The chromosome-level draft genome of Dalbergia odorifera.
Identifieur interne : 000075 ( Main/Exploration ); précédent : 000074; suivant : 000076The chromosome-level draft genome of Dalbergia odorifera.
Auteurs : Zhou Hong [République populaire de Chine] ; Jiang Li [République populaire de Chine] ; Xiaojin Liu [République populaire de Chine] ; Jinmin Lian [République populaire de Chine] ; Ningnan Zhang [République populaire de Chine] ; Zengjiang Yang [République populaire de Chine] ; Yongchao Niu [République populaire de Chine] ; Zhiyi Cui [République populaire de Chine] ; Daping Xu [République populaire de Chine]Source :
- GigaScience [ 2047-217X ] ; 2020.
Abstract
BACKGROUND
Dalbergia odorifera T. Chen (Fabaceae) is an International Union for Conservation of Nature red-listed tree. This tree is of high medicinal and commercial value owing to its officinal, insect-proof, durable heartwood. However, there is a lack of genome reference, which has hindered development of studies on the heartwood formation.
FINDINGS
We presented the first chromosome-scale genome assembly of D. odorifera obtained on the basis of Illumina paired-end sequencing, Pacific Biosciences single-molecule real-time sequencing, 10x Genomics linked reads, and Hi-C technology. We assembled 97.68% of the 653.45 Mb D. odorifera genome with scaffold N50 and contig sizes of 56.16 and 5.92 Mb, respectively. Ten super-scaffolds corresponding to the 10 chromosomes were assembled, with the longest scaffold reaching 79.61 Mb. Repetitive elements account for 54.17% of the genome, and 30,310 protein-coding genes were predicted from the genome, of which ∼92.6% were functionally annotated. The phylogenetic tree showed that D. odorifera diverged from the ancestor of Arabidopsis thaliana and Populus trichocarpa and then separated from Glycine max and Cajanus cajan.
CONCLUSIONS
We sequence and reveal the first chromosome-level de novo genome of D. odorifera. These studies provide valuable genomic resources for the research of heartwood formation in D. odorifera and other timber trees. The high-quality assembled genome can also be used as reference for comparative genomics analysis and future population genetic studies of D. odorifera.
DOI: 10.1093/gigascience/giaa084
PubMed: 32808664
PubMed Central: PMC7433187
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Li, Jiang" sort="Li, Jiang" uniqKey="Li J" first="Jiang" last="Li">Jiang Li</name><affiliation wicri:level="1"><nlm:affiliation>Biozeron Shenzhen Inc., Shenzhen 518000, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Biozeron Shenzhen Inc., Shenzhen 518000</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Liu, Xiaojin" sort="Liu, Xiaojin" uniqKey="Liu X" first="Xiaojin" last="Liu">Xiaojin Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Lian, Jinmin" sort="Lian, Jinmin" uniqKey="Lian J" first="Jinmin" last="Lian">Jinmin Lian</name><affiliation wicri:level="1"><nlm:affiliation>Biozeron Shenzhen Inc., Shenzhen 518000, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Biozeron Shenzhen Inc., Shenzhen 518000</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Zhang, Ningnan" sort="Zhang, Ningnan" uniqKey="Zhang N" first="Ningnan" last="Zhang">Ningnan Zhang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Yang, Zengjiang" sort="Yang, Zengjiang" uniqKey="Yang Z" first="Zengjiang" last="Yang">Zengjiang Yang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Niu, Yongchao" sort="Niu, Yongchao" uniqKey="Niu Y" first="Yongchao" last="Niu">Yongchao Niu</name><affiliation wicri:level="1"><nlm:affiliation>Biozeron Shenzhen Inc., Shenzhen 518000, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Biozeron Shenzhen Inc., Shenzhen 518000</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Cui, Zhiyi" sort="Cui, Zhiyi" uniqKey="Cui Z" first="Zhiyi" last="Cui">Zhiyi Cui</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Xu, Daping" sort="Xu, Daping" uniqKey="Xu D" first="Daping" last="Xu">Daping Xu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author></analytic><series><title level="j">GigaScience</title><idno type="eISSN">2047-217X</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"><p><b>BACKGROUND</b></p><p>Dalbergia odorifera T. Chen (Fabaceae) is an International Union for Conservation of Nature red-listed tree. This tree is of high medicinal and commercial value owing to its officinal, insect-proof, durable heartwood. However, there is a lack of genome reference, which has hindered development of studies on the heartwood formation.</p></div><div type="abstract" xml:lang="en"><p><b>FINDINGS</b></p><p>We presented the first chromosome-scale genome assembly of D. odorifera obtained on the basis of Illumina paired-end sequencing, Pacific Biosciences single-molecule real-time sequencing, 10x Genomics linked reads, and Hi-C technology. We assembled 97.68% of the 653.45 Mb D. odorifera genome with scaffold N50 and contig sizes of 56.16 and 5.92 Mb, respectively. Ten super-scaffolds corresponding to the 10 chromosomes were assembled, with the longest scaffold reaching 79.61 Mb. Repetitive elements account for 54.17% of the genome, and 30,310 protein-coding genes were predicted from the genome, of which ∼92.6% were functionally annotated. The phylogenetic tree showed that D. odorifera diverged from the ancestor of Arabidopsis thaliana and Populus trichocarpa and then separated from Glycine max and Cajanus cajan.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>We sequence and reveal the first chromosome-level de novo genome of D. odorifera. These studies provide valuable genomic resources for the research of heartwood formation in D. odorifera and other timber trees. The high-quality assembled genome can also be used as reference for comparative genomics analysis and future population genetic studies of D. odorifera.</p></div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32808664</PMID><DateRevised><Year>2020</Year><Month>08</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">2047-217X</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>8</Issue><PubDate><Year>2020</Year><Month>Aug</Month><Day>01</Day></PubDate></JournalIssue><Title>GigaScience</Title><ISOAbbreviation>Gigascience</ISOAbbreviation></Journal><ArticleTitle>The chromosome-level draft genome of Dalbergia odorifera.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">giaa084</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1093/gigascience/giaa084</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Dalbergia odorifera T. Chen (Fabaceae) is an International Union for Conservation of Nature red-listed tree. This tree is of high medicinal and commercial value owing to its officinal, insect-proof, durable heartwood. However, there is a lack of genome reference, which has hindered development of studies on the heartwood formation.</AbstractText><AbstractText Label="FINDINGS" NlmCategory="RESULTS">We presented the first chromosome-scale genome assembly of D. odorifera obtained on the basis of Illumina paired-end sequencing, Pacific Biosciences single-molecule real-time sequencing, 10x Genomics linked reads, and Hi-C technology. We assembled 97.68% of the 653.45 Mb D. odorifera genome with scaffold N50 and contig sizes of 56.16 and 5.92 Mb, respectively. Ten super-scaffolds corresponding to the 10 chromosomes were assembled, with the longest scaffold reaching 79.61 Mb. Repetitive elements account for 54.17% of the genome, and 30,310 protein-coding genes were predicted from the genome, of which ∼92.6% were functionally annotated. The phylogenetic tree showed that D. odorifera diverged from the ancestor of Arabidopsis thaliana and Populus trichocarpa and then separated from Glycine max and Cajanus cajan.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">We sequence and reveal the first chromosome-level de novo genome of D. odorifera. These studies provide valuable genomic resources for the research of heartwood formation in D. odorifera and other timber trees. The high-quality assembled genome can also be used as reference for comparative genomics analysis and future population genetic studies of D. odorifera.</AbstractText><CopyrightInformation>© The Author(s) 2020. Published by Oxford University Press.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hong</LastName><ForeName>Zhou</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Jiang</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Biozeron Shenzhen Inc., Shenzhen 518000, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Xiaojin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lian</LastName><ForeName>Jinmin</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Biozeron Shenzhen Inc., Shenzhen 518000, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Ningnan</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Zengjiang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Niu</LastName><ForeName>Yongchao</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Biozeron Shenzhen Inc., Shenzhen 518000, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cui</LastName><ForeName>Zhiyi</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Daping</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Gigascience</MedlineTA><NlmUniqueID>101596872</NlmUniqueID><ISSNLinking>2047-217X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Dalbergia odorifera T. Chen</Keyword><Keyword MajorTopicYN="N">de novo sequencing</Keyword><Keyword MajorTopicYN="N">annotation</Keyword><Keyword MajorTopicYN="N">chromosome-level genome assembly</Keyword><Keyword MajorTopicYN="N">phylogeny</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>03</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>05</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>07</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>8</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>8</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Chine</li></country><region><li>Guangdong</li></region><settlement><li>Jiangmen</li><li>Shenzhen</li></settlement></list><tree><country name="République populaire de Chine"><region name="Guangdong"><name sortKey="Hong, Zhou" sort="Hong, Zhou" uniqKey="Hong Z" first="Zhou" last="Hong">Zhou Hong</name></region><name sortKey="Cui, Zhiyi" sort="Cui, Zhiyi" uniqKey="Cui Z" first="Zhiyi" last="Cui">Zhiyi Cui</name><name sortKey="Li, Jiang" sort="Li, Jiang" uniqKey="Li J" first="Jiang" last="Li">Jiang Li</name><name sortKey="Lian, Jinmin" sort="Lian, Jinmin" uniqKey="Lian J" first="Jinmin" last="Lian">Jinmin Lian</name><name sortKey="Liu, Xiaojin" sort="Liu, Xiaojin" uniqKey="Liu X" first="Xiaojin" last="Liu">Xiaojin Liu</name><name sortKey="Niu, Yongchao" sort="Niu, Yongchao" uniqKey="Niu Y" first="Yongchao" last="Niu">Yongchao Niu</name><name sortKey="Xu, Daping" sort="Xu, Daping" uniqKey="Xu D" first="Daping" last="Xu">Daping Xu</name><name sortKey="Yang, Zengjiang" sort="Yang, Zengjiang" uniqKey="Yang Z" first="Zengjiang" last="Yang">Zengjiang Yang</name><name sortKey="Zhang, Ningnan" sort="Zhang, Ningnan" uniqKey="Zhang N" first="Ningnan" last="Zhang">Ningnan Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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