Two Highly Similar Poplar Paleo-subgenomes Suggest an Autotetraploid Ancestor of Salicaceae Plants.
Identifieur interne : 001141 ( Main/Exploration ); précédent : 001140; suivant : 001142Two Highly Similar Poplar Paleo-subgenomes Suggest an Autotetraploid Ancestor of Salicaceae Plants.
Auteurs : Yinzhe Liu [République populaire de Chine] ; Jinpeng Wang [République populaire de Chine] ; Weina Ge [République populaire de Chine] ; Zhenyi Wang [République populaire de Chine] ; Yuxian Li [République populaire de Chine] ; Nanshan Yang [République populaire de Chine] ; Sangrong Sun [République populaire de Chine] ; Liwei Zhang [République populaire de Chine] ; Xiyin Wang [République populaire de Chine]Source :
- Frontiers in plant science [ 1664-462X ] ; 2017.
Abstract
As a model plant to study perennial trees in the Salicaceae family, the poplar (Populus trichocarpa) genome was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment of its genome to a well-selected reference genome would help us better understand poplar's genome structure and gene family evolution. Here, by adopting the relatively simpler grape (Vitis vinifera) genome as reference, and by inferring both intra- and inter-genomic gene collinearity, we produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation. We uncovered homologous blocks in the grape and poplar genomes and also between them. Moreover, we characterized the genes missing and found that poplar had two considerably similar subgenomes (≤0.05 difference in gene deletion) produced by the Salicaceae-common tetraploidization, suggesting its autotetraploid nature. Taken together, this work provides a timely and valuable dataset of orthologous and paralogous genes for further study of the genome structure and functional evolution of poplar and other Salicaceae plants.
DOI: 10.3389/fpls.2017.00571
PubMed: 28446920
PubMed Central: PMC5388744
Affiliations:
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first="Yinzhe" last="Liu">Yinzhe Liu</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jinpeng" sort="Wang, Jinpeng" uniqKey="Wang J" first="Jinpeng" last="Wang">Jinpeng Wang</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation></author><author><name sortKey="Ge, Weina" sort="Ge, Weina" uniqKey="Ge W" first="Weina" last="Ge">Weina Ge</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Zhenyi" sort="Wang, Zhenyi" uniqKey="Wang Z" first="Zhenyi" last="Wang">Zhenyi Wang</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation></author><author><name sortKey="Li, Yuxian" sort="Li, Yuxian" uniqKey="Li Y" first="Yuxian" last="Li">Yuxian Li</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Nanshan" sort="Yang, Nanshan" uniqKey="Yang N" first="Nanshan" last="Yang">Nanshan Yang</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation></author><author><name sortKey="Sun, Sangrong" sort="Sun, Sangrong" uniqKey="Sun S" first="Sangrong" last="Sun">Sangrong Sun</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Liwei" sort="Zhang, Liwei" uniqKey="Zhang L" first="Liwei" last="Zhang">Liwei Zhang</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Xiyin" sort="Wang, Xiyin" uniqKey="Wang X" first="Xiyin" last="Wang">Xiyin Wang</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan</wicri:regionArea><wicri:noRegion>North China University of Science and TechnologyTangshan</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">As a model plant to study perennial trees in the Salicaceae family, the poplar (<i>Populus trichocarpa</i>) genome was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment of its genome to a well-selected reference genome would help us better understand poplar's genome structure and gene family evolution. Here, by adopting the relatively simpler grape (<i>Vitis vinifera</i>) genome as reference, and by inferring both intra- and inter-genomic gene collinearity, we produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation. We uncovered homologous blocks in the grape and poplar genomes and also between them. Moreover, we characterized the genes missing and found that poplar had two considerably similar subgenomes (≤0.05 difference in gene deletion) produced by the Salicaceae-common tetraploidization, suggesting its autotetraploid nature. Taken together, this work provides a timely and valuable dataset of orthologous and paralogous genes for further study of the genome structure and functional evolution of poplar and other Salicaceae plants.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">28446920</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>01</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Two Highly Similar Poplar Paleo-subgenomes Suggest an Autotetraploid Ancestor of Salicaceae Plants.</ArticleTitle><Pagination><MedlinePgn>571</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2017.00571</ELocationID><Abstract><AbstractText>As a model plant to study perennial trees in the Salicaceae family, the poplar (<i>Populus trichocarpa</i>) genome was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment of its genome to a well-selected reference genome would help us better understand poplar's genome structure and gene family evolution. Here, by adopting the relatively simpler grape (<i>Vitis vinifera</i>) genome as reference, and by inferring both intra- and inter-genomic gene collinearity, we produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation. We uncovered homologous blocks in the grape and poplar genomes and also between them. Moreover, we characterized the genes missing and found that poplar had two considerably similar subgenomes (≤0.05 difference in gene deletion) produced by the Salicaceae-common tetraploidization, suggesting its autotetraploid nature. Taken together, this work provides a timely and valuable dataset of orthologous and paralogous genes for further study of the genome structure and functional evolution of poplar and other Salicaceae plants.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Yinzhe</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jinpeng</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ge</LastName><ForeName>Weina</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Zhenyi</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yuxian</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Nanshan</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Sangrong</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Liwei</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xiyin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>School of Life Science, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>04</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">fractionation</Keyword><Keyword MajorTopicYN="N">gene collinearity</Keyword><Keyword MajorTopicYN="N">genome alignment</Keyword><Keyword MajorTopicYN="N">genomic homology</Keyword><Keyword MajorTopicYN="N">grape</Keyword><Keyword MajorTopicYN="N">polyploid</Keyword><Keyword MajorTopicYN="N">poplar</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>01</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>03</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>4</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>4</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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last="Ge">Weina Ge</name><name sortKey="Li, Yuxian" sort="Li, Yuxian" uniqKey="Li Y" first="Yuxian" last="Li">Yuxian Li</name><name sortKey="Li, Yuxian" sort="Li, Yuxian" uniqKey="Li Y" first="Yuxian" last="Li">Yuxian Li</name><name sortKey="Liu, Yinzhe" sort="Liu, Yinzhe" uniqKey="Liu Y" first="Yinzhe" last="Liu">Yinzhe Liu</name><name sortKey="Sun, Sangrong" sort="Sun, Sangrong" uniqKey="Sun S" first="Sangrong" last="Sun">Sangrong Sun</name><name sortKey="Wang, Jinpeng" sort="Wang, Jinpeng" uniqKey="Wang J" first="Jinpeng" last="Wang">Jinpeng Wang</name><name sortKey="Wang, Jinpeng" sort="Wang, Jinpeng" uniqKey="Wang J" first="Jinpeng" last="Wang">Jinpeng Wang</name><name sortKey="Wang, Xiyin" sort="Wang, Xiyin" uniqKey="Wang X" first="Xiyin" last="Wang">Xiyin Wang</name><name sortKey="Wang, Xiyin" sort="Wang, Xiyin" uniqKey="Wang X" first="Xiyin" last="Wang">Xiyin Wang</name><name sortKey="Wang, Zhenyi" sort="Wang, Zhenyi" uniqKey="Wang Z" first="Zhenyi" last="Wang">Zhenyi Wang</name><name sortKey="Wang, Zhenyi" sort="Wang, Zhenyi" uniqKey="Wang Z" first="Zhenyi" last="Wang">Zhenyi Wang</name><name sortKey="Yang, Nanshan" sort="Yang, Nanshan" uniqKey="Yang N" first="Nanshan" last="Yang">Nanshan Yang</name><name sortKey="Zhang, Liwei" sort="Zhang, Liwei" uniqKey="Zhang L" first="Liwei" last="Zhang">Liwei Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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