干旱区生态环境知识资源中心(Arid): Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica)

Arid

DOI	10.1111/1755-0998.13142
	Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica)
	Zhang, Zhiyang 1; Chen, Yang 1; Zhang, Junlin 1; Ma, Xinzhi 1; Li, Yiling 1; Li, Mengmeng 1; Wang, Deyan 1; Kang, Minghui 1; Wu, Haolin 1; Yang, Yongzhi 2,3; Olson, Matthew S.4; DiFazio, Stephen P.5; Wan, Dongshi 2,3; Liu, Jianquan 1,2,3; Ma, Tao 1
通讯作者	Ma, Tao
来源期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
EISSN	1755-0998
出版年	2020
卷号	20 期号:3
英文摘要	Populus euphratica is well adapted to extreme desert environments and is an important model species for elucidating the mechanisms of abiotic stress resistance in trees. The current assembly of P. euphratica genome is highly fragmented with many gaps and errors, thereby impeding downstream applications. Here, we report an improved chromosome-level reference genome of P. euphratica (v2.0) using single-molecule sequencing and chromosome conformation capture (Hi-C) technologies. Relative to the previous reference genome, our assembly represents a nearly 60-fold improvement in contiguity, with a scaffold N50 size of 28.59 Mb. Using this genome, we have found that extensive expansion of Gypsy elements in P. euphratica led to its rapid increase in genome size compared to any other Salicaceae species studied to date, and potentially contributed to adaptive divergence driven by insertions near genes involved in stress tolerance. We also detected a wide range of unique structural rearrangements in P. euphratica, including 2,549 translocations, 454 inversions, 121 tandem and 14 segmental duplications. Several key genes likely to be involved in tolerance to abiotic stress were identified within these regions. This high-quality genome represents a valuable resource for poplar breeding and genetic improvement in the future, as well as comparative genomic analysis with other Salicaceae species.
英文关键词	environmental adaptation genome assembly Populus euphratica repeat expansion structural variation
类型	Article
语种	英语
国家	Peoples R China ; USA
收录类别	SCI-E
WOS记录号	WOS:000529782200004
WOS关键词	ARABIDOPSIS-THALIANA ; PHOSPHOLIPASES D-ZETA-1 ; ANNOTATION ; IDENTIFICATION ; TRANSCRIPTOME ; DATABASE ; ACCURATE ; GROWTH ; RNA ; RECONSTRUCTION
WOS类目	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS研究方向	Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
来源机构	兰州大学
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/319020
作者单位	1.Sichuan Univ, Key Lab Bioresource & Ecoenvironm, State Key Lab Hydraul & Mt River Engn, Minist Educ,Coll Life Sci, Chengdu, Peoples R China; 2.Lanzhou Univ, State Key Lab Grassland Agroecosyst, Inst Innovat Ecol, Lanzhou, Peoples R China; 3.Lanzhou Univ, Coll Life Sci, Lanzhou, Peoples R China; 4.Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA; 5.West Virginia Univ, Dept Biol, Morgantown, WV 26506 USA
推荐引用方式 GB/T 7714	Zhang, Zhiyang,Chen, Yang,Zhang, Junlin,et al. Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica)[J]. 兰州大学,2020,20(3).
APA	Zhang, Zhiyang.,Chen, Yang.,Zhang, Junlin.,Ma, Xinzhi.,Li, Yiling.,...&Ma, Tao.(2020).Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica).MOLECULAR ECOLOGY RESOURCES,20(3).
MLA	Zhang, Zhiyang,et al."Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica)".MOLECULAR ECOLOGY RESOURCES 20.3(2020).