to as a living fossil. An important general question is whether long-term stasis in morphological evolution is associated with stasis in genome evolution. To this end we have used targeted genome sequencing for acquiring 1,612,752 bp of high quality finished sequence encompassing the four HOX clusters of the Indonesian coelacanth Latimeria menadoensis. Detailed analyses were carried out on genomic structure, gene and repeat contents, conserved noncoding regions, and relative rates of sequence evolution in both coding and noncoding tracts. Our results demonstrate conclusively that the coelacanth HOX clusters are evolving comparatively slowly and that this taxon should serve as a viable outgroup for interpretation of the genomes of tetrapod species. PMID:20139301

  4. Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics.

    TOXLINE Toxicology Bibliographic Information

    Orsi RH; den Bakker HC; Wiedmann M

    2011-02-01

    Listeria monocytogenes consists of at least 4 evolutionary lineages (I, II, III, and IV) with different but overlapping ecological niches. Most L. monocytogenes isolates seem to belong to lineages I and II, which harbor the serotypes more commonly associated with human clinical cases, including serotype 1/2a (lineage II) and serotypes 1/2b and 4b (lineage I). Lineage II strains are common in foods, seem to be widespread in the natural and farm environments, and are also commonly isolated from animal listeriosis cases and sporadic human clinical cases. Most human listeriosis outbreaks are associated with lineage I isolates though. In addition, a number of studies indicate that, in many countries, lineage I strains are overrepresented among human isolates, as compared to lineage II strains. Lineage III and IV strains on the other hand are rare and predominantly isolated from animal sources. The apparent differences in the distribution of strains representing the L. monocytogenes lineages has lead to a number of studies aimed at identifying phenotypic differences among the different lineages. Interestingly, lineage II isolates seem to carry more plasmids than lineage I isolates and these plasmids often confer resistance to toxic metals and possibly other compounds that may be found in the environment. Moreover, lineage II isolates seem to be more resistant to bacteriocins than lineage I isolates, which probably confers an advantage in environments where bacteriocin-producing organisms are abundant. A large number of lineage II isolates and strains have been shown to be virulence-attenuated due to premature stop codon mutations in inlA and mutations in prfA. A subset of lineage I isolates carry a listeriolysin S hemolysin, which is not present in isolates belonging to lineages II, III, or IV. While lineage II isolates also show higher recombination rates than lineage I isolates, possibly facilitating adaptation of lineage II strains to diverse environments, lineage I isolates are clonal and show a low prevalence of plasmids and IS elements, suggesting that lineage I isolates may have mechanisms that limit the acquisition of foreign DNA by horizontal gene transfer. Diversifying selection has also been shown to have played an important role during evolution of the L. monocytogenes lineages and during divergence of L. monocytogenes from the non-pathogenic species L. innocua. Overall evidence thus suggests that the 4 L. monocytogenes lineages identified so far represent distinct ecologic, genetic, and phenotypic characteristics, which appear to affect their ability to be transmitted through foods and to cause human disease. Further insights into the ecology, evolution, and characteristics of these lineages will thus not only provide an improved understanding of the evolution of this foodborne pathogen, but may also facilitate improved control of foodborne listeriosis.

  5. Genome Evolution and Phylogenomic Analysis of Candidatus Kinetoplastibacterium, the Betaproteobacterial Endosymbionts of Strigomonas and Angomonas

    PubMed Central

    Alves, Joo M.P.; Serrano, Myrna G.; Maia da Silva, Flvia; Voegtly, Logan J.; Matveyev, Andrey V.; Teixeira, Marta M.G.; Camargo, Erney P.; Buck, Gregory A.

    2013-01-01

    It has been long known that insect-infecting trypanosomatid flagellates from the genera Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont]) that supplement the host metabolism. Based on previous analyses of other bacterial endosymbiont genomes from other lineages, a stereotypical path of genome evolution in such bacteria over the duration of their association with the eukaryotic host has been characterized. In this work, we sequence and analyze the genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic analyses with all available Betaproteobacteria, and compare the TPEs with their nearest betaproteobacterial relatives. We also identify a number of housekeeping and central metabolism genes that seem to have undergone positive selection. Our genome structure analyses show total synteny among the five TPEs despite millions of years of divergence, and that this lineage follows the common path of genome evolution observed in other endosymbionts of diverse ancestries. As previously suggested by cell biology and biochemistry experiments, Ca. Kinetoplastibacterium spp. preferentially maintain those genes necessary for the biosynthesis of compounds needed by their hosts. We have also shown that metabolic and informational genes related to the cooperation with the host are overrepresented amongst genes shown to be under positive selection. Finally, our phylogenomic analysis shows that, while being in the Alcaligenaceae family of Betaproteobacteria, the closest relatives of these endosymbionts are not in the genus Bordetella as previously reported, but more likely in the Taylorella genus. PMID:23345457

  6. Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites.

    PubMed

    Haag, Karen L; James, Timothy Y; Pombert, Jean-Franois; Larsson, Ronny; Schaer, Tobias M M; Refardt, Dominik; Ebert, Dieter

    2014-10-28

    Intracellular parasitism results in extreme adaptations, whose evolutionary history is difficult to understand, because the parasites and their known free-living relatives are so divergent from one another. Microsporidia are intracellular parasites of humans and other animals, which evolved highly specialized morphological structures, but also extreme physiologic and genomic simplification. They are suggested to be an early-diverging branch on the fungal tree, but comparisons to other species are difficult because their rates of molecular evolution are exceptionally high. Mitochondria in microsporidia have degenerated into organelles called mitosomes, which have lost a genome and the ability to produce ATP. Here we describe a gut parasite of the crustacean Daphnia that despite having remarkable morphological similarity to the microsporidia, has retained genomic features of its fungal ancestors. This parasite, which we name Mitosporidium daphniae gen. et sp. nov., possesses a mitochondrial genome including genes for oxidative phosphorylation, yet a spore stage with a highly specialized infection apparatus--the polar tube--uniquely known only from microsporidia. Phylogenomics places M. daphniae at the root of the microsporidia. A comparative genomic analysis suggests that the reduction in energy metabolism, a prominent feature of microsporidian evolution, was preceded by a reduction in the machinery controlling cell cycle, DNA recombination, repair, and gene expression. These data show that the morphological features unique to M. daphniae and other microsporidia were already present before the lineage evolved the extreme host metabolic dependence and loss of mitochondrial respiration for which microsporidia are well known. PMID:25313038

  7. Identification, Diversity and Evolution of MITEs in the Genomes of Microsporidian Nosema Parasites

    PubMed Central

    He, Qiang; Ma, Zhenggang; Dang, Xiaoqun; Xu, Jinshan; Zhou, Zeyang

    2015-01-01

    Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous DNA transposons, which are widespread in most eukaryotic genomes. However, genome-wide identification, origin and evolution of MITEs remain largely obscure in microsporidia. In this study, we investigated structural features for de novo identification of MITEs in genomes of silkworm microsporidia Nosema bombycis and Nosema antheraeae, as well as a honeybee microsporidia Nosema ceranae. A total of 1490, 149 and 83 MITE-related sequences from 89, 17 and five families, respectively, were found in the genomes of the above-mentioned species. Species-specific MITEs are predominant in each genome of microsporidian Nosema, with the exception of three MITE families that were shared by N. bombycis and N. antheraeae. One or multiple rounds of amplification occurred for MITEs in N. bombycis after divergence between N. bombycis and the other two species, suggesting that the more abundant families in N. bombycis could be attributed to the recent amplification of new MITEs. Significantly, some MITEs that inserted into the homologous protein-coding region of N. bombycis were recruited as introns, indicating that gene expansion occurred during the evolution of microsporidia. NbS31 and NbS24 had polymorphisms in different geographical strains of N. bombycis, indicating that they could still be active. In addition, several small RNAs in the MITEs in N. bombycis are mainly produced from both ends of the MITEs sequence. PMID:25898273

  8. Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites

    PubMed Central

    Haag, Karen L.; James, Timothy Y.; Pombert, Jean-François; Larsson, Ronny; Schaer, Tobias M. M.; Refardt, Dominik; Ebert, Dieter

    2014-01-01

    Intracellular parasitism results in extreme adaptations, whose evolutionary history is difficult to understand, because the parasites and their known free-living relatives are so divergent from one another. Microsporidia are intracellular parasites of humans and other animals, which evolved highly specialized morphological structures, but also extreme physiologic and genomic simplification. They are suggested to be an early-diverging branch on the fungal tree, but comparisons to other species are difficult because their rates of molecular evolution are exceptionally high. Mitochondria in microsporidia have degenerated into organelles called mitosomes, which have lost a genome and the ability to produce ATP. Here we describe a gut parasite of the crustacean Daphnia that despite having remarkable morphological similarity to the microsporidia, has retained genomic features of its fungal ancestors. This parasite, which we name Mitosporidium daphniae gen. et sp. nov., possesses a mitochondrial genome including genes for oxidative phosphorylation, yet a spore stage with a highly specialized infection apparatus—the polar tube—uniquely known only from microsporidia. Phylogenomics places M. daphniae at the root of the microsporidia. A comparative genomic analysis suggests that the reduction in energy metabolism, a prominent feature of microsporidian evolution, was preceded by a reduction in the machinery controlling cell cycle, DNA recombination, repair, and gene expression. These data show that the morphological features unique to M. daphniae and other microsporidia were already present before the lineage evolved the extreme host metabolic dependence and loss of mitochondrial respiration for which microsporidia are well known. PMID:25313038

  9. Identification, Diversity and Evolution of MITEs in the Genomes of Microsporidian Nosema Parasites.

    PubMed

    He, Qiang; Ma, Zhenggang; Dang, Xiaoqun; Xu, Jinshan; Zhou, Zeyang

    2015-01-01

    Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous DNA transposons, which are widespread in most eukaryotic genomes. However, genome-wide identification, origin and evolution of MITEs remain largely obscure in microsporidia. In this study, we investigated structural features for de novo identification of MITEs in genomes of silkworm microsporidia Nosema bombycis and Nosema antheraeae, as well as a honeybee microsporidia Nosema ceranae. A total of 1490, 149 and 83 MITE-related sequences from 89, 17 and five families, respectively, were found in the genomes of the above-mentioned species. Species-specific MITEs are predominant in each genome of microsporidian Nosema, with the exception of three MITE families that were shared by N. bombycis and N. antheraeae. One or multiple rounds of amplification occurred for MITEs in N. bombycis after divergence between N. bombycis and the other two species, suggesting that the more abundant families in N. bombycis could be attributed to the recent amplification of new MITEs. Significantly, some MITEs that inserted into the homologous protein-coding region of N. bombycis were recruited as introns, indicating that gene expansion occurred during the evolution of microsporidia. NbS31 and NbS24 had polymorphisms in different geographical strains of N. bombycis, indicating that they could still be active. In addition, several small RNAs in the MITEs in N. bombycis are mainly produced from both ends of the MITEs sequence. PMID:25898273

  10. Massively Convergent Evolution for Ribosomal Protein Gene Content in Plastid and Mitochondrial Genomes

    PubMed Central

    Maier, Uwe-G; Zauner, Stefan; Woehle, Christian; Bolte, Kathrin; Hempel, Franziska; Allen, John F.; Martin, William F.

    2013-01-01

    Plastid and mitochondrial genomes have undergone parallel evolution to encode the same functional set of genes. These encode conserved protein components of the electron transport chain in their respective bioenergetic membranes and genes for the ribosomes that express them. This highly convergent aspect of organelle genome evolution is partly explained by the redox regulation hypothesis, which predicts a separate plastid or mitochondrial location for genes encoding bioenergetic membrane proteins of either photosynthesis or respiration. Here we show that convergence in organelle genome evolution is far stronger than previously recognized, because the same set of genes for ribosomal proteins is independently retained by both plastid and mitochondrial genomes. A hitherto unrecognized selective pressure retains genes for the same ribosomal proteins in both organelles. On the Escherichia coli ribosome assembly map, the retained proteins are implicated in 30S and 50S ribosomal subunit assembly and initial rRNA binding. We suggest that ribosomal assembly imposes functional constraints that govern the retention of ribosomal protein coding genes in organelles. These constraints are subordinate to redox regulation for electron transport chain components, which anchor the ribosome to the organelle genome in the first place. As organelle genomes undergo reduction, the rRNAs also become smaller. Below size thresholds of approximately 1,300 nucleotides (16S rRNA) and 2,100 nucleotides (26S rRNA), all ribosomal protein coding genes are lost from organelles, while electron transport chain components remain organelle encoded as long as the organelles use redox chemistry to generate a proton motive force. PMID:24259312

  11. Patterns of evolutionary conservation of microsatellites (SSRs) suggest a faster rate of genome evolution in Hymenoptera than in Diptera.

    PubMed

    Stolle, Eckart; Kidner, Jonathan H; Moritz, Robin F A

    2013-01-01

    Microsatellites, or simple sequence repeats (SSRs), are common and widespread DNA elements in genomes of many organisms. However, their dynamics in genome evolution is unclear, whereby they are thought to evolve neutrally. More available genome sequences along with dated phylogenies allowed for studying the evolution of these repetitive DNA elements along evolutionary time scales. This could be used to compare rates of genome evolution. We show that SSRs in insects can be retained for several hundred million years. Different types of microsatellites seem to be retained longer than others. By comparing Dipteran with Hymenopteran species, we found very similar patterns of SSR loss during their evolution, but both taxa differ profoundly in the rate. Relative to divergence time, Diptera lost SSRs twice as fast as Hymenoptera. The loss of SSRs on the Drosophila melanogaster X-chromosome was higher than on the other chromosomes. However, accounting for generation time, the Diptera show an 8.5-fold slower rate of SSR loss than the Hymenoptera, which, in contrast to previous studies, suggests a faster genome evolution in the latter. This shows that generation time differences can have a profound effect. A faster genome evolution in these insects could be facilitated by several factors very different to Diptera, which is discussed in light of our results on the haplodiploid D. melanogaster X-chromosome. Furthermore, large numbers of SSRs can be found to be in synteny and thus could be exploited as a tool to investigate genome structure and evolution. PMID:23292136

  12. Patterns of Evolutionary Conservation of Microsatellites (SSRs) Suggest a Faster Rate of Genome Evolution in Hymenoptera Than in Diptera

    PubMed Central

    Stolle, Eckart; Kidner, Jonathan H.; Moritz, Robin F.A.

    2013-01-01

    Microsatellites, or simple sequence repeats (SSRs), are common and widespread DNA elements in genomes of many organisms. However, their dynamics in genome evolution is unclear, whereby they are thought to evolve neutrally. More available genome sequences along with dated phylogenies allowed for studying the evolution of these repetitive DNA elements along evolutionary time scales. This could be used to compare rates of genome evolution. We show that SSRs in insects can be retained for several hundred million years. Different types of microsatellites seem to be retained longer than others. By comparing Dipteran with Hymenopteran species, we found very similar patterns of SSR loss during their evolution, but both taxa differ profoundly in the rate. Relative to divergence time, Diptera lost SSRs twice as fast as Hymenoptera. The loss of SSRs on the Drosophila melanogaster X-chromosome was higher than on the other chromosomes. However, accounting for generation time, the Diptera show an 8.5-fold slower rate of SSR loss than the Hymenoptera, which, in contrast to previous studies, suggests a faster genome evolution in the latter. This shows that generation time differences can have a profound effect. A faster genome evolution in these insects could be facilitated by several factors very different to Diptera, which is discussed in light of our results on the haplodiploid D. melanogaster X-chromosome. Furthermore, large numbers of SSRs can be found to be in synteny and thus could be exploited as a tool to investigate genome structure and evolution. PMID:23292136

  13. Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

    PubMed Central

    Voloch, Carolina M.; Capello, Renata T.; Mello, Beatriz; Schrago, Carlos G.

    2014-01-01

    Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups. PMID:25415197

  14. Analysis of adaptive evolution in Lyssavirus genomes reveals pervasive diversifying selection during species diversification.

    PubMed

    Voloch, Carolina M; Capello, Renata T; Mello, Beatriz; Schrago, Carlos G

    2014-11-01

    Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups. PMID:25415197

  15. Vertebrate genome evolution and the zebrafish gene map.

    PubMed

    Postlethwait, J H; Yan, Y L; Gates, M A; Horne, S; Amores, A; Brownlie, A; Donovan, A; Egan, E S; Force, A; Gong, Z; Goutel, C; Fritz, A; Kelsh, R; Knapik, E; Liao, E; Paw, B; Ransom, D; Singer, A; Thomson, M; Abduljabbar, T S; Yelick, P; Beier, D; Joly, J S; Larhammar, D; Rosa, F; Westerfield, M; Zon, L I; Johnson, S L; Talbot, W S

    1998-04-01

    In chordate phylogeny, changes in the nervous system, jaws, and appendages transformed meek filter feeders into fearsome predators. Gene duplication is thought to promote such innovation. Vertebrate ancestors probably had single copies of genes now found in multiple copies in vertebrates and gene maps suggest that this occurred by polyploidization. It has been suggested that one genome duplication event occurred before, and one after the divergence of ray-finned and lobe-finned fishes. Holland et al., however, have argued that because various vertebrates have several HOX clusters, two rounds of duplication occurred before the origin of jawed fishes. Such gene-number data, however, do not distinguish between tandem duplications and polyploidization events, nor whether independent duplications occurred in different lineages. To investigate these matters, we mapped 144 zebrafish genes and compared the resulting map with mammalian maps. Comparison revealed large conserved chromosome segments. Because duplicated chromosome segments in zebrafish often correspond with specific chromosome segments in mammals, it is likely that two polyploidization events occurred prior to the divergence of fish and mammal lineages. This zebrafish gene map will facilitate molecular identification of mutated zebrafish genes, which can suggest functions for human genes known only by sequence. PMID:9537416

  16. Genetics, genomics and evolution of ergot alkaloid diversity.

    PubMed

    Young, Carolyn A; Schardl, Christopher L; Panaccione, Daniel G; Florea, Simona; Takach, Johanna E; Charlton, Nikki D; Moore, Neil; Webb, Jennifer S; Jaromczyk, Jolanta

    2015-04-01

    The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine. PMID:25875294

  17. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

    PubMed Central

    Young, Carolyn A.; Schardl, Christopher L.; Panaccione, Daniel G.; Florea, Simona; Takach, Johanna E.; Charlton, Nikki D.; Moore, Neil; Webb, Jennifer S.; Jaromczyk, Jolanta

    2015-01-01

    The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine. PMID:25875294

  18. Population genetics and evolution of the pan-genome of Streptococcus pneumoniae.

    PubMed

    Muzzi, Alessandro; Donati, Claudio

    2011-12-01

    The genetic variability in bacterial species is much larger than in other kingdoms of life. The gene content between pairs of isolates can diverge by as much as 30% in species like Escherichia coli or Streptococcus pneumoniae. This unexpected finding led to the introduction of the concept of the pan-genome, the set of genes that can be found in a given bacterial species. The genome of any isolate is thus composed by a "core genome" shared by all strains and characteristic of the species, and a "dispensable genome" that accounts for many of the phenotypic differences between strains. The pan-genome is usually much larger than the genome of any single isolate and, given the ability of many bacteria to exchange genetic material with the environment, constitutes a reservoir that could enhance their ability to survive in a mutating environment. To understand the evolution of the pan-genome of an important pathogen and its interactions with the commensal microbial flora, we have analyzed the genomes of 44 strains of Streptococcus pneumoniae, one of the most important causes of microbial diseases in humans. Despite evidence of extensive homologous recombination, the S. pneumoniae phylogenetic tree reconstructed from polymorphisms in the core genome identified major groups of genetically related strains. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant evolutionary process of the core genome of S. pneumoniae. Genetic exchange with related species sharing the same ecological niche was the main mechanism of evolution of S. pneumonia; and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome of S. pneumoniae increased logarithmically with the number of strains and linearly with the variability of the sample, suggesting that acquired genes accumulate proportionately to the age of clones. PMID:22000739

  19. Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution

    PubMed Central

    Spang, Anja; Saw, Jimmy H.; Lind, Anders E.; Ettema, Thijs J. G.

    2013-01-01

    The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life. PMID:24348093

  20. A systems approach to understanding human rhinovirus and influenza virus infection.

    PubMed

    Kim, Taek-Kyun; Bheda-Malge, Anjali; Lin, Yakang; Sreekrishna, Koti; Adams, Rachel; Robinson, Michael K; Bascom, Charles C; Tiesman, Jay P; Isfort, Robert J; Gelinas, Richard

    2015-12-01

    Human rhinovirus and influenza virus infections of the upper airway lead to colds and the flu and can trigger exacerbations of lower airway diseases including asthma and chronic obstructive pulmonary disease. Novel diagnostic and therapeutic targets are still needed to differentiate between the cold and the flu, since the clinical course of influenza can be severe while that of rhinovirus is usually more mild. In our investigation of influenza and rhinovirus infection of human respiratory epithelial cells, we used a systems approach to identify the temporally changing patterns of host gene expression from these viruses. After infection of human bronchial epithelial cells (BEAS-2B) with rhinovirus, influenza virus or co-infection with both viruses, we studied the time-course of host gene expression changes over three days. We modeled host responses to these viral infections with time and documented the qualitative and quantitative differences in innate immune activation and regulation. PMID:26437235

  1. Evolution of a Pathogen: A Comparative Genomics Analysis Identifies a Genetic Pathway to Pathogenesis in Acinetobacter

    PubMed Central

    Sahl, Jason W.; Gillece, John D.; Schupp, James M.; Waddell, Victor G.; Driebe, Elizabeth M.; Engelthaler, David M.; Keim, Paul

    2013-01-01

    Acinetobacter baumannii is an emergent and global nosocomial pathogen. In addition to A. baumannii, other Acinetobacter species, especially those in the Acinetobacter calcoaceticus-baumannii (Acb) complex, have also been associated with serious human infection. Although mechanisms of attachment, persistence on abiotic surfaces, and pathogenesis in A. baumannii have been identified, the genetic mechanisms that explain the emergence of A. baumannii as the most widespread and virulent Acinetobacter species are not fully understood. Recent whole genome sequencing has provided insight into the phylogenetic structure of the genus Acinetobacter. However, a global comparison of genomic features between Acinetobacter spp. has not been described in the literature. In this study, 136 Acinetobacter genomes, including 67 sequenced in this study, were compared to identify the acquisition and loss of genes in the expansion of the Acinetobacter genus. A whole genome phylogeny confirmed that A. baumannii is a monophyletic clade and that the larger Acb complex is also a well-supported monophyletic group. The whole genome phylogeny provided the framework for a global genomic comparison based on a blast score ratio (BSR) analysis. The BSR analysis demonstrated that specific genes have been both lost and acquired in the evolution of A. baumannii. In addition, several genes associated with A. baumannii pathogenesis were found to be more conserved in the Acb complex, and especially in A. baumannii, than in other Acinetobacter genomes; until recently, a global analysis of the distribution and conservation of virulence factors across the genus was not possible. The results demonstrate that the acquisition of specific virulence factors has likely contributed to the widespread persistence and virulence of A. baumannii. The identification of novel features associated with transcriptional regulation and acquired by clades in the Acb complex presents targets for better understanding the evolution of pathogenesis and virulence in the expansion of the genus. PMID:23365658

  2. Ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family

    PubMed Central

    Tanaka-Kunishima, Motoko; Ishida, Yoshihiro; Takahashi, Kunitaro; Honda, Motoo; Oonuma, Takashi

    2007-01-01

    Background In spite of the recent accumulation of genomic data, the evolutionary pathway in the individual genes of present-day living taxa is still elusive for most genes. Among ion channels, inward K+ rectifier (IRK) channels are the fundamental and well-defined protein group. We analyzed the genomic structures of this group and compared them among a phylogenetically wide range with our sequenced Halocynthia roretzi, a tunicate, IRK genomic genes. Results A total of 131 IRK genomic genes were analyzed. The phylogenic trees of amino acid sequences revealed a clear diversification of deuterostomic IRKs from protostomic IRKs and suggested that the tunicate IRKs are possibly representatives of the descendants of ancestor forms of three major groups of IRKs in the vertebrate. However, the exon-intron structures of the tunicate IRK genomes showed considerable similarities to those of Caenorhabditis. In the vertebrate clade, the members in each major group increased at least four times those in the tunicate by various types of global gene duplication. The generation of some major groups was inferred to be due to anti-tandem (palindromic) duplication in early history. The intron insertion points greatly decreased during the evolution of the vertebrates, remaining as a unique conservation of an intron insertion site in the portion of protein-protein interaction within the coding regions of all vertebrate G-protein-activated IRK genes. Conclusion From the genomic survey of a family of IRK genes, it was suggested that the ancient intron insertion sites and the unique palindromic genomic duplication evolutionally shaped this membrane protein family. PMID:17708769

  3. Evolution of a noncoding region of the chloroplast genome.

    PubMed

    Golenberg, E M; Clegg, M T; Durbin, M L; Doebley, J; Ma, D P

    1993-03-01

    The relative rate of occurrence of nucleotide substitutions versus indel (insertion/deletion) events is investigated by comparing complete DNA sequence data from the noncoding portion of the chloroplast genome that maps between the genes rbcL and atp beta. The sequence data are obtained from nine species that represent three tribes of the grass family. Indels could be categorized by those that are deletions or duplications of adjacent or proximal sequences and those that do not appear to be permutations of adjacent sequences. The first category represents 82% of the recorded indels. These indels may also be characterized by being direct duplications of one to several bases usually within runs of As or Ts or by being duplications or deletions of more complex sequences. When viewed from within groups of closely related taxa, indel events appear to occur at an equal or slightly faster rate than do nucleotide substitution events. However, the apparent rate of accumulation of indels in more distantly related species is significantly slower than that of nucleotide substitutions. This difference in apparent accumulation rates between indel events and nucleotide substitutions suggests that the proportion of superimposed changes has been higher among all indel events than among all nucleotide substitution events. Indeed the indels involving more complex sequences were found to be confined across taxa to a number of highly labile sites. Independent, though similar, indel events occur at identical sites in unrelated taxa, yet may not be shared among related taxa, resulting in a type of molecular parallelism. As a result, the phylogenetic tree based on indel events represents an evolutionary hypothesis which is inconsistent with the accepted phylogeny of these grasses. The phylogenetic tree based on nucleotide substitutions is consistent with accepted phylogeny. PMID:8081547

  4. Insights and inferences about integron evolution from genomic data

    PubMed Central

    Nemergut, Diana R; Robeson, Michael S; Kysela, Robert F; Martin, Andrew P; Schmidt, Steven K; Knight, Rob

    2008-01-01

    Background Integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign DNA. These are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. Here, we provide a systematic analysis of the distribution and diversity of integron intI genes and integron-containing bacteria. Results We found integrons in 103 different pathogenic and non-pathogenic bacteria, in six major phyla. Integrons were widely scattered, and their presence was not confined to specific clades within bacterial orders. Nearly 1/3 of the intI genes that we identified were pseudogenes, containing either an internal stop codon or a frameshift mutation that would render the protein product non-functional. Additionally, 20% of bacteria contained more than one integrase gene. dN/dS ratios revealed mutational hotspots in clades of Vibrio and Shewanella intI genes. Finally, we characterized the gene cassettes associated with integrons in Methylobacillus flagellatus KT and Dechloromonas aromatica RCB, and found a heavy metal efflux gene as well as genes involved in protein folding and stability. Conclusion Our analysis suggests that the present distribution of integrons is due to multiple losses and gene transfer events. While, in some cases, the ability to integrate and excise foreign DNA may be selectively advantageous, the gain, loss, or rearrangment of gene cassettes could also be deleterious, selecting against functional integrases. Thus, such a high fraction of pseudogenes may suggest that the selective impact of integrons on genomes is variable, oscillating between beneficial and deleterious, possibly depending on environmental conditions. PMID:18513439

  5. Modeling of the human rhinovirus C capsid suggests possible causes for antiviral drug resistance.

    PubMed

    Basta, Holly A; Ashraf, Shamaila; Sgro, Jean-Yves; Bochkov, Yury A; Gern, James E; Palmenberg, Ann C

    2014-01-01

    Human rhinoviruses of the RV-C species are recently discovered pathogens with greater clinical significance than isolates in the RV-A+B species. The RV-C cannot be propagated in typical culture systems; so much of the virology is necessarily derivative, relying on comparative genomics, relative to the better studied RV-A+B. We developed a bioinformatics-based structural model for a C15 isolate. The model showed the VP1-3 capsid proteins retain their fundamental cores relative to the RV-A+B, but conserved, internal RV-C residues affect the shape and charge of the VP1 hydrophobic pocket that confers antiviral drug susceptibility. When predictions of the model were tested in organ cultures or ALI systems with recombinant C15 virus, there was a resistance to capsid-binding drugs, including pleconaril, BTA-188, WIN56291, WIN52035 and WIN52084. Unique to all RV-C, the model predicts conserved amino acids within the pocket and capsid surface pore leading to the pocket may correlate with this activity. PMID:24314639

  6. Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms.

    PubMed

    Puttick, Mark N; Clark, James; Donoghue, Philip C J

    2015-12-01

    Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity. PMID:26631568

  7. Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms

    PubMed Central

    Puttick, Mark N.; Clark, James; Donoghue, Philip C. J.

    2015-01-01

    Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity. PMID:26631568

  8. Genomic and Metagenomic Approaches for Predicting Pathogen Evolution.

    PubMed

    Casas, Veronica; Maloy, Stanley

    2014-02-01

    Global climate change can alter the distribution of microbial pathogens and vectors that transmit infectious diseases, exposing humans to newly emerging or reemerging diseases. Early detection of potential pathogens and vectors in the environment can facilitate upstream interventions that limit the spread of infectious disease. Metagenomics is the analysis of DNA sequences from a population of microorganisms in a particular environment, followed by the computational reconstruction of the data to determine what organisms are present and predict their role in the environment. Defining the microbial populations associated with humans, animals, and their environment provides insight into the structure of microbial communities in any particular niche, including the abundance, diversity, and composition of the microbes and viruses present. It can also reveal the distribution of virulence genes within that niche. These data can be used to identify reservoirs of pathogens in an environment and predict environments with a high probability for evolution of new pathogens or outbreaks caused by known pathogens, thereby facilitating approaches to prevent infections of animals or humans before serious outbreaks of infectious disease. PMID:26082117

  9. Early evolution of efficient enzymes and genome organization

    PubMed Central

    2012-01-01

    Background Cellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specificities: they were generalist. When and under what conditions could primordial metabolism run by generalist enzymes evolve to contemporary-type metabolism run by specific enzymes? Results Here we show by numerical simulation of an enzyme-catalyzed reaction chain that specialist enzymes spread after the invention of the chromosome because protocells harbouring unlinked genes maintain largely non-specific enzymes to reduce their assortment load. When genes are linked on chromosomes, high enzyme specificity evolves because it increases biomass production, also by reducing taxation by side reactions. Conclusion The constitution of the genetic system has a profound influence on the limits of metabolic efficiency. The major evolutionary transition to chromosomes is thus proven to be a prerequisite for a complex metabolism. Furthermore, the appearance of specific enzymes opens the door for the evolution of their regulation. Reviewers This article was reviewed by Sndor Pongor, Gspr Jkely, and Rob Knight. PMID:23114029

  10. Epidemiology of virus-induced asthma exacerbations: with special reference to the role of human rhinovirus

    PubMed Central

    Saraya, Takeshi; Kurai, Daisuke; Ishii, Haruyuki; Ito, Anri; Sasaki, Yoshiko; Niwa, Shoichi; Kiyota, Naoko; Tsukagoshi, Hiroyuki; Kozawa, Kunihisa; Goto, Hajime; Takizawa, Hajime

    2014-01-01

    Viral respiratory infections may be associated with the virus-induced asthma in adults as well as children. Particularly, human rhinovirus is strongly suggested a major candidate for the associations of the virus-induced asthma. Thus, in this review, we reviewed and focused on the epidemiology, pathophysiology, and treatment of virus-induced asthma with special reference on human rhinovirus. Furthermore, we added our preliminary data regarding the clinical and virological findings in the present review. PMID:24904541

  11. Outgrowth of the Bacterial Airway Microbiome after Rhinovirus Exacerbation of Chronic Obstructive Pulmonary Disease

    PubMed Central

    Molyneaux, Philip L.; Mallia, Patrick; Cox, Michael J.; Footitt, Joseph; Willis-Owen, Saffron A. G.; Homola, Daniel; Trujillo-Torralbo, Maria-Belen; Elkin, Sarah; Kon, Onn Min; Cookson, William O. C.; Johnston, Sebastian L.

    2013-01-01

    Rationale: Rhinovirus infection is followed by significantly increased frequencies of positive, potentially pathogenic sputum cultures in chronic obstructive pulmonary disease (COPD). However, it remains unclear whether these represent de novo infections or an increased load of organisms from the complex microbial communities (microbiome) in the lower airways. Objectives: To investigate the effect of rhinovirus infection on the airway bacterial microbiome. Methods: Subjects with COPD (n = 14) and healthy control subjects with normal lung function (n = 17) were infected with rhinovirus. Induced sputum was collected at baseline before rhinovirus inoculation and again on Days 5, 15, and 42 after rhinovirus infection and DNA was extracted. The V3V5 region of the bacterial 16S ribosomal RNA gene was amplified and pyrosequenced, resulting in 370,849 high-quality reads from 112 of the possible 124 time points. Measurements and Main Results: At 15 days after rhinovirus infection, there was a sixfold increase in 16S copy number (P = 0.007) and a 16% rise in numbers of proteobacterial sequences, most notably in potentially pathogenic Haemophilus influenzae (P = 2.7 10-20), from a preexisting community. These changes occurred only in the sputum microbiome of subjects with COPD and were still evident 42 days after infection. This was in contrast to the temporal stability demonstrated in the microbiome of healthy smokers and nonsmokers. Conclusions: After rhinovirus infection, there is a rise in bacterial burden and a significant outgrowth of Haemophilus influenzae from the existing microbiota of subjects with COPD. This is not observed in healthy individuals. Our findings suggest that rhinovirus infection in COPD alters the respiratory microbiome and may precipitate secondary bacterial infections. PMID:23992479

  12. The bovine lactation genome: insights into the evolution of mammalian milk

    PubMed Central

    Lemay, Danielle G; Lynn, David J; Martin, William F; Neville, Margaret C; Casey, Theresa M; Rincon, Gonzalo; Kriventseva, Evgenia V; Barris, Wesley C; Hinrichs, Angie S; Molenaar, Adrian J; Pollard, Katherine S; Maqbool, Nauman J; Singh, Kuljeet; Murney, Regan; Zdobnov, Evgeny M; Tellam, Ross L; Medrano, Juan F; German, J Bruce; Rijnkels, Monique

    2009-01-01

    Background The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. Results Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome. Intersection of these genes with 238 milk production quantitative trait loci curated from the literature decreased the search space for milk trait effectors by more than an order of magnitude. Genome location analysis revealed a tendency for milk protein genes to be clustered with other mammary genes. Using the genomes of a monotreme (platypus), a marsupial (opossum), and five placental mammals (bovine, human, dog, mice, rat), gene loss and duplication, phylogeny, sequence conservation, and evolution were examined. Compared with other genes in the bovine genome, milk and mammary genes are: more likely to be present in all mammals; more likely to be duplicated in therians; more highly conserved across Mammalia; and evolving more slowly along the bovine lineage. The most divergent proteins in milk were associated with nutritional and immunological components of milk, whereas highly conserved proteins were associated with secretory processes. Conclusions Although both copy number and sequence variation contribute to the diversity of milk protein composition across species, our results suggest that this diversity is primarily due to other mechanisms. Our findings support the essentiality of milk to the survival of mammalian neonates and the establishment of milk secretory mechanisms more than 160 million years ago. PMID:19393040

  13. Genome evolution and speciation: toward quantitative descriptions of pattern and process.

    PubMed

    Nosil, Patrik; Feder, Jeffrey L

    2013-09-01

    Studies of patterns of differentiation across genomes are accumulating, yet integrative work that combines approaches and fully capitalizes on new technologies to test explicit hypotheses is still rare. Thus, debates persist about the rate, magnitude, and causes of genomic change. This special section is devoted to helping resolve these debates. The eight studies contained within demonstrate how we can begin to move away from vague metaphors toward quantitative and more precise descriptors of patterns of genetic architecture and divergence. However, a particular genomic pattern can often arise via different combinations of various processes such as selection, gene flow, recombination, mutation, genetic drift, and demographic variability. Thus, substantial challenges remain in elucidating which evolutionary processes generated observed genomic patterns. Nonetheless, the studies in this section demonstrate ways forward toward bridging pattern and process, including experimental work, genetic mapping, increased knowledge of natural history and demography, and comparative studies spanning taxa at different points in the speciation continuum. Such collective work will lead to more powerful hypothesis testing. Future work can also help better integrate the contributions of ecology, genome structure (e.g., inversions and translocations), and genetic conflict to genome evolution. PMID:24033160

  14. Genome of the Rusty Millipede, Trigoniulus corallinus, Illuminates Diplopod, Myriapod, and Arthropod Evolution

    PubMed Central

    Kenny, Nathan J.; Shen, Xin; Chan, Thomas T.H.; Wong, Nicola W.Y.; Chan, Ting Fung; Chu, Ka Hou; Lam, Hon-Ming; Hui, Jerome H.L.

    2015-01-01

    The increasing availability of genomic information from the Arthropoda continues to revolutionize our understanding of the biology of this most diverse animal phylum. However, our sampling of arthropod diversity remains uneven, and key clade such as the Myriapoda are severely underrepresented. Here we present the genome of the cosmopolitanly distributed Rusty Millipede Trigoniulus corallinus, which represents the first diplopod genome to be published, and the second example from the Myriapoda as a whole. This genomic resource contains the majority of core eukaryotic genes (94.3%), and key transcription factor classes that were thought to be lost in the Ecdysozoa. Mitochondrial genome and gene family (transcription factor, Dscam, circadian clock-driving protein, odorant receptor cassette, bioactive compound, and cuticular protein) analyses were also carried out to shed light on their states in the Diplopoda and Myriapoda. The ready availability of T. corallinus recommends it as a new model for evolutionary developmental biology, and the data set described here will be of widespread utility in investigating myriapod and arthropod genomics and evolution. PMID:25900922

  15. The sacred lotus genome provides insights into the evolution of flowering plants.

    PubMed

    Wang, Yun; Fan, Guangyi; Liu, Yiman; Sun, Fengming; Shi, Chengcheng; Liu, Xin; Peng, Jing; Chen, Wenbin; Huang, Xinfang; Cheng, Shifeng; Liu, Yuping; Liang, Xinming; Zhu, Honglian; Bian, Chao; Zhong, Lan; Lv, Tian; Dong, Hongxia; Liu, Weiqing; Zhong, Xiao; Chen, Jing; Quan, Zhiwu; Wang, Zhihong; Tan, Benzhong; Lin, Chufa; Mu, Feng; Xu, Xun; Ding, Yi; Guo, An-Yuan; Wang, Jun; Ke, Weidong

    2013-11-01

    Sacred lotus (Nelumbo nucifera) is an ornamental plant that is also used for food and medicine. This basal eudicot species is especially important from an evolutionary perspective, as it occupies a critical phylogenetic position in flowering plants. Here we report the draft genome of a wild strain of sacred lotus. The assembled genome is 792 Mb, which is approximately 85-90% of genome size estimates. We annotated 392 Mb of repeat sequences and 36,385 protein-coding genes within the genome. Using these sequence data, we constructed a phylogenetic tree and confirmed the basal location of sacred lotus within eudicots. Importantly, we found evidence for a relatively recent whole-genome duplication event; any indication of the ancient paleo-hexaploid event was, however, absent. Genomic analysis revealed evidence of positive selection within 28 embryo-defective genes and one annexin gene that may be related to the long-term viability of sacred lotus seed. We also identified a significant expansion of starch synthase genes, which probably elevated starch levels within the rhizome of sacred lotus. Sequencing this strain of sacred lotus thus provided important insights into the evolution of flowering plant and revealed genetic mechanisms that influence seed dormancy and starch synthesis. PMID:23952714

  16. Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology.

    PubMed

    Rogalski, Marcelo; do Nascimento Vieira, Leila; Fraga, Hugo P; Guerra, Miguel P

    2015-01-01

    During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ?130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field. PMID:26284102

  17. Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology

    PubMed Central

    Rogalski, Marcelo; do Nascimento Vieira, Leila; Fraga, Hugo P.; Guerra, Miguel P.

    2015-01-01

    During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100–220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field. PMID:26284102

  18. Game of clones: the genomic evolution of severe congenital neutropenia.

    PubMed

    Touw, Ivo P

    2015-12-01

    Severe congenital neutropenia (SCN) is a genetically heterogeneous condition of bone marrow failure usually diagnosed in early childhood and characterized by a chronic and severe shortage of neutrophils. It is now well-established that mutations in HAX1 and ELANE (and more rarely in other genes) are the genetic cause of SCN. In contrast, it has remained unclear how these mutations affect neutrophil development. Innovative models based on induced pluripotent stem cell technology are being explored to address this issue. These days, most SCN patients receive life-long treatment with granulocyte colony-stimulating factor (G-CSF, CSF3). CSF3 therapy has greatly improved the life expectancy of SCN patients, but also unveiled a high frequency of progression toward myelodysplastic syndrome (MDS) and therapy refractory acute myeloid leukemia (AML). Expansion of hematopoietic clones with acquired mutations in the gene encoding the G-CSF receptor (CSF3R) is regularly seen in SCN patients and AML usually descends from one of these CSF3R mutant clones. These findings raised the questions how CSF3R mutations affect CSF3 responses of myeloid progenitors, how they contribute to the pre-leukemic state of SCN, and which additional events are responsible for progression to leukemia. The vast (sub)clonal heterogeneity of AML and the presence of AML-associated mutations in normally aged hematopoietic clones make it often difficult to determine which mutations are responsible for the leukemic process. Leukemia predisposition syndromes such as SCN are unique disease models to identify the sequential acquisition of these mutations and to interrogate how they contribute to clonal selection and leukemic evolution. PMID:26637693

  19. Outcomes of Hematopoietic Stem Cell Transplant Recipients with Rhinovirus Infection: A Matched, Case-Control Study

    PubMed Central

    Abandeh, Foad I.; Lustberg, Mark; Devine, Steven; Elder, Pat; Andritsos, Leslie; Martin, Stanley I.

    2015-01-01

    The impact of rhinovirus in hematopoietic stem cell transplant (HSCT) recipients is not well defined. A retrospective, matched, case-control study of HSCT recipients with rhinovirus was conducted between 2009 and 2011. Controls were matched for timing relative to transplant, malignancy, and stem cell source. There were 47 cases and 94 controls. Cases and controls did not differ with respect to age, gender, ethnicity, donor source, malignancy, conditioning regimen, immunosuppression, antimicrobial prophylaxis, or significant comorbidities. There were no differences in need for ICU care, 100 day mortality, hospice discharge, relapse of disease, GVHD or development of disease or infection due to CMV or EBV. Other infectious complications after rhinovirus diagnosis were also equal. However, there was an increased number of recurrent hospitalizations from any cause among cases (46.8% vs. 24.5%, P=0.007). Recurrent hospitalizations due to any infection were also more common in cases (34% vs. 14.9%, P=0.015). For patients who were diagnosed with rhinovirus pre-transplant (n=13), there was no difference in outcomes compared to matched controls. HSCT recipients with rhinovirus have an increased risk of hospital readmission. However, there was no difference in outcomes compared to matched controls. Transplantation in patients with active rhinovirus infection appears to be safe. PMID:23872740

  20. Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia.

    PubMed

    Kugelman, Jeffrey R; Wiley, Michael R; Mate, Suzanne; Ladner, Jason T; Beitzel, Brett; Fakoli, Lawrence; Taweh, Fahn; Prieto, Karla; Diclaro, Joseph W; Minogue, Timothy; Schoepp, Randal J; Schaecher, Kurt E; Pettitt, James; Bateman, Stacey; Fair, Joseph; Kuhn, Jens H; Hensley, Lisa; Park, Daniel J; Sabeti, Pardis C; Sanchez-Lockhart, Mariano; Bolay, Fatorma K; Palacios, Gustavo

    2015-07-01

    To support Liberia's response to the ongoing Ebola virus (EBOV) disease epidemic in Western Africa, we established in-country advanced genomic capabilities to monitor EBOV evolution. Twenty-five EBOV genomes were sequenced at the Liberian Institute for Biomedical Research, which provided an in-depth view of EBOV diversity in Liberia during September 2014-February 2015. These sequences were consistent with a single virus introduction to Liberia; however, shared ancestry with isolates from Mali indicated at least 1 additional instance of movement into or out of Liberia. The pace of change is generally consistent with previous estimates of mutation rate. We observed 23 nonsynonymous mutations and 1 nonsense mutation. Six of these changes are within known binding sites for sequence-based EBOV medical countermeasures; however, the diagnostic and therapeutic impact of EBOV evolution within Liberia appears to be low. PMID:26079255

  1. The genomics of selection in dogs and the parallel evolution between dogs and humans.

    PubMed

    Wang, Guo-dong; Zhai, Weiwei; Yang, He-chuan; Fan, Ruo-xi; Cao, Xue; Zhong, Li; Wang, Lu; Liu, Fei; Wu, Hong; Cheng, Lu-guang; Poyarkov, Andrei D; Poyarkov, Nikolai A; Tang, Shu-sheng; Zhao, Wen-ming; Gao, Yun; Lv, Xue-mei; Irwin, David M; Savolainen, Peter; Wu, Chung-I; Zhang, Ya-ping

    2013-01-01

    The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution. PMID:23673645

  2. Rhinovirus and Asthma: A Storied History of Incompatibility

    PubMed Central

    Hammond, Catherine; Kurten, Megan; Kennedy, Joshua L.

    2015-01-01

    Human Rhinovirus (HRV) is commonly associated with loss of asthma symptom control requiring escalation of care and emergency room visits in many patients. While the association is clear, the mechanisms behind HRV-induced asthma exacerbations remain uncertain. Immune dysregulation via aberrant immune responses, both deficient and exaggerated, have been proposed as mechanisms for HRV-induced exacerbations of asthma. Epithelial-derived innate immune cytokines that bias Th2 responses, including interleukin (IL)-25, IL-33, and thymic stromal lymphopoietin (TSLP), have also been implicated as a means to bridge allergic conditions with asthma exacerbations. In this review, we discuss the literature supporting these positions. We also discuss new and emerging biotherapeutics that may target viral-induced exacerbations of asthma. PMID:25612798

  3. Challenges in developing a cross-serotype rhinovirus vaccine.

    PubMed

    Glanville, Nicholas; Johnston, Sebastian L

    2015-04-01

    A great burden of disease is attributable to human rhinovirus (HRV) infections which are the major cause of the common cold, exacerbations of both asthma and chronic obstructive pulmonary disease (COPD), and are associated with asthma development. Despite this there is currently no vaccine for HRV. The first vaccine studies showed some promise in terms of serotype-specific protection against cold symptoms, but antigenic heterogeneity amongst the >150 HRVs has been regarded as a major barrier to effective vaccine development and has resulted in little progress over 50 years. Here we review those vaccine studies conducted to date, discuss the difficulties posed by antigenic heterogeneity and describe some recent advances in generating cross-reactive antibodies and T cell responses using peptide immunogens. PMID:25829255

  4. Method for measuring the size distribution of airborne rhinovirus

    SciTech Connect

    Russell, M.L.; Goth-Goldstein, R.; Apte, M.G.; Fisk, W.J.

    2002-01-01

    About 50% of viral-induced respiratory illnesses are caused by the human rhinovirus (HRV). Measurements of the concentrations and sizes of bioaerosols are critical for research on building characteristics, aerosol transport, and mitigation measures. We developed a quantitative reverse transcription-coupled polymerase chain reaction (RT-PCR) assay for HRV and verified that this assay detects HRV in nasal lavage samples. A quantitation standard was used to determine a detection limit of 5 fg of HRV RNA with a linear range over 1000-fold. To measure the size distribution of HRV aerosols, volunteers with a head cold spent two hours in a ventilated research chamber. Airborne particles from the chamber were collected using an Andersen Six-Stage Cascade Impactor. Each stage of the impactor was analyzed by quantitative RT-PCR for HRV. For the first two volunteers with confirmed HRV infection, but with mild symptoms, we were unable to detect HRV on any stage of the impactor.

  5. Nematode and Arthropod Genomes Provide New Insights into the Evolution of Class 2 B1 GPCRs

    PubMed Central

    Cardoso, Joo C. R.; Flix, Rute C.; Power, Deborah M.

    2014-01-01

    Nematodes and arthropods are the most speciose animal groups and possess Class 2 B1 G-protein coupled receptors (GPCRs). Existing models of invertebrate Class 2 B1 GPCR evolution are mainly centered on Caenorhabditis elegans and Drosophila melanogaster and a few other nematode and arthropod representatives. The present study reevaluates the evolution of metazoan Class 2 B1 GPCRs and orthologues by exploring the receptors in several nematode and arthropod genomes and comparing them to the human receptors. Three novel receptor phylogenetic clusters were identified and designated cluster A, cluster B and PDF-R-related cluster. Clusters A and B were identified in several nematode and arthropod genomes but were absent from D. melanogaster and Culicidae genomes, whereas the majority of the members of the PDF-R-related cluster were from nematodes. Cluster A receptors were nematode and arthropod-specific but shared a conserved gene environment with human receptor loci. Cluster B members were orthologous to human GCGR, PTHR and Secretin members with which they probably shared a common origin. PDF-R and PDF-R related clusters were present in representatives of both nematodes and arthropods. The results of comparative analysis of GPCR evolution and diversity in protostomes confirm previous notions that C. elegans and D. melanogaster genomes are not good representatives of nematode and arthropod phyla. We hypothesize that at least four ancestral Class 2 B1 genes emerged early in the metazoan radiation, which after the protostome-deuterostome split underwent distinct selective pressures that resulted in duplication and deletion events that originated the current Class 2 B1 GPCRs in nematode and arthropod genomes. PMID:24651821

  6. Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

    PubMed Central

    2012-01-01

    The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens. PMID:22923046

  7. [Evolution of non-coding nucleotide sequences in Newcastle disease virus genomes ].

    PubMed

    Xu, Huaiying; Qin, Zhuoming; Qi, Lihong; Zhang, Wei; Wang, Youling; Liu, Jinhua

    2014-09-01

    [OBJECTIVE] Although much is done in the coding genes of Newcastle disease virus (NDV) , limited papers can be found with non-coding sequences. In this paper, the evolution tendency of non-coding sequences was studied. [METHODS] NDV strain LC12 isolated from duck with egg drop syndrome in 2012, and others 35 strains genome cDNA of different NDV genotype were sought and obtained from GenBank. Analytical approaches including nucleotide homology, nucleotide alignment and phylogenetic tree were associated with the leading sequences, trailer sequences, intergenic sequences (IGS), and coding gene between 5 'and 3' UTR nucleotide, respectively. [RESULTS] The location and the length of the non-coding sequences highly conserve, and the variation trend of non-coding sequences is synchronous with the entire genomes and coding genes. [ CONCLUSION] The molecular variation of the coding gene was indistinguishable with the non-coding gene in view of the NDV genome. PMID:25522596

  8. SNP Formation Bias in the Murine Genome Provides Evidence for Parallel Evolution.

    PubMed

    Plyler, Zackery E; Hill, Aubrey E; McAtee, Christopher W; Cui, Xiangqin; Moseley, Leah A; Sorscher, Eric J

    2015-09-01

    In this study, we show novel DNA motifs that promote single nucleotide polymorphism (SNP) formation and are conserved among exons, introns, and intergenic DNA from mice (Sanger Mouse Genomes Project), human genes (1000 Genomes), and tumor-specific somatic mutations (data from TCGA). We further characterize SNPs likely to be very recent in origin (i.e., formed in otherwise congenic mice) and show enrichment for both synonymous and parallel DNA variants occurring under circumstances not attributable to purifying selection. The findings provide insight regarding SNP contextual bias and eukaryotic codon usage as strategies that favor long-term exonic stability. The study also furnishes new information concerning rates of murine genomic evolution and features of DNA mutagenesis (at the time of SNP formation) that should be viewed as "adaptive." PMID:26253317

  9. Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish.

    PubMed

    Reichwald, Kathrin; Petzold, Andreas; Koch, Philipp; Downie, Bryan R; Hartmann, Nils; Pietsch, Stefan; Baumgart, Mario; Chalopin, Domitille; Felder, Marius; Bens, Martin; Sahm, Arne; Szafranski, Karol; Taudien, Stefan; Groth, Marco; Arisi, Ivan; Weise, Anja; Bhatt, Samarth S; Sharma, Virag; Kraus, Johann M; Schmid, Florian; Priebe, Steffen; Liehr, Thomas; Grlach, Matthias; Than, Manuel E; Hiller, Michael; Kestler, Hans A; Volff, Jean-Nicolas; Schartl, Manfred; Cellerino, Alessandro; Englert, Christoph; Platzer, Matthias

    2015-12-01

    The killifish Nothobranchius furzeri is the shortest-lived vertebrate that can be bred in the laboratory. Its rapid growth, early sexual maturation, fast aging, and arrested embryonic development (diapause) make it an attractive model organism in biomedical research. Here, we report a draft sequence of its genome that allowed us to uncover an intra-species Y chromosome polymorphism representing-in real time-different stages of sex chromosome formation that display features of early mammalian XY evolution "in action." Our data suggest that gdf6Y, encoding a TGF-? family growth factor, is the master sex-determining gene in N.furzeri. Moreover, we observed genomic clustering of aging-related genes, identified genes under positive selection, and revealed significant similarities of gene expression profiles between diapause and aging, particularly for genes controlling cell cycle and translation. The annotated genome sequence is provided as an online resource (http://www.nothobranchius.info/NFINgb). PMID:26638077

  10. SNP Formation Bias in the Murine Genome Provides Evidence for Parallel Evolution

    PubMed Central

    Plyler, Zackery E.; Hill, Aubrey E.; McAtee, Christopher W.; Cui, Xiangqin; Moseley, Leah A.; Sorscher, Eric J.

    2015-01-01

    In this study, we show novel DNA motifs that promote single nucleotide polymorphism (SNP) formation and are conserved among exons, introns, and intergenic DNA from mice (Sanger Mouse Genomes Project), human genes (1000 Genomes), and tumor-specific somatic mutations (data from TCGA). We further characterize SNPs likely to be very recent in origin (i.e., formed in otherwise congenic mice) and show enrichment for both synonymous and parallel DNA variants occurring under circumstances not attributable to purifying selection. The findings provide insight regarding SNP contextual bias and eukaryotic codon usage as strategies that favor long-term exonic stability. The study also furnishes new information concerning rates of murine genomic evolution and features of DNA mutagenesis (at the time of SNP formation) that should be viewed as adaptive. PMID:26253317

  11. The Complete Chloroplast Genome of Banana (Musa acuminata, Zingiberales): Insight into Plastid Monocotyledon Evolution

    PubMed Central

    Martin, Guillaume; Baurens, Franc-Christophe; Cardi, Cline; Aury, Jean-Marc; DHont, Anglique

    2013-01-01

    Background Banana (genus Musa) is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-)specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus. Methodology/Principal Findings The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp) and a Small Single Copy region (SSC, 10,768 bp) separated by Inverted Repeat regions (IRs, 35,433 bp). Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1) and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed. Conclusion The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas. PMID:23840670

  12. Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus aculeatus

    PubMed Central

    Terekhanova, Nadezhda V.; Logacheva, Maria D.; Penin, Aleksey A.; Neretina, Tatiana V.; Barmintseva, Anna E.; Bazykin, Georgii A.; Kondrashov, Alexey S.; Mugue, Nikolai S.

    2014-01-01

    Adaptation is driven by natural selection; however, many adaptations are caused by weak selection acting over large timescales, complicating its study. Therefore, it is rarely possible to study selection comprehensively in natural environments. The threespine stickleback (Gasterosteus aculeatus) is a well-studied model organism with a short generation time, small genome size, and many genetic and genomic tools available. Within this originally marine species, populations have recurrently adapted to freshwater all over its range. This evolution involved extensive parallelism: pre-existing alleles that adapt sticklebacks to freshwater habitats, but are also present at low frequencies in marine populations, have been recruited repeatedly. While a number of genomic regions responsible for this adaptation have been identified, the details of selection remain poorly understood. Using whole-genome resequencing, we compare pooled genomic samples from marine and freshwater populations of the White Sea basin, and identify 19 short genomic regions that are highly divergent between them, including three known inversions. 17 of these regions overlap protein-coding genes, including a number of genes with predicted functions that are relevant for adaptation to the freshwater environment. We then analyze four additional independently derived young freshwater populations of known ages, two natural and two artificially established, and use the observed shifts of allelic frequencies to estimate the strength of positive selection. Adaptation turns out to be quite rapid, indicating strong selection acting simultaneously at multiple regions of the genome, with selection coefficients of up to 0.27. High divergence between marine and freshwater genotypes, lack of reduction in polymorphism in regions responsible for adaptation, and high frequencies of freshwater alleles observed even in young freshwater populations are all consistent with rapid assembly of G. aculeatus freshwater genotypes from pre-existing genomic regions of adaptive variation, with strong selection that favors this assembly acting simultaneously at multiple loci. PMID:25299485

  13. Fast evolution from precast bricks: genomics of young freshwater populations of threespine stickleback Gasterosteus aculeatus.

    PubMed

    Terekhanova, Nadezhda V; Logacheva, Maria D; Penin, Aleksey A; Neretina, Tatiana V; Barmintseva, Anna E; Bazykin, Georgii A; Kondrashov, Alexey S; Mugue, Nikolai S

    2014-10-01

    Adaptation is driven by natural selection; however, many adaptations are caused by weak selection acting over large timescales, complicating its study. Therefore, it is rarely possible to study selection comprehensively in natural environments. The threespine stickleback (Gasterosteus aculeatus) is a well-studied model organism with a short generation time, small genome size, and many genetic and genomic tools available. Within this originally marine species, populations have recurrently adapted to freshwater all over its range. This evolution involved extensive parallelism: pre-existing alleles that adapt sticklebacks to freshwater habitats, but are also present at low frequencies in marine populations, have been recruited repeatedly. While a number of genomic regions responsible for this adaptation have been identified, the details of selection remain poorly understood. Using whole-genome resequencing, we compare pooled genomic samples from marine and freshwater populations of the White Sea basin, and identify 19 short genomic regions that are highly divergent between them, including three known inversions. 17 of these regions overlap protein-coding genes, including a number of genes with predicted functions that are relevant for adaptation to the freshwater environment. We then analyze four additional independently derived young freshwater populations of known ages, two natural and two artificially established, and use the observed shifts of allelic frequencies to estimate the strength of positive selection. Adaptation turns out to be quite rapid, indicating strong selection acting simultaneously at multiple regions of the genome, with selection coefficients of up to 0.27. High divergence between marine and freshwater genotypes, lack of reduction in polymorphism in regions responsible for adaptation, and high frequencies of freshwater alleles observed even in young freshwater populations are all consistent with rapid assembly of G. aculeatus freshwater genotypes from pre-existing genomic regions of adaptive variation, with strong selection that favors this assembly acting simultaneously at multiple loci. PMID:25299485

  14. Finite Genome Length Corrections for the Mean Fitness and Gene Probabilities in Evolution Models

    NASA Astrophysics Data System (ADS)

    Kirakosyan, Zara; Saakian, David B.; Hu, Chin-Kun

    2011-07-01

    Using the Hamilton-Jacobi equation approach to study genomes of length L, we obtain 1/ L corrections for the steady state population distributions and mean fitness functions for horizontal gene transfer model, as well as for the diploid evolution model with general fitness landscapes. Our numerical solutions confirm the obtained analytic equations. Our method could be applied to the general case of nonlinear Markov models.

  15. Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

    PubMed Central

    Galardini, Marco; Brilli, Matteo; Spini, Giulia; Rossi, Matteo; Roncaglia, Bianca; Bani, Alessia; Chiancianesi, Manuela; Moretto, Marco; Engelen, Kristof; Bacci, Giovanni; Pini, Francesco; Biondi, Emanuele G.; Bazzicalupo, Marco; Mengoni, Alessio

    2015-01-01

    Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. The evolution of such networks within and outside the species boundary is however still obscure. Sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a significant knowledge of its transcription factors (TF). Each replicon has a specific functional and evolutionary mark; which might also emerge from the analysis of their regulatory signatures. Here we have studied the plasticity of the regulatory network within and outside the S. meliloti species, looking for the presence of 41 TFs binding motifs in 51 strains and 5 related rhizobial species. We have detected a preference of several TFs for one of the three replicons, and the function of regulated genes was found to be in accordance with the overall replicon functional signature: house-keeping functions for the chromosome, metabolism for the chromid, symbiosis for the megaplasmid. This therefore suggests a replicon-specific wiring of the regulatory network in the S. meliloti species. At the same time a significant part of the predicted regulatory network is shared between the chromosome and the chromid, thus adding an additional layer by which the chromid integrates itself in the core genome. Furthermore, the regulatory network distance was found to be correlated with both promoter regions and accessory genome evolution inside the species, indicating that both pangenome compartments are involved in the regulatory network evolution. We also observed that genes which are not included in the species regulatory network are more likely to belong to the accessory genome, indicating that regulatory interactions should also be considered to predict gene conservation in bacterial pangenomes. PMID:26340565

  16. Revisiting the evolution of mouse LINE-1 in the genomic era

    PubMed Central

    2013-01-01

    Background LINE-1 (L1) is the dominant category of transposable elements in placental mammals. L1 has significantly affected the size and structure of all mammalian genomes and understanding the nature of the interactions between L1 and its mammalian host remains a question of crucial importance in comparative genomics. For this reason, much attention has been dedicated to the evolution of L1. Among the most studied elements is the mouse L1 which has been the subject of a number of studies in the 1980s and 1990s. These seminal studies, performed in the pre-genomic era when only a limited number of L1 sequences were available, have significantly improved our understanding of L1 evolution. Yet, no comprehensive study on the evolution of L1 in mouse has been performed since the completion of this genome sequence. Results Using the Genome Parsing Suite we performed the first evolutionary analysis of mouse L1 over the entire length of the element. This analysis indicates that the mouse L1 has recruited novel 5UTR sequences more frequently than previously thought and that the simultaneous activity of non-homologous promoters seems to be one of the conditions for the co-existence of multiple L1 families or lineages. In addition the exchange of genetic information between L1 families is not limited to the 5UTR as evidence of inter-family recombination was observed in ORF1, ORF2, and the 3UTR. In contrast to the human L1, there was little evidence of rapid amino-acid replacement in the coiled-coil of ORF1, although this region is structurally unstable. We propose that the structural instability of the coiled-coil domain might be adaptive and that structural changes in this region are selectively equivalent to the rapid evolution at the amino-acid level reported in the human lineage. Conclusions The pattern of evolution of L1 in mouse shows some similarity with human suggesting that the nature of the interactions between L1 and its host might be similar in these two species. Yet, some notable differences, particularly in the evolution of ORF1, suggest that the molecular mechanisms involved in host-L1 interactions might be different in these two species. PMID:23286374

  17. Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution

    SciTech Connect

    Richards, Stephen; Liu, Yue; Bettencourt, Brian R.; Hradecky, Pavel; Letovsky, Stan; Nielsen, Rasmus; Thornton, Kevin; Todd, Melissa J.; Chen, Rui; Meisel, Richard P.; Couronne, Olivier; Hua, Sujun; Smith, Mark A.; Bussemaker, Harmen J.; van Batenburg, Marinus F.; Howells, Sally L.; Scherer, Steven E.; Sodergren, Erica; Matthews, Beverly B.; Crosby, Madeline A.; Schroeder, Andrew J.; Ortiz-Barrientos, Daniel; Rives, Catherine M.; Metzker, Michael L.; Muzny, Donna M.; Scott, Graham; Steffen, David; Wheeler, David A.; Worley, Kim C.; Havlak, Paul; Durbin, K. James; Egan, Amy; Gill, Rachel; Hume, Jennifer; Morgan, Margaret B.; Miner, George; Hamilton, Cerissa; Huang, Yanmei; Waldron, Lenee; Verduzco, Daniel; Blankenburg, Kerstin P.; Dubchak, Inna; Noor, Mohamed A.F.; Anderson, Wyatt; White, Kevin P.; Clark, Andrew G.; Schaeffer, Stephen W.; Gelbart, William; Weinstock, George M.; Gibbs, Richard A.

    2004-04-01

    The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have remained on the same arm, but within each arm gene order has been extensively reshuffled leading to the identification of approximately 1300 syntenic blocks. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 35 My since divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome wide average consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than control sequences between the species but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a picture of repeat mediated chromosomal rearrangement, and high co-adaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

  18. The Ectocarpus genome and the independent evolution of multicellularity in brown algae.

    PubMed

    Cock, J Mark; Sterck, Lieven; Rouzé, Pierre; Scornet, Delphine; Allen, Andrew E; Amoutzias, Grigoris; Anthouard, Veronique; Artiguenave, François; Aury, Jean-Marc; Badger, Jonathan H; Beszteri, Bank; Billiau, Kenny; Bonnet, Eric; Bothwell, John H; Bowler, Chris; Boyen, Catherine; Brownlee, Colin; Carrano, Carl J; Charrier, Bénédicte; Cho, Ga Youn; Coelho, Susana M; Collén, Jonas; Corre, Erwan; Da Silva, Corinne; Delage, Ludovic; Delaroque, Nicolas; Dittami, Simon M; Doulbeau, Sylvie; Elias, Marek; Farnham, Garry; Gachon, Claire M M; Gschloessl, Bernhard; Heesch, Svenja; Jabbari, Kamel; Jubin, Claire; Kawai, Hiroshi; Kimura, Kei; Kloareg, Bernard; Küpper, Frithjof C; Lang, Daniel; Le Bail, Aude; Leblanc, Catherine; Lerouge, Patrice; Lohr, Martin; Lopez, Pascal J; Martens, Cindy; Maumus, Florian; Michel, Gurvan; Miranda-Saavedra, Diego; Morales, Julia; Moreau, Hervé; Motomura, Taizo; Nagasato, Chikako; Napoli, Carolyn A; Nelson, David R; Nyvall-Collén, Pi; Peters, Akira F; Pommier, Cyril; Potin, Philippe; Poulain, Julie; Quesneville, Hadi; Read, Betsy; Rensing, Stefan A; Ritter, Andrés; Rousvoal, Sylvie; Samanta, Manoj; Samson, Gaelle; Schroeder, Declan C; Ségurens, Béatrice; Strittmatter, Martina; Tonon, Thierry; Tregear, James W; Valentin, Klaus; von Dassow, Peter; Yamagishi, Takahiro; Van de Peer, Yves; Wincker, Patrick

    2010-06-01

    Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. PMID:20520714

  19. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

    PubMed Central

    2013-01-01

    Background The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan. Results Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms. Conclusions Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host. PMID:23375108

  20. Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae

    PubMed Central

    Turmel, Monique; Otis, Christian; Lemieux, Claude

    2015-01-01

    Previous studies of trebouxiophycean chloroplast genomes revealed little information regarding the evolutionary dynamics of this genome because taxon sampling was too sparse and the relationships between the sampled taxa were unknown. We recently sequenced the chloroplast genomes of 27 trebouxiophycean and 2 pedinophycean green algae to resolve the relationships among the main lineages recognized for the Trebouxiophyceae. These taxa and the previously sampled members of the Pedinophyceae and Trebouxiophyceae are included in the comparative chloroplast genome analysis we report here. The 38 genomes examined display considerable variability at all levels, except gene content. Our results highlight the high propensity of the rDNA-containing large inverted repeat (IR) to vary in size, gene content and gene order as well as the repeated losses it experienced during trebouxiophycean evolution. Of the seven predicted IR losses, one event demarcates a superclade of 11 taxa representing 5 late-diverging lineages. IR expansions/contractions account not only for changes in gene content in this region but also for changes in gene order and gene duplications. Inversions also led to gene rearrangements within the IR, including the reversal or disruption of the rDNA operon in some lineages. Most of the 20 IR-less genomes are more rearranged compared with their IR-containing homologs and tend to show an accelerated rate of sequence evolution. In the IR-less superclade, several ancestral operons were disrupted, a few genes were fragmented, and a subgroup of taxa features a G+C-biased nucleotide composition. Our analyses also unveiled putative cases of gene acquisitions through horizontal transfer. PMID:26139832

  1. Genome Duplication and Gene Loss Affect the Evolution of Heat Shock Transcription Factor Genes in Legumes

    PubMed Central

    Jin, Jing; Jin, Xiaolei; Jiang, Haiyang; Yan, Hanwei; Cheng, Beijiu

    2014-01-01

    Whole-genome duplication events (polyploidy events) and gene loss events have played important roles in the evolution of legumes. Here we show that the vast majority of Hsf gene duplications resulted from whole genome duplication events rather than tandem duplication, and significant differences in gene retention exist between species. By searching for intraspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found that genome duplications accounted for 42 of 46 Hsf-containing segments in Glycine max, while paired segments were rarely identified in Lotus japonicas, Medicago truncatula and Cajanus cajan. However, by comparing interspecies microsynteny, we determined that the great majority of Hsf-containing segments in Lotus japonicas, Medicago truncatula and Cajanus cajan show extensive conservation with the duplicated regions of Glycine max. These segments formed 17 groups of orthologous segments. These results suggest that these regions shared ancient genome duplication with Hsf genes in Glycine max, but more than half of the copies of these genes were lost. On the other hand, the Glycine max Hsf gene family retained approximately 75% and 84% of duplicated genes produced from the ancient genome duplication and recent Glycine-specific genome duplication, respectively. Continuous purifying selection has played a key role in the maintenance of Hsf genes in Glycine max. Expression analysis of the Hsf genes in Lotus japonicus revealed their putative involvement in multiple tissue-/developmental stages and responses to various abiotic stimuli. This study traces the evolution of Hsf genes in legume species and demonstrates that the rates of gene gain and loss are far from equilibrium in different species. PMID:25047803

  2. Evolution of the mitochondrial genome in snakes: Gene rearrangements and phylogenetic relationships

    PubMed Central

    Yan, Jie; Li, Hongdan; Zhou, Kaiya

    2008-01-01

    Background Snakes as a major reptile group display a variety of morphological characteristics pertaining to their diverse behaviours. Despite abundant analyses of morphological characters, molecular studies using mitochondrial and nuclear genes are limited. As a result, the phylogeny of snakes remains controversial. Previous studies on mitochondrial genomes of snakes have demonstrated duplication of the control region and translocation of trnL to be two notable features of the alethinophidian (all serpents except blindsnakes and threadsnakes) mtDNAs. Our purpose is to further investigate the gene organizations, evolution of the snake mitochondrial genome, and phylogenetic relationships among several major snake families. Results The mitochondrial genomes were sequenced for four taxa representing four different families, and each had a different gene arrangement. Comparative analyses with other snake mitochondrial genomes allowed us to summarize six types of mitochondrial gene arrangement in snakes. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (BI, ML, MP, NJ) arrived at a similar topology, which was used to reconstruct the evolution of mitochondrial gene arrangements in snakes. Conclusion The phylogenetic relationships among the major families of snakes are in accordance with the mitochondrial genomes in terms of gene arrangements. The gene arrangement in Ramphotyphlops braminus mtDNA is inferred to be ancestral for snakes. After the divergence of the early Ramphotyphlops lineage, three types of rearrangements occurred. These changes involve translocations within the IQM tRNA gene cluster and the duplication of the CR. All phylogenetic methods support the placement of Enhydris plumbea outside of the (Colubridae + Elapidae) cluster, providing mitochondrial genomic evidence for the familial rank of Homalopsidae. PMID:19038056

  3. Accelerated Evolution of Mitochondrial but Not Nuclear Genomes of Hymenoptera: New Evidence from Crabronid Wasps

    PubMed Central

    Kaltenpoth, Martin; Showers Corneli, Patrice; Dunn, Diane M.; Weiss, Robert B.

    2012-01-01

    Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae), and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera) based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase). The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes). Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes. PMID:22412929

  4. Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps.

    PubMed

    Kaltenpoth, Martin; Showers Corneli, Patrice; Dunn, Diane M; Weiss, Robert B; Strohm, Erhard; Seger, Jon

    2012-01-01

    Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae), and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera) based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase). The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes). Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes. PMID:22412929

  5. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

    PubMed Central

    Vonk, Freek J.; Casewell, Nicholas R.; Henkel, Christiaan V.; Heimberg, Alysha M.; Jansen, Hans J.; McCleary, Ryan J. R.; Kerkkamp, Harald M. E.; Vos, Rutger A.; Guerreiro, Isabel; Calvete, Juan J.; Wster, Wolfgang; Woods, Anthony E.; Logan, Jessica M.; Harrison, Robert A.; Castoe, Todd A.; de Koning, A. P. Jason; Pollock, David D.; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B.; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S.; Ribeiro, Jos M. C.; Arntzen, Jan W.; van den Thillart, Guido E. E. J. M.; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P.; Spaink, Herman P.; Duboule, Denis; McGlinn, Edwina; Kini, R. Manjunatha; Richardson, Michael K.

    2013-01-01

    Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection. PMID:24297900

  6. Genomic Evidence for the Emergence and Evolution of Pathogenicity and Niche Preferences in the Genus Campylobacter

    PubMed Central

    Iraola, Gregorio; Pérez, Ruben; Naya, Hugo; Paolicchi, Fernando; Pastor, Eugenia; Valenzuela, Sebastián; Calleros, Lucía; Velilla, Alejandra; Hernández, Martín; Morsella, Claudia

    2014-01-01

    The genus Campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. Nowadays, the available genomic data for the genus comprise a wide variety of species with different pathogenic potential and niche preferences. In this work, we contribute to enlarge this available information presenting the first genome for the species Campylobacter sputorum bv. sputorum and use this and the already sequenced organisms to analyze the emergence and evolution of pathogenicity and niche preferences among Campylobacter species. We found that campylobacters can be unequivocally distinguished in established and putative pathogens depending on their repertory of virulence genes, which have been horizontally acquired from other bacteria because the nonpathogenic Campylobacter ancestor emerged, and posteriorly interchanged between some members of the genus. Additionally, we demonstrated the role of both horizontal gene transfers and diversifying evolution in niche preferences, being able to distinguish genetic features associated to the tropism for oral, genital, and gastrointestinal tissues. In particular, we highlight the role of nonsynonymous evolution of disulphide bond proteins, the invasion antigen B (CiaB), and other secreted proteins in the determination of niche preferences. Our results arise from assessing the previously unmet goal of considering the whole available Campylobacter diversity for genome comparisons, unveiling notorious genetic features that could explain particular phenotypes and set the basis for future research in Campylobacter biology. PMID:25193310

  7. Genomic evidence for the emergence and evolution of pathogenicity and niche preferences in the genus Campylobacter.

    PubMed

    Iraola, Gregorio; Pérez, Ruben; Naya, Hugo; Paolicchi, Fernando; Pastor, Eugenia; Valenzuela, Sebastián; Calleros, Lucía; Velilla, Alejandra; Hernández, Martín; Morsella, Claudia

    2014-09-01

    The genus Campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. Nowadays, the available genomic data for the genus comprise a wide variety of species with different pathogenic potential and niche preferences. In this work, we contribute to enlarge this available information presenting the first genome for the species Campylobacter sputorum bv. sputorum and use this and the already sequenced organisms to analyze the emergence and evolution of pathogenicity and niche preferences among Campylobacter species. We found that campylobacters can be unequivocally distinguished in established and putative pathogens depending on their repertory of virulence genes, which have been horizontally acquired from other bacteria because the nonpathogenic Campylobacter ancestor emerged, and posteriorly interchanged between some members of the genus. Additionally, we demonstrated the role of both horizontal gene transfers and diversifying evolution in niche preferences, being able to distinguish genetic features associated to the tropism for oral, genital, and gastrointestinal tissues. In particular, we highlight the role of nonsynonymous evolution of disulphide bond proteins, the invasion antigen B (CiaB), and other secreted proteins in the determination of niche preferences. Our results arise from assessing the previously unmet goal of considering the whole available Campylobacter diversity for genome compariso