De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China
文献类型：期刊论文
| 作者 | Liu, Yan-Jing; Wang, Xiao-Ru; Zeng, Qing-Yin |
| 刊名 | SCIENCE CHINA-LIFE SCIENCES
 |
| 出版日期 | 2019 |
| 卷号 | 62期号:5页码:609-618 |
| 关键词 | Populus alba de novo assembly genetic diversity population expansion |
| ISSN号 | 1674-7305 |
| DOI | 10.1007/s11427-018-9455-2 |
| 文献子类 | Article |
| 英文摘要 | 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. |
| 学科主题 | Biology |
| 出版地 | BEIJING |
| 电子版国际标准刊号 | 1869-1889 |
| WOS关键词 | POPULUS-ALBA ; PHYLOGENETIC ANALYSIS ; DRAFT GENOME ; ANNOTATION ; PATTERNS ; RESOURCE ; SEQUENCE ; DIVERGENCE ; SALICACEAE ; EVOLUTION |
| WOS研究方向 | Life Sciences & Biomedicine - Other Topics |
| 语种 | 英语 |
| WOS记录号 | WOS:000467172000001 |
| 出版者 | SCIENCE PRESS |
| 资助机构 | 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] |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/19717]  |
| 专题 | 植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文 |
| 作者单位 | 1.Umea Univ, UPSC, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden 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.[Liu, Yan-Jing |
| 推荐引用方式 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. |
入库方式： OAI收割
来源：植物研究所
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