De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China.
Identifieur interne : 000A45 ( Main/Exploration ); précédent : 000A44; suivant : 000A46De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China.
Auteurs : Yan-Jing Liu [République populaire de Chine] ; Xiao-Ru Wang [Suède] ; Qing-Yin Zeng [République populaire de Chine]Source :
- Science China. Life sciences [ 1869-1889 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- MESH :
- chemical : DNA, Plant.
- geographic : China.
- classification : Populus.
- genetics : Populus.
- Genetic Variation, Genome, Plant, Geography, Polymorphism, Single Nucleotide, Rivers, Sequence Analysis, DNA.
Abstract
The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred ~5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (~ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170±0.014, which was lower than that in Italy (0.271±0.051) and Hungary (0.264±0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.
DOI: 10.1007/s11427-018-9455-2
PubMed: 30661181
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred ~5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (~ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170±0.014, which was lower than that in Italy (0.271±0.051) and Hungary (0.264±0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30661181</PMID><DateCompleted><Year>2020</Year><Month>04</Month><Day>10</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1869-1889</ISSN><JournalIssue CitedMedium="Internet"><Volume>62</Volume><Issue>5</Issue><PubDate><Year>2019</Year><Month>May</Month></PubDate></JournalIssue><Title>Science China. Life sciences</Title><ISOAbbreviation>Sci China Life Sci</ISOAbbreviation></Journal><ArticleTitle>De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China.</ArticleTitle><Pagination><MedlinePgn>609-618</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s11427-018-9455-2</ELocationID><Abstract><AbstractText>The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred ~5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (~ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170±0.014, which was lower than that in Italy (0.271±0.051) and Hungary (0.264±0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Yan-Jing</ForeName><Initials>YJ</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xiao-Ru</ForeName><Initials>XR</Initials><AffiliationInfo><Affiliation>Department of Ecology and Environmental Science, UPSC, Umeå University, 90187, SE, Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author 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MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D045483" MajorTopicYN="N">Rivers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus alba</Keyword><Keyword MajorTopicYN="N">de novo assembly</Keyword><Keyword MajorTopicYN="N">genetic diversity</Keyword><Keyword MajorTopicYN="N">population expansion</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>11</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>12</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>1</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>1</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30661181</ArticleId><ArticleId IdType="doi">10.1007/s11427-018-9455-2</ArticleId><ArticleId IdType="pii">10.1007/s11427-018-9455-2</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li><li>Suède</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Liu, Yan Jing" sort="Liu, Yan Jing" uniqKey="Liu Y" first="Yan-Jing" last="Liu">Yan-Jing Liu</name></noRegion><name sortKey="Liu, Yan Jing" sort="Liu, Yan Jing" uniqKey="Liu Y" first="Yan-Jing" last="Liu">Yan-Jing Liu</name><name sortKey="Zeng, Qing Yin" sort="Zeng, Qing Yin" uniqKey="Zeng Q" first="Qing-Yin" last="Zeng">Qing-Yin Zeng</name><name sortKey="Zeng, Qing Yin" sort="Zeng, Qing Yin" uniqKey="Zeng Q" first="Qing-Yin" last="Zeng">Qing-Yin Zeng</name></country><country name="Suède"><noRegion><name sortKey="Wang, Xiao Ru" sort="Wang, Xiao Ru" uniqKey="Wang X" first="Xiao-Ru" last="Wang">Xiao-Ru Wang</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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