A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

doi:10.1016/j.molp.2020.09.019

	A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era
	Chen, Yongming ; Song, Wanjun 1; Xie, Xiaoming ; Wang, Zihao ; Guan, Panfeng ; Peng, Huiru ; Jiao, Yuannian2,3 ; Ni, Zhongfu ; Sun, Qixin ; Guo, Weilong
	2020
发表期刊	MOLECULAR PLANT
ISSN	1674-2052
卷号	13 期号:12 页码:1694-1708
摘要	Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for Glade-specific homology inference and analysis have increased in the pangenomic era. Here we present a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. The Triticeae tribe is a typical allopolyploid-rich Glade with complex species relationships that includes many important crops, such as wheat, barley, and rye. We built Triticeae-GeneTribe (https://wheat.cau.edu.cn/TGT/), a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2, which evolved as a combined result of genome translocation, duplication, and polyploidization and gene loss events. Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources.
关键词	homology inference collinearity database pangenome Triticeae tribe polyploid
学科领域	Biochemistry & Molecular Biology ; Plant Sciences
DOI	10.1016/j.molp.2020.09.019
收录类别	SCI
语种	英语
WOS关键词	PAN-GENOME ; ORTHOLOGY ANALYSIS ; R PACKAGE ; WHEAT ; GENE ; DATABASE ; ANNOTATION ; EVOLUTION ; SEQUENCE ; VISUALIZATION
WOS研究方向	Biochemistry & Molecular Biology ; Plant Sciences
WOS记录号	WOS:000596734100008
出版者	CELL PRESS
文献子类	Article
出版地	CAMBRIDGE
EISSN	1752-9867
资助机构	Major Program of the National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31991210] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31701415]
作者邮箱	guoweilong@cau.edu.cn
引用统计	被引频次：107[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/2S10CLM1/21501
专题	系统与进化植物学国家重点实验室
作者单位	1.China Agr Univ, Key Lab Crop Heterosis & Utilizat, State Key Lab Agrobiotechnol, Beijing Key Lab Crop Genet Improvement, Beijing 100193, Peoples R China 2.Beijing Geek Gene Technol Co Ltd, Beijing 100193, Peoples R China 3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Chen, Yongming,Song, Wanjun,Xie, Xiaoming,et al. A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era[J]. MOLECULAR PLANT,2020,13(12):1694-1708.
APA	Chen, Yongming.,Song, Wanjun.,Xie, Xiaoming.,Wang, Zihao.,Guan, Panfeng.,...&Guo, Weilong.(2020).A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era.MOLECULAR PLANT,13(12),1694-1708.
MLA	Chen, Yongming,et al."A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era".MOLECULAR PLANT 13.12(2020):1694-1708.

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