文献类型：期刊文献

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

作者：Liu, Yan-Jing[1,2] Wang, Xiao-Ru[3] Zeng, Qing-Yin[1,2]

第一作者：Liu, Yan-Jing;刘妍婧

通信作者：Zeng, QY[1];Zeng, QY[2]

机构：[1]Chinese Acad Forestry, State Key Lab Tree Genet & Breeding, Beijing 100091, Peoples R China;[2]Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China;[3]Umea Univ, UPSC, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden

年份：2019

卷号：62

期号：5

起止页码：609-618

外文期刊名：SCIENCE CHINA-LIFE SCIENCES

收录：;Scopus(收录号：2-s2.0-85060339083);WOS:【SCI-EXPANDED(收录号:WOS:000467172000001)】；

基金：We thank Dr. Jian Wang for assisting with the population sampling from Irtysh River basin. This work was supported by the National Science Fund for Distinguished Young Scholars (31425006) and Chinese Academy of Forestry (CAFYBB2018ZX001).

语种：英文

外文关键词：Populus alba; de novo assembly; genetic diversity; population expansion

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.