Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.
Identifieur interne : 001749 ( Main/Exploration ); précédent : 001748; suivant : 001750Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.
Auteurs : Jaqueline Hess [Norvège] ; Inger Skrede [Norvège] ; Benjamin E. Wolfe [États-Unis] ; Kurt Labutti [États-Unis] ; Robin A. Ohm [États-Unis] ; Igor V. Grigoriev [États-Unis] ; Anne Pringle [États-Unis]Source :
- Genome biology and evolution [ 1759-6653 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Amanita, Biote, Mycorhizes, Symbiose, Éléments transposables d'ADN.
- Phylogenèse.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA Transposable Elements.
- genetics : Amanita, Biota, Mycorrhizae, Symbiosis.
- Phylogeny.
Abstract
Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species' natural histories may have in shaping genome architecture.
DOI: 10.1093/gbe/evu121
PubMed: 24923322
PubMed Central: PMC4122921
Affiliations:
Links toward previous steps (curation, corpus...)
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Wolfe</name><affiliation wicri:level="4"><nlm:affiliation>Department of Organismic and Evolutionary Biology, Harvard UniversityFAS Center for Systems Biology, Harvard University.</nlm:affiliation><country>États-Unis</country><placeName><settlement type="city">Cambridge (Massachusetts)</settlement><region type="state">Massachusetts</region></placeName><orgName type="university">Université Harvard</orgName></affiliation></author><author><name sortKey="Labutti, Kurt" sort="Labutti, Kurt" uniqKey="Labutti K" first="Kurt" last="Labutti">Kurt Labutti</name><affiliation wicri:level="2"><nlm:affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, California.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>U.S. Department of Energy Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Ohm, Robin A" sort="Ohm, Robin A" uniqKey="Ohm R" first="Robin A" last="Ohm">Robin A. Ohm</name><affiliation wicri:level="2"><nlm:affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, California.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>U.S. Department of Energy Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Grigoriev, Igor V" sort="Grigoriev, Igor V" uniqKey="Grigoriev I" first="Igor V" last="Grigoriev">Igor V. Grigoriev</name><affiliation wicri:level="2"><nlm:affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, California.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>U.S. Department of Energy Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Pringle, Anne" sort="Pringle, Anne" uniqKey="Pringle A" first="Anne" last="Pringle">Anne Pringle</name><affiliation wicri:level="4"><nlm:affiliation>Department of Organismic and Evolutionary Biology, Harvard University.</nlm:affiliation><country>États-Unis</country><placeName><settlement type="city">Cambridge (Massachusetts)</settlement><region type="state">Massachusetts</region></placeName><orgName type="university">Université Harvard</orgName></affiliation></author></analytic><series><title level="j">Genome biology and evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amanita (genetics)</term><term>Biota (genetics)</term><term>DNA Transposable Elements (genetics)</term><term>Mycorrhizae (genetics)</term><term>Phylogeny (MeSH)</term><term>Symbiosis (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amanita (génétique)</term><term>Biote (génétique)</term><term>Mycorhizes (génétique)</term><term>Phylogenèse (MeSH)</term><term>Symbiose (génétique)</term><term>Éléments transposables d'ADN (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Transposable Elements</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Amanita</term><term>Biota</term><term>Mycorrhizae</term><term>Symbiosis</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Amanita</term><term>Biote</term><term>Mycorhizes</term><term>Symbiose</term><term>Éléments transposables d'ADN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Phylogenèse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species' natural histories may have in shaping genome architecture. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24923322</PMID><DateCompleted><Year>2015</Year><Month>04</Month><Day>01</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1759-6653</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><Issue>7</Issue><PubDate><Year>2014</Year><Month>Jun</Month><Day>12</Day></PubDate></JournalIssue><Title>Genome biology and evolution</Title><ISOAbbreviation>Genome Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.</ArticleTitle><Pagination><MedlinePgn>1564-78</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gbe/evu121</ELocationID><Abstract><AbstractText>Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species' natural histories may have in shaping genome architecture. </AbstractText><CopyrightInformation>© The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hess</LastName><ForeName>Jaqueline</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Organismic and Evolutionary Biology, Harvard University jaqueline.hess@ibv.uio.no.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Skrede</LastName><ForeName>Inger</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Organismic and Evolutionary Biology, Harvard UniversitySection for Genetics and Evolutionary Biology, University of Oslo, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wolfe</LastName><ForeName>Benjamin E</ForeName><Initials>BE</Initials><AffiliationInfo><Affiliation>Department of Organismic and Evolutionary Biology, Harvard UniversityFAS Center for Systems Biology, Harvard University.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>LaButti</LastName><ForeName>Kurt</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, California.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ohm</LastName><ForeName>Robin A</ForeName><Initials>RA</Initials><AffiliationInfo><Affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, California.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grigoriev</LastName><ForeName>Igor V</ForeName><Initials>IV</Initials><AffiliationInfo><Affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, California.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pringle</LastName><ForeName>Anne</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Organismic and Evolutionary Biology, Harvard University.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>06</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol Evol</MedlineTA><NlmUniqueID>101509707</NlmUniqueID><ISSNLinking>1759-6653</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004251">DNA Transposable Elements</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000545" MajorTopicYN="N">Amanita</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058448" MajorTopicYN="N">Biota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004251" MajorTopicYN="N">DNA Transposable Elements</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013559" MajorTopicYN="N">Symbiosis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">ecological genomics</Keyword><Keyword MajorTopicYN="N">evolution of symbiosis</Keyword><Keyword MajorTopicYN="N">genome architecture</Keyword><Keyword MajorTopicYN="N">phylogeny</Keyword><Keyword MajorTopicYN="N">repetitive DNA</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>6</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>6</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>4</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24923322</ArticleId><ArticleId IdType="pii">evu121</ArticleId><ArticleId IdType="doi">10.1093/gbe/evu121</ArticleId><ArticleId IdType="pmc">PMC4122921</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Bioinformatics. 2006 Nov 1;22(21):2688-90</Citation><ArticleIdList><ArticleId 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Wolfe</name></region><name sortKey="Grigoriev, Igor V" sort="Grigoriev, Igor V" uniqKey="Grigoriev I" first="Igor V" last="Grigoriev">Igor V. Grigoriev</name><name sortKey="Labutti, Kurt" sort="Labutti, Kurt" uniqKey="Labutti K" first="Kurt" last="Labutti">Kurt Labutti</name><name sortKey="Ohm, Robin A" sort="Ohm, Robin A" uniqKey="Ohm R" first="Robin A" last="Ohm">Robin A. Ohm</name><name sortKey="Pringle, Anne" sort="Pringle, Anne" uniqKey="Pringle A" first="Anne" last="Pringle">Anne Pringle</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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