Knowledge Management System Of Institute Of Botany,CAS
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 | |
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 | |
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. |
条目包含的文件 | ||||||
文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
1-s2.0-S167420522030(2673KB) | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 请求全文 |
除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。
修改评论