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

作　　者：Yongming Chen Wanjun Song Xiaoming Xie Zihao Wang Panfeng Guan Huiru Peng Yuannian Jiao Zhongfu Ni Qixin Sun Weilong Guo 

机构地区：[1]Key Laboratory of Crop Heterosis and Utilization,State Key Laboratory for Agrobiotechnology,Beijing Key Laboratory of Crop Genetic Improvement,China Agricultural University,Beijing 100193,China [2]Beijing Geek Gene Technology Co Ltd,Beijing 100193,China [3]State Key Laboratory of Systematic and Evolutionary Botany,Institute of Botany,Chinese Academy of Sciences,Beijing 100093,China [4]University of Chinese Academy of Sciences,Beijing 100049,China

出　　处：《Molecular Plant》2020年第12期1694-1708,共15页分子植物（英文版）

基　　金：the Major Program of the National Natural Science Foundation of China(grant no.31991210)to Q.S.and by the National Natural Science Foundation of China(grant no.31701415)to W.G.

摘　　要：Plant genome sequencing has dramatically increased,and some species even have multiple high-quality reference versions.Demands for clade-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 bet-ter performance than traditional sequence-similarity-based methods in terms of accuracy and scalability.The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops,such as wheat,barley,and rye.We built Triticeae-GeneTribe(http://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 Vm2,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 re-sources.

关 键 词：homology inference COLLINEARITY database pangenome Triticeae tribe POLYPLOID 

分 类 号：Q94[生物学—植物学]