The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution.
Identifieur interne : 000074 ( Main/Exploration ); précédent : 000073; suivant : 000075The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution.
Auteurs : Suyun Wei [République populaire de Chine] ; Yonghua Yang [République populaire de Chine] ; Tongming Yin [République populaire de Chine]Source :
- Horticulture research [ 2052-7276 ] ; 2020.
Abstract
Salix suchowensis is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of S. suchowensis was assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of S. suchowensis generated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was ~65-fold higher than that reported previously. The contiguity and completeness of the genome were significantly improved. By applying Hi-C data, 339.67 Mb (95.29%) of the assembled sequences were allocated to the 19 chromosomes of haploid willow. With the chromosome-scale assembly, we revealed a series of major chromosomal fissions and fusions that explain the genome divergence between the sister genera of Salix and Populus. The more complete and accurate willow reference genome obtained in this study provides a fundamental resource for studying many genetic and genomic characteristics of woody plants.
DOI: 10.1038/s41438-020-0268-6
PubMed: 32257231
PubMed Central: PMC7109076
Affiliations:
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wicri:level="1"><nlm:affiliation>2College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>2College of Information Science and Technology, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Yonghua" sort="Yang, Yonghua" uniqKey="Yang Y" first="Yonghua" last="Yang">Yonghua Yang</name><affiliation wicri:level="1"><nlm:affiliation>3College of Life Sciences, Nanjing University, Nanjing, 210093 China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>3College of Life Sciences, Nanjing University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name><affiliation wicri:level="1"><nlm:affiliation>1Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author></analytic><series><title level="j">Horticulture research</title><idno type="ISSN">2052-7276</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>Salix suchowensis</i> is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of <i>S. suchowensis</i> was assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of <i>S. suchowensis</i> generated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was ~65-fold higher than that reported previously. The contiguity and completeness of the genome were significantly improved. By applying Hi-C data, 339.67 Mb (95.29%) of the assembled sequences were allocated to the 19 chromosomes of haploid willow. With the chromosome-scale assembly, we revealed a series of major chromosomal fissions and fusions that explain the genome divergence between the sister genera of <i>Salix</i> and <i>Populus</i>. The more complete and accurate willow reference genome obtained in this study provides a fundamental resource for studying many genetic and genomic characteristics of woody plants.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32257231</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2052-7276</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Horticulture research</Title><ISOAbbreviation>Hortic Res</ISOAbbreviation></Journal><ArticleTitle>The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution.</ArticleTitle><Pagination><MedlinePgn>45</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41438-020-0268-6</ELocationID><Abstract><AbstractText><i>Salix suchowensis</i> is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of <i>S. suchowensis</i> was assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of <i>S. suchowensis</i> generated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was ~65-fold higher than that reported previously. The contiguity and completeness of the genome were significantly improved. By applying Hi-C data, 339.67 Mb (95.29%) of the assembled sequences were allocated to the 19 chromosomes of haploid willow. With the chromosome-scale assembly, we revealed a series of major chromosomal fissions and fusions that explain the genome divergence between the sister genera of <i>Salix</i> and <i>Populus</i>. The more complete and accurate willow reference genome obtained in this study provides a fundamental resource for studying many genetic and genomic characteristics of woody plants.</AbstractText><CopyrightInformation>© The Author(s) 2020.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Suyun</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0003-3262-2771</Identifier><AffiliationInfo><Affiliation>1Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo><AffiliationInfo><Affiliation>2College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Yonghua</ForeName><Initials>Y</Initials><Identifier Source="ORCID">0000-0002-8647-1158</Identifier><AffiliationInfo><Affiliation>3College of Life Sciences, Nanjing University, Nanjing, 210093 China.</Affiliation><Identifier Source="ISNI">0000 0001 2314 964X</Identifier><Identifier Source="GRID">grid.41156.37</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yin</LastName><ForeName>Tongming</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>1Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate 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sortKey="Yang, Yonghua" sort="Yang, Yonghua" uniqKey="Yang Y" first="Yonghua" last="Yang">Yonghua Yang</name><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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