De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections.
Identifieur interne : 000612 ( Main/Exploration ); précédent : 000611; suivant : 000613De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections.
Auteurs : Hainan Wu [République populaire de Chine] ; Dan Yao [République populaire de Chine] ; Yuhua Chen [République populaire de Chine] ; Wenguo Yang [République populaire de Chine] ; Wei Zhao [République populaire de Chine] ; Hua Gao [République populaire de Chine] ; Chunfa Tong [République populaire de Chine]Source :
- G3 (Bethesda, Md.) [ 2160-1836 ] ; 2020.
Abstract
Populus simonii is an important tree in the genus Populus, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of P. simonii using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the P. simonii assembly. Genomic repeat analysis revealed that 41.47% of the P. simonii genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the P. simonii genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that P. simonii and Populus trichocarpa should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different Populus species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F1 hybrid population derived by crossing P. simonii with other Populus species.
DOI: 10.1534/g3.119.400913
PubMed: 31806765
PubMed Central: PMC7003099
Affiliations:
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Assembly of <i>Populus simonii</i> Further Supports That <i>Populus simonii</i> and <i>Populus trichocarpa</i> Belong to Different Sections.</title><author><name sortKey="Wu, Hainan" sort="Wu, Hainan" uniqKey="Wu H" first="Hainan" last="Wu">Hainan Wu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037</wicri:regionArea><wicri:noRegion>Nanjing 210037</wicri:noRegion></affiliation></author><author><name sortKey="Yao, Dan" sort="Yao, Dan" uniqKey="Yao D" first="Dan" last="Yao">Dan Yao</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037</wicri:regionArea><wicri:noRegion>Nanjing 210037</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Yuhua" sort="Chen, Yuhua" uniqKey="Chen Y" first="Yuhua" last="Chen">Yuhua Chen</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037</wicri:regionArea><wicri:noRegion>Nanjing 210037</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Wenguo" sort="Yang, Wenguo" uniqKey="Yang W" first="Wenguo" last="Yang">Wenguo Yang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037</wicri:regionArea><wicri:noRegion>Nanjing 210037</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Wei" sort="Zhao, Wei" uniqKey="Zhao W" first="Wei" last="Zhao">Wei Zhao</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037</wicri:regionArea><wicri:noRegion>Nanjing 210037</wicri:noRegion></affiliation></author><author><name sortKey="Gao, Hua" sort="Gao, Hua" uniqKey="Gao H" first="Hua" last="Gao">Hua Gao</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037</wicri:regionArea><wicri:noRegion>Nanjing 210037</wicri:noRegion></affiliation></author><author><name sortKey="Tong, Chunfa" sort="Tong, Chunfa" uniqKey="Tong C" first="Chunfa" last="Tong">Chunfa Tong</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China tongchf@njfu.edu.cn.</nlm:affiliation><country wicri:rule="url">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037</wicri:regionArea><wicri:noRegion>Nanjing 210037</wicri:noRegion></affiliation></author></analytic><series><title level="j">G3 (Bethesda, Md.)</title><idno type="eISSN">2160-1836</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Populus simonii</i> is an important tree in the genus <i>Populus</i>, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of <i>P. simonii</i> using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the <i>P. simonii</i> assembly. Genomic repeat analysis revealed that 41.47% of the <i>P. simonii</i> genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the <i>P. simonii</i> genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that <i>P. simonii</i> and <i>Populus trichocarpa</i> should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different <i>Populus</i> species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F<sub>1</sub> hybrid population derived by crossing <i>P. simonii</i> with other <i>Populus</i> species.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">31806765</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>14</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2160-1836</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>2</Issue><PubDate><Year>2020</Year><Month>02</Month><Day>06</Day></PubDate></JournalIssue><Title>G3 (Bethesda, Md.)</Title><ISOAbbreviation>G3 (Bethesda)</ISOAbbreviation></Journal><ArticleTitle><i>De Novo</i> Genome Assembly of <i>Populus simonii</i> Further Supports That <i>Populus simonii</i> and <i>Populus trichocarpa</i> Belong to Different Sections.</ArticleTitle><Pagination><MedlinePgn>455-466</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1534/g3.119.400913</ELocationID><Abstract><AbstractText><i>Populus simonii</i> is an important tree in the genus <i>Populus</i>, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of <i>P. simonii</i> using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the <i>P. simonii</i> assembly. Genomic repeat analysis revealed that 41.47% of the <i>P. simonii</i> genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the <i>P. simonii</i> genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that <i>P. simonii</i> and <i>Populus trichocarpa</i> should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different <i>Populus</i> species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F<sub>1</sub> hybrid population derived by crossing <i>P. simonii</i> with other <i>Populus</i> species.</AbstractText><CopyrightInformation>Copyright © 2020 Wu et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Hainan</ForeName><Initials>H</Initials><Identifier Source="ORCID">0000-0003-2890-9702</Identifier><AffiliationInfo><Affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yao</LastName><ForeName>Dan</ForeName><Initials>D</Initials><Identifier Source="ORCID">0000-0001-5937-3467</Identifier><AffiliationInfo><Affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Yuhua</ForeName><Initials>Y</Initials><Identifier Source="ORCID">0000-0002-4530-8653</Identifier><AffiliationInfo><Affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Wenguo</ForeName><Initials>W</Initials><Identifier Source="ORCID">0000-0002-5191-828X</Identifier><AffiliationInfo><Affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Wei</ForeName><Initials>W</Initials><Identifier Source="ORCID">0000-0002-7130-7670</Identifier><AffiliationInfo><Affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Hua</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tong</LastName><ForeName>Chunfa</ForeName><Initials>C</Initials><Identifier Source="ORCID">0000-0001-9795-211X</Identifier><AffiliationInfo><Affiliation>Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China tongchf@njfu.edu.cn.</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>2020</Year><Month>02</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>G3 (Bethesda)</MedlineTA><NlmUniqueID>101566598</NlmUniqueID><ISSNLinking>2160-1836</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Illumina sequencing</Keyword><Keyword MajorTopicYN="Y">PacBio sequencing</Keyword><Keyword MajorTopicYN="Y">Populus simonii</Keyword><Keyword MajorTopicYN="Y">genetic linkage maps</Keyword><Keyword MajorTopicYN="Y">genome assembly</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>12</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>12</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>12</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31806765</ArticleId><ArticleId IdType="pii">g3.119.400913</ArticleId><ArticleId IdType="doi">10.1534/g3.119.400913</ArticleId><ArticleId 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Wenguo" sort="Yang, Wenguo" uniqKey="Yang W" first="Wenguo" last="Yang">Wenguo Yang</name><name sortKey="Yao, Dan" sort="Yao, Dan" uniqKey="Yao D" first="Dan" last="Yao">Dan Yao</name><name sortKey="Zhao, Wei" sort="Zhao, Wei" uniqKey="Zhao W" first="Wei" last="Zhao">Wei Zhao</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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