Poxvirus genome evolution by gene gain and loss.
Identifieur interne : 000D97 ( Main/Exploration ); précédent : 000D96; suivant : 000D98Poxvirus genome evolution by gene gain and loss.
Auteurs : Austin L. Hughes [États-Unis] ; Robert FriedmanSource :
- Molecular phylogenetics and evolution [ 1055-7903 ] ; 2005.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Poxviridae.
- classification : Duplication de gène, Délétion de gène, Génome viral, Phylogenèse, Poxviridae, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- classification : Poxviridae.
- genetics : Poxviridae.
- Evolution, Molecular, Gene Deletion, Gene Duplication, Genome, Viral, Phylogeny.
Abstract
The poxviruses (Poxviridae) are a family of viruses with double-stranded DNA genomes and substantial numbers (often >200) of genes per genome. We studied the patterns of gene gain and loss over the evolutionary history of 17 poxvirus complete genomes. A phylogeny based on gene family presence/absence showed good agreement with families based on concatenated amino acid sequences of conserved single-copy genes. Gene duplications in poxviruses were often lineage specific, and the most extensively duplicated viral gene families were found in only a few of the genomes analyzed. A total of 34 gene families were found to include a member in at least one of the poxvirus genomes analyzed and at least one animal genome; in 16 (47%) of these families, there was evidence of recent horizontal gene transfer (HGT) from host to virus. Gene families with evidence of HGT included several involved in host immune defense mechanisms (the MHC class I, interleukin-10, interleukin-24, interleukin-18, the interferon gamma receptor, and tumor necrosis factor receptor II) and others (glutaredoxin and glutathione peroxidase) involved in resistance of cells to oxidative stress. Thus "capture" of host genes by HGT has been a recurrent feature of poxvirus evolution and has played an important role in adapting the virus to survive host antiviral defense mechanisms.
DOI: 10.1016/j.ympev.2004.12.008
PubMed: 15737590
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Hughes</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA. austin@biol.sc.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, University of South Carolina, Columbia, SC 29208</wicri:regionArea><placeName><region type="state">Caroline du Sud</region><settlement type="city">Columbia (Caroline du Sud)</settlement></placeName><orgName type="university">Université de Caroline du Sud</orgName></affiliation></author><author><name sortKey="Friedman, Robert" sort="Friedman, Robert" uniqKey="Friedman R" first="Robert" last="Friedman">Robert Friedman</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:15737590</idno><idno type="pmid">15737590</idno><idno type="doi">10.1016/j.ympev.2004.12.008</idno><idno type="wicri:Area/Main/Corpus">000E24</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000E24</idno><idno type="wicri:Area/Main/Curation">000E24</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000E24</idno><idno type="wicri:Area/Main/Exploration">000E24</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Poxvirus genome evolution by gene gain and loss.</title><author><name sortKey="Hughes, Austin L" sort="Hughes, Austin L" uniqKey="Hughes A" first="Austin L" last="Hughes">Austin L. Hughes</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA. austin@biol.sc.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, University of South Carolina, Columbia, SC 29208</wicri:regionArea><placeName><region type="state">Caroline du Sud</region><settlement type="city">Columbia (Caroline du Sud)</settlement></placeName><orgName type="university">Université de Caroline du Sud</orgName></affiliation></author><author><name sortKey="Friedman, Robert" sort="Friedman, Robert" uniqKey="Friedman R" first="Robert" last="Friedman">Robert Friedman</name></author></analytic><series><title level="j">Molecular phylogenetics and evolution</title><idno type="ISSN">1055-7903</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Evolution, Molecular (MeSH)</term><term>Gene Deletion (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Genome, Viral (MeSH)</term><term>Phylogeny (MeSH)</term><term>Poxviridae (classification)</term><term>Poxviridae (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Duplication de gène (MeSH)</term><term>Délétion de gène (MeSH)</term><term>Génome viral (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Poxviridae (classification)</term><term>Poxviridae (génétique)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Poxviridae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Poxviridae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Poxviridae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Deletion</term><term>Gene Duplication</term><term>Genome, Viral</term><term>Phylogeny</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Duplication de gène</term><term>Délétion de gène</term><term>Génome viral</term><term>Phylogenèse</term><term>Poxviridae</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The poxviruses (Poxviridae) are a family of viruses with double-stranded DNA genomes and substantial numbers (often >200) of genes per genome. We studied the patterns of gene gain and loss over the evolutionary history of 17 poxvirus complete genomes. A phylogeny based on gene family presence/absence showed good agreement with families based on concatenated amino acid sequences of conserved single-copy genes. Gene duplications in poxviruses were often lineage specific, and the most extensively duplicated viral gene families were found in only a few of the genomes analyzed. A total of 34 gene families were found to include a member in at least one of the poxvirus genomes analyzed and at least one animal genome; in 16 (47%) of these families, there was evidence of recent horizontal gene transfer (HGT) from host to virus. Gene families with evidence of HGT included several involved in host immune defense mechanisms (the MHC class I, interleukin-10, interleukin-24, interleukin-18, the interferon gamma receptor, and tumor necrosis factor receptor II) and others (glutaredoxin and glutathione peroxidase) involved in resistance of cells to oxidative stress. Thus "capture" of host genes by HGT has been a recurrent feature of poxvirus evolution and has played an important role in adapting the virus to survive host antiviral defense mechanisms.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15737590</PMID><DateCompleted><Year>2005</Year><Month>09</Month><Day>27</Day></DateCompleted><DateRevised><Year>2007</Year><Month>11</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1055-7903</ISSN><JournalIssue CitedMedium="Print"><Volume>35</Volume><Issue>1</Issue><PubDate><Year>2005</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Molecular phylogenetics and evolution</Title><ISOAbbreviation>Mol Phylogenet Evol</ISOAbbreviation></Journal><ArticleTitle>Poxvirus genome evolution by gene gain and loss.</ArticleTitle><Pagination><MedlinePgn>186-95</MedlinePgn></Pagination><Abstract><AbstractText>The poxviruses (Poxviridae) are a family of viruses with double-stranded DNA genomes and substantial numbers (often >200) of genes per genome. We studied the patterns of gene gain and loss over the evolutionary history of 17 poxvirus complete genomes. A phylogeny based on gene family presence/absence showed good agreement with families based on concatenated amino acid sequences of conserved single-copy genes. Gene duplications in poxviruses were often lineage specific, and the most extensively duplicated viral gene families were found in only a few of the genomes analyzed. A total of 34 gene families were found to include a member in at least one of the poxvirus genomes analyzed and at least one animal genome; in 16 (47%) of these families, there was evidence of recent horizontal gene transfer (HGT) from host to virus. Gene families with evidence of HGT included several involved in host immune defense mechanisms (the MHC class I, interleukin-10, interleukin-24, interleukin-18, the interferon gamma receptor, and tumor necrosis factor receptor II) and others (glutaredoxin and glutathione peroxidase) involved in resistance of cells to oxidative stress. Thus "capture" of host genes by HGT has been a recurrent feature of poxvirus evolution and has played an important role in adapting the virus to survive host antiviral defense mechanisms.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hughes</LastName><ForeName>Austin L</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA. austin@biol.sc.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Friedman</LastName><ForeName>Robert</ForeName><Initials>R</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>GM43940</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2005</Year><Month>01</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Phylogenet Evol</MedlineTA><NlmUniqueID>9304400</NlmUniqueID><ISSNLinking>1055-7903</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017353" MajorTopicYN="N">Gene Deletion</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="Y">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011212" MajorTopicYN="N">Poxviridae</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2004</Year><Month>04</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2004</Year><Month>11</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2004</Year><Month>12</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2005</Year><Month>3</Month><Day>2</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2005</Year><Month>9</Month><Day>28</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2005</Year><Month>3</Month><Day>2</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15737590</ArticleId><ArticleId IdType="pii">S1055-7903(04)00395-1</ArticleId><ArticleId IdType="doi">10.1016/j.ympev.2004.12.008</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Caroline du Sud</li></region><settlement><li>Columbia (Caroline du Sud)</li></settlement><orgName><li>Université de Caroline du Sud</li></orgName></list><tree><noCountry><name sortKey="Friedman, Robert" sort="Friedman, Robert" uniqKey="Friedman R" first="Robert" last="Friedman">Robert Friedman</name></noCountry><country name="États-Unis"><region name="Caroline du Sud"><name sortKey="Hughes, Austin L" sort="Hughes, Austin L" uniqKey="Hughes A" first="Austin L" last="Hughes">Austin L. 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