umu.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.ORCID iD: 0000-0002-6150-7046
2019 (English)In: Science China Life Sciences, ISSN 1674-7305, E-ISSN 1869-1889, Vol. 62, no 5, p. 609-618Article in journal (Refereed) Published
Abstract [en]

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 similar to 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 (similar to 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.

Place, publisher, year, edition, pages
2019. Vol. 62, no 5, p. 609-618
Keywords [en]
Populus alba, de novo assembly, genetic diversity, population expansion
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:umu:diva-159401DOI: 10.1007/s11427-018-9455-2ISI: 000467172000001PubMedID: 30661181OAI: oai:DiVA.org:umu-159401DiVA, id: diva2:1322058
Available from: 2019-06-10 Created: 2019-06-10 Last updated: 2019-06-10Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMed

Authority records BETA

Wang, Xiao-Ru

Search in DiVA

By author/editor
Wang, Xiao-Ru
By organisation
Department of Ecology and Environmental Sciences
In the same journal
Science China Life Sciences
Evolutionary Biology

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 13 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf