De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China

doi:10.1007/s11427-018-9455-2

	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
发表期刊	SCIENCE CHINA-LIFE SCIENCES
ISSN	1674-7305
卷号	62 期号:5 页码:609-618
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.
关键词	Populus alba de novo assembly genetic diversity population expansion
学科领域	Biology
DOI	10.1007/s11427-018-9455-2
收录类别	SCI
语种	英语
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
WOS记录号	WOS:000467172000001
出版者	SCIENCE PRESS
文献子类	Article
出版地	BEIJING
EISSN	1869-1889
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]
作者邮箱	qingyin.zeng@caf.ac.cn
引用统计	被引频次：49[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/19717
专题	系统与进化植物学国家重点实验室
作者单位	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
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.

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