Knowledge Management System Of Institute Of Botany,CAS
| De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China | |
| Liu, Yan-Jing; Wang, Xiao-Ru; Zeng, Qing-Yin | |
| 2019 | |
| Source Publication | SCIENCE CHINA-LIFE SCIENCES
 |
| ISSN | 1674-7305 |
| Volume | 62Issue:5Pages:609-618 |
| 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 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. |
| Keyword | Populus alba de novo assembly genetic diversity population expansion |
| Subject Area | Biology |
| DOI | 10.1007/s11427-018-9455-2 |
| Indexed By | SCI |
| Language | 英语 |
| WOS Keyword | POPULUS-ALBA ; PHYLOGENETIC ANALYSIS ; DRAFT GENOME ; ANNOTATION ; PATTERNS ; RESOURCE ; SEQUENCE ; DIVERGENCE ; SALICACEAE ; EVOLUTION |
| WOS Research Area | Life Sciences & Biomedicine - Other Topics |
| WOS ID | WOS:000467172000001 |
| Publisher | SCIENCE PRESS |
| Subtype | Article |
| Publication Place | BEIJING |
| EISSN | 1869-1889 |
| Funding Organization | National Science Fund for Distinguished Young ScholarsNational Natural Science Foundation of China (NSFC)National Science Fund for Distinguished Young Scholars [31425006] ; Chinese Academy of Forestry [CAFYBB2018ZX001] |
| Corresponding Author Email | qingyin.zeng@caf.ac.cn |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ibcas.ac.cn/handle/2S10CLM1/19717 |
| Collection | 系统与进化植物学国家重点实验室 |
| Affiliation | 1.[Liu, Yan-Jing 2.Chinese Acad Forestry, State Key Lab Tree Genet & Breeding, Beijing 100091, Peoples R China 3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 4.Umea Univ, UPSC, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden |
| Recommended Citation GB/T 7714 | Liu, Yan-Jing,Wang, Xiao-Ru,Zeng, Qing-Yin. De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China[J]. SCIENCE CHINA-LIFE SCIENCES,2019,62(5):609-618. |
| APA | Liu, Yan-Jing,Wang, Xiao-Ru,&Zeng, Qing-Yin.(2019).De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China.SCIENCE CHINA-LIFE SCIENCES,62(5),609-618. |
| MLA | Liu, Yan-Jing,et al."De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China".SCIENCE CHINA-LIFE SCIENCES 62.5(2019):609-618. |
| Files in This Item: | ||||||
| File Name/Size | DocType | Version | Access | License | ||
| Liu-2019-De novo ass（2091KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.
Edit Comment