IB-CAS  > 系统与进化植物学国家重点实验室
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, Wanjun1; Xie, Xiaoming; Wang, Zihao; Guan, Panfeng; Peng, Huiru; Jiao, Yuannian2,3; Ni, Zhongfu; Sun, Qixin; Guo, Weilong
2020
Source PublicationMOLECULAR PLANT
ISSN1674-2052
Volume13Issue:12Pages:1694-1708
AbstractPlant 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.
Keywordhomology inference collinearity database pangenome Triticeae tribe polyploid
Subject AreaBiochemistry & Molecular Biology ; Plant Sciences
DOI10.1016/j.molp.2020.09.019
Indexed BySCI
Language英语
WOS KeywordPAN-GENOME ; ORTHOLOGY ANALYSIS ; R PACKAGE ; WHEAT ; GENE ; DATABASE ; ANNOTATION ; EVOLUTION ; SEQUENCE ; VISUALIZATION
WOS Research AreaBiochemistry & Molecular Biology ; Plant Sciences
WOS IDWOS:000596734100008
PublisherCELL PRESS
SubtypeArticle
Publication PlaceCAMBRIDGE
EISSN1752-9867
Funding OrganizationMajor 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]
Corresponding Author Emailguoweilong@cau.edu.cn
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Cited Times:21[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ibcas.ac.cn/handle/2S10CLM1/21501
Collection系统与进化植物学国家重点实验室
Affiliation1.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
Recommended Citation
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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