The poplar pangenome provides insights into the evolutionary history of the genus.
Identifieur interne : 000672 ( Main/Exploration ); précédent : 000671; suivant : 000673The poplar pangenome provides insights into the evolutionary history of the genus.
Auteurs : Bingyu Zhang [République populaire de Chine] ; Wenxu Zhu [République populaire de Chine] ; Shu Diao [République populaire de Chine] ; Xiaojuan Wu [République populaire de Chine] ; Junqian Lu [République populaire de Chine] ; Changjun Ding [République populaire de Chine] ; Xiaohua Su [République populaire de Chine]Source :
- Communications biology [ 2399-3642 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Populus.
- classification : Gene Ontology, Génome végétal, Phylogenèse, Polymorphisme de nucléotide simple, Populus, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- classification : Populus.
- genetics : Populus.
- Evolution, Molecular, Gene Ontology, Genome, Plant, Phylogeny, Polymorphism, Single Nucleotide.
Abstract
The genus Populus comprises a complex amalgam of ancient and modern species that has become a prime model for evolutionary and taxonomic studies. Here we sequenced the genomes of 10 species from five sections of the genus Populus, identified 71 million genomic variations, and observed new correlations between the single-nucleotide polymorphism-structural variation (SNP-SV) density and indel-SV density to complement the SNP-indel density correlation reported in mammals. Disease resistance genes (R genes) with heterozygous loss-of-function (LOF) were significantly enriched in the 10 species, which increased the diversity of poplar R genes during evolution. Heterozygous LOF mutations in the self-incompatibility genes were closely related to the self-fertilization of poplar, suggestive of genomic control of self-fertilization in dioecious plants. The phylogenetic genome-wide SNPs tree also showed possible ancient hybridization among species in sections Tacamahaca, Aigeiros, and Leucoides. The pangenome resource also provided information for poplar genetics and breeding.
DOI: 10.1038/s42003-019-0474-7
PubMed: 31240253
PubMed Central: PMC6581948
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Su, Xiaohua" sort="Su, Xiaohua" uniqKey="Su X" first="Xiaohua" last="Su">Xiaohua Su</name><affiliation wicri:level="1"><nlm:affiliation>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">Communications biology</title><idno type="eISSN">2399-3642</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Evolution, Molecular (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Phylogeny (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Gene Ontology (MeSH)</term><term>Génome végétal (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Ontology</term><term>Genome, Plant</term><term>Phylogeny</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Gene Ontology</term><term>Génome végétal</term><term>Phylogenèse</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The genus <i>Populus</i> comprises a complex amalgam of ancient and modern species that has become a prime model for evolutionary and taxonomic studies. Here we sequenced the genomes of 10 species from five sections of the genus <i>Populus</i>, identified 71 million genomic variations, and observed new correlations between the single-nucleotide polymorphism-structural variation (SNP-SV) density and indel-SV density to complement the SNP-indel density correlation reported in mammals. Disease resistance genes (R genes) with heterozygous loss-of-function (LOF) were significantly enriched in the 10 species, which increased the diversity of poplar R genes during evolution. Heterozygous LOF mutations in the self-incompatibility genes were closely related to the self-fertilization of poplar, suggestive of genomic control of self-fertilization in dioecious plants. The phylogenetic genome-wide SNPs tree also showed possible ancient hybridization among species in sections Tacamahaca, Aigeiros, and Leucoides. The pangenome resource also provided information for poplar genetics and breeding.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31240253</PMID><DateCompleted><Year>2020</Year><Month>04</Month><Day>23</Day></DateCompleted><DateRevised><Year>2020</Year><Month>05</Month><Day>25</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">2399-3642</ISSN><JournalIssue CitedMedium="Internet"><Volume>2</Volume><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>Communications biology</Title><ISOAbbreviation>Commun Biol</ISOAbbreviation></Journal><ArticleTitle>The poplar pangenome provides insights into the evolutionary history of the genus.</ArticleTitle><Pagination><MedlinePgn>215</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s42003-019-0474-7</ELocationID><Abstract><AbstractText>The genus <i>Populus</i> comprises a complex amalgam of ancient and modern species that has become a prime model for evolutionary and taxonomic studies. Here we sequenced the genomes of 10 species from five sections of the genus <i>Populus</i>, identified 71 million genomic variations, and observed new correlations between the single-nucleotide polymorphism-structural variation (SNP-SV) density and indel-SV density to complement the SNP-indel density correlation reported in mammals. Disease resistance genes (R genes) with heterozygous loss-of-function (LOF) were significantly enriched in the 10 species, which increased the diversity of poplar R genes during evolution. Heterozygous LOF mutations in the self-incompatibility genes were closely related to the self-fertilization of poplar, suggestive of genomic control of self-fertilization in dioecious plants. The phylogenetic genome-wide SNPs tree also showed possible ancient hybridization among species in sections Tacamahaca, Aigeiros, and Leucoides. The pangenome resource also provided information for poplar genetics and breeding.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Bingyu</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Wenxu</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Diao</LastName><ForeName>Shu</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Xiaojuan</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Junqian</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ding</LastName><ForeName>ChangJun</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Su</LastName><ForeName>Xiaohua</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>1State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091 Beijing, China.</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>2019</Year><Month>06</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Commun Biol</MedlineTA><NlmUniqueID>101719179</NlmUniqueID><ISSNLinking>2399-3642</ISSNLinking></MedlineJournalInfo><MeshHeadingList><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D063990" MajorTopicYN="N">Gene Ontology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Plant evolution</Keyword><Keyword MajorTopicYN="Y">Plant sciences</Keyword></KeywordList><CoiStatement>Competing interestsThe authors declare no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>05</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>05</Month><Day>23</Day></PubMedPubDate><PubMedPubDate 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Diao</name><name sortKey="Diao, Shu" sort="Diao, Shu" uniqKey="Diao S" first="Shu" last="Diao">Shu Diao</name><name sortKey="Ding, Changjun" sort="Ding, Changjun" uniqKey="Ding C" first="Changjun" last="Ding">Changjun Ding</name><name sortKey="Ding, Changjun" sort="Ding, Changjun" uniqKey="Ding C" first="Changjun" last="Ding">Changjun Ding</name><name sortKey="Lu, Junqian" sort="Lu, Junqian" uniqKey="Lu J" first="Junqian" last="Lu">Junqian Lu</name><name sortKey="Lu, Junqian" sort="Lu, Junqian" uniqKey="Lu J" first="Junqian" last="Lu">Junqian Lu</name><name sortKey="Su, Xiaohua" sort="Su, Xiaohua" uniqKey="Su X" first="Xiaohua" last="Su">Xiaohua Su</name><name sortKey="Su, Xiaohua" sort="Su, Xiaohua" uniqKey="Su X" first="Xiaohua" last="Su">Xiaohua Su</name><name sortKey="Wu, Xiaojuan" sort="Wu, Xiaojuan" uniqKey="Wu X" first="Xiaojuan" last="Wu">Xiaojuan Wu</name><name sortKey="Wu, Xiaojuan" sort="Wu, Xiaojuan" uniqKey="Wu X" first="Xiaojuan" last="Wu">Xiaojuan Wu</name><name sortKey="Zhang, Bingyu" sort="Zhang, Bingyu" uniqKey="Zhang B" first="Bingyu" last="Zhang">Bingyu Zhang</name><name sortKey="Zhu, Wenxu" sort="Zhu, Wenxu" uniqKey="Zhu W" first="Wenxu" last="Zhu">Wenxu Zhu</name><name sortKey="Zhu, Wenxu" sort="Zhu, Wenxu" uniqKey="Zhu W" first="Wenxu" last="Zhu">Wenxu Zhu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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