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

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	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, Yuannian 2,3; Ni, Zhongfu ; Sun, Qixin ; Guo, Weilong
刊名	MOLECULAR PLANT
	2020
卷号	13 期号:12 页码:1694-1708
关键词	homology inference collinearity database pangenome Triticeae tribe polyploid
ISSN号	1674-2052
DOI	10.1016/j.molp.2020.09.019
文献子类	Article
英文摘要	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.
学科主题	Biochemistry & Molecular Biology ; Plant Sciences
电子版国际标准刊号	1752-9867
出版地	CAMBRIDGE
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
语种	英语
出版者	CELL PRESS
WOS记录号	WOS:000596734100008
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]
内容类型	期刊论文
源URL	[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.