Genome sequence and genetic transformation of a widely distributed and cultivated poplar.
Identifieur interne : 000942 ( Main/Exploration ); précédent : 000941; suivant : 000943Genome sequence and genetic transformation of a widely distributed and cultivated poplar.
Auteurs : Jianchao Ma [République populaire de Chine] ; Dongshi Wan [République populaire de Chine] ; Bingbing Duan [République populaire de Chine] ; Xiaotao Bai [République populaire de Chine] ; Qiuxian Bai [République populaire de Chine] ; Ningning Chen [République populaire de Chine] ; Tao Ma [République populaire de Chine]Source :
- Plant biotechnology journal [ 1467-7652 ] ; 2019.
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Abstract
Populus alba is widely distributed and cultivated in Europe and Asia. This species has been used for diverse studies. In this study, we assembled a de novo genome sequence of P. alba var. pyramidalis (= P. bolleana) and confirmed its high transformation efficiency and short transformation time by experiments. Through a process of hybrid genome assembly, a total of 464 M of the genome was assembled. Annotation analyses predicted 37 901 protein-coding genes. This genome is highly collinear to that of P. trichocarpa, with most genes having orthologs in the two species. We found a marked expansion of gene families related to histone and the hormone auxin but loss of disease resistance genes in P. alba if compared with the closely related P. trichocarpa. The genome sequence presented here represents a valuable resource for further molecular functional analyses of this species as a new tree model, poplar breeding practices and comparative genomic analyses across different poplars.
DOI: 10.1111/pbi.12989
PubMed: 30044051
PubMed Central: PMC6335071
Affiliations:
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Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Duan, Bingbing" sort="Duan, Bingbing" uniqKey="Duan B" first="Bingbing" last="Duan">Bingbing Duan</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Bai, Xiaotao" sort="Bai, Xiaotao" uniqKey="Bai X" first="Xiaotao" last="Bai">Xiaotao Bai</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Bai, Qiuxian" sort="Bai, Qiuxian" uniqKey="Bai Q" first="Qiuxian" last="Bai">Qiuxian Bai</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Ningning" sort="Chen, Ningning" uniqKey="Chen N" first="Ningning" last="Chen">Ningning Chen</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu</wicri:regionArea><wicri:noRegion>Chengdu</wicri:noRegion></affiliation></author></analytic><series><title level="j">Plant biotechnology journal</title><idno type="eISSN">1467-7652</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genome, Plant (genetics)</term><term>Genomics (MeSH)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Populus (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Transformation, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Annotation de séquence moléculaire (MeSH)</term><term>Génome végétal (génétique)</term><term>Génomique (MeSH)</term><term>Populus (génétique)</term><term>Transformation génétique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Plant</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Génome végétal</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genomics</term><term>Molecular Sequence Annotation</term><term>Sequence Analysis, DNA</term><term>Transformation, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Annotation de séquence moléculaire</term><term>Génomique</term><term>Transformation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Populus alba is widely distributed and cultivated in Europe and Asia. This species has been used for diverse studies. In this study, we assembled a de novo genome sequence of P. alba var. pyramidalis (= P. bolleana) and confirmed its high transformation efficiency and short transformation time by experiments. Through a process of hybrid genome assembly, a total of 464 M of the genome was assembled. Annotation analyses predicted 37 901 protein-coding genes. This genome is highly collinear to that of P. trichocarpa, with most genes having orthologs in the two species. We found a marked expansion of gene families related to histone and the hormone auxin but loss of disease resistance genes in P. alba if compared with the closely related P. trichocarpa. The genome sequence presented here represents a valuable resource for further molecular functional analyses of this species as a new tree model, poplar breeding practices and comparative genomic analyses across different poplars.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30044051</PMID><DateCompleted><Year>2019</Year><Month>06</Month><Day>03</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>09</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1467-7652</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><Issue>2</Issue><PubDate><Year>2019</Year><Month>02</Month></PubDate></JournalIssue><Title>Plant biotechnology journal</Title><ISOAbbreviation>Plant Biotechnol J</ISOAbbreviation></Journal><ArticleTitle>Genome sequence and genetic transformation of a widely distributed and cultivated poplar.</ArticleTitle><Pagination><MedlinePgn>451-460</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/pbi.12989</ELocationID><Abstract><AbstractText>Populus alba is widely distributed and cultivated in Europe and Asia. This species has been used for diverse studies. In this study, we assembled a de novo genome sequence of P. alba var. pyramidalis (= P. bolleana) and confirmed its high transformation efficiency and short transformation time by experiments. Through a process of hybrid genome assembly, a total of 464 M of the genome was assembled. Annotation analyses predicted 37 901 protein-coding genes. This genome is highly collinear to that of P. trichocarpa, with most genes having orthologs in the two species. We found a marked expansion of gene families related to histone and the hormone auxin but loss of disease resistance genes in P. alba if compared with the closely related P. trichocarpa. The genome sequence presented here represents a valuable resource for further molecular functional analyses of this species as a new tree model, poplar breeding practices and comparative genomic analyses across different poplars.</AbstractText><CopyrightInformation>© 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Jianchao</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wan</LastName><ForeName>Dongshi</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Duan</LastName><ForeName>Bingbing</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bai</LastName><ForeName>Xiaotao</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bai</LastName><ForeName>Qiuxian</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Ningning</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, 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>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>2013AA102605</GrantID><Agency>National High-Tech Research and Development Program of China</Agency><Country>International</Country></Grant><Grant><GrantID>31561123001</GrantID><Agency>National Science Foundation of China</Agency><Country>International</Country></Grant><Grant><GrantID>31470620</GrantID><Agency>National Science Foundation of China</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>10</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant Biotechnol J</MedlineTA><NlmUniqueID>101201889</NlmUniqueID><ISSNLinking>1467-7644</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014170" MajorTopicYN="N">Transformation, Genetic</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus alba
</Keyword><Keyword MajorTopicYN="Y">Populus bolleana
</Keyword><Keyword MajorTopicYN="Y">comparative genomics</Keyword><Keyword MajorTopicYN="Y">gene families</Keyword><Keyword MajorTopicYN="Y">transformation efficiency</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>09</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>07</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>07</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>7</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>6</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>7</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId 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IdType="pubmed">20525638</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Ma, Jianchao" sort="Ma, Jianchao" uniqKey="Ma J" first="Jianchao" last="Ma">Jianchao Ma</name></noRegion><name sortKey="Bai, Qiuxian" sort="Bai, Qiuxian" uniqKey="Bai Q" first="Qiuxian" last="Bai">Qiuxian Bai</name><name sortKey="Bai, Xiaotao" sort="Bai, Xiaotao" uniqKey="Bai X" first="Xiaotao" last="Bai">Xiaotao Bai</name><name sortKey="Chen, Ningning" sort="Chen, Ningning" uniqKey="Chen N" first="Ningning" last="Chen">Ningning Chen</name><name sortKey="Duan, Bingbing" sort="Duan, Bingbing" uniqKey="Duan B" first="Bingbing" last="Duan">Bingbing Duan</name><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao 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