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Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection.

Identifieur interne : 000212 ( Main/Exploration ); précédent : 000211; suivant : 000213

Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection.

Auteurs : Mingcheng Wang [République populaire de Chine] ; Lei Zhang [République populaire de Chine] ; Zhiyang Zhang [République populaire de Chine] ; Mengmeng Li [République populaire de Chine] ; Deyan Wang [République populaire de Chine] ; Xu Zhang [République populaire de Chine] ; Zhenxiang Xi [République populaire de Chine] ; Ken Keefover-Ring [États-Unis] ; Lawrence B. Smart [États-Unis] ; Stephen P. Difazio [États-Unis] ; Matthew S. Olson [États-Unis] ; Tongming Yin [République populaire de Chine] ; Jianquan Liu [République populaire de Chine] ; Tao Ma [République populaire de Chine]

Source :

RBID : pubmed:31550399

Abstract

Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere. We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re-sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple-species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence. We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection-mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.

DOI: 10.1111/nph.16215
PubMed: 31550399


Affiliations:


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Le document en format XML

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<div type="abstract" xml:lang="en">Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere. We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re-sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple-species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence. We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection-mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.</div>
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<Abstract>
<AbstractText>Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere. We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re-sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple-species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence. We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection-mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.</AbstractText>
<CopyrightInformation>© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Wang</LastName>
<ForeName>Mingcheng</ForeName>
<Initials>M</Initials>
<Identifier Source="ORCID">0000-0002-3631-9174</Identifier>
<AffiliationInfo>
<Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhang</LastName>
<ForeName>Lei</ForeName>
<Initials>L</Initials>
<AffiliationInfo>
<Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhang</LastName>
<ForeName>Zhiyang</ForeName>
<Initials>Z</Initials>
<Identifier Source="ORCID">0000-0002-9466-9439</Identifier>
<AffiliationInfo>
<Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Li</LastName>
<ForeName>Mengmeng</ForeName>
<Initials>M</Initials>
<AffiliationInfo>
<Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Wang</LastName>
<ForeName>Deyan</ForeName>
<Initials>D</Initials>
<AffiliationInfo>
<Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhang</LastName>
<ForeName>Xu</ForeName>
<Initials>X</Initials>
<AffiliationInfo>
<Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Xi</LastName>
<ForeName>Zhenxiang</ForeName>
<Initials>Z</Initials>
<Identifier Source="ORCID">0000-0002-2851-5474</Identifier>
<AffiliationInfo>
<Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Keefover-Ring</LastName>
<ForeName>Ken</ForeName>
<Initials>K</Initials>
<AffiliationInfo>
<Affiliation>Departments of Botany and Geography, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI, 53706, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Smart</LastName>
<ForeName>Lawrence B</ForeName>
<Initials>LB</Initials>
<AffiliationInfo>
<Affiliation>Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>DiFazio</LastName>
<ForeName>Stephen P</ForeName>
<Initials>SP</Initials>
<Identifier Source="ORCID">0000-0003-4077-1590</Identifier>
<AffiliationInfo>
<Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 25606, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Olson</LastName>
<ForeName>Matthew S</ForeName>
<Initials>MS</Initials>
<Identifier Source="ORCID">0000-0002-0798-145X</Identifier>
<AffiliationInfo>
<Affiliation>Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Yin</LastName>
<ForeName>Tongming</ForeName>
<Initials>T</Initials>
<AffiliationInfo>
<Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Liu</LastName>
<ForeName>Jianquan</ForeName>
<Initials>J</Initials>
<Identifier Source="ORCID">0000-0002-4237-7418</Identifier>
<AffiliationInfo>
<Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Ma</LastName>
<ForeName>Tao</ForeName>
<Initials>T</Initials>
<Identifier Source="ORCID">0000-0002-7094-6868</Identifier>
<AffiliationInfo>
<Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<DataBankList CompleteYN="Y">
<DataBank>
<DataBankName>GENBANK</DataBankName>
<AccessionNumberList>
<AccessionNumber>CRA001510</AccessionNumber>
</AccessionNumberList>
</DataBank>
</DataBankList>
<PublicationTypeList>
<PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2019</Year>
<Month>10</Month>
<Day>31</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>England</Country>
<MedlineTA>New Phytol</MedlineTA>
<NlmUniqueID>9882884</NlmUniqueID>
<ISSNLinking>0028-646X</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<KeywordList Owner="NOTNLM">
<Keyword MajorTopicYN="Y">Populus </Keyword>
<Keyword MajorTopicYN="Y">balancing selection</Keyword>
<Keyword MajorTopicYN="Y">gene flow</Keyword>
<Keyword MajorTopicYN="Y">phylogenomics</Keyword>
<Keyword MajorTopicYN="Y">trans-specific polymorphisms</Keyword>
</KeywordList>
</MedlineCitation>
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<Year>2019</Year>
<Month>02</Month>
<Day>09</Day>
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<PubMedPubDate PubStatus="accepted">
<Year>2019</Year>
<Month>09</Month>
<Day>16</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed">
<Year>2019</Year>
<Month>9</Month>
<Day>25</Day>
<Hour>6</Hour>
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<ArticleId IdType="doi">10.1111/nph.16215</ArticleId>
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<name sortKey="Zhang, Xu" sort="Zhang, Xu" uniqKey="Zhang X" first="Xu" last="Zhang">Xu Zhang</name>
<name sortKey="Zhang, Zhiyang" sort="Zhang, Zhiyang" uniqKey="Zhang Z" first="Zhiyang" last="Zhang">Zhiyang Zhang</name>
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