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

查看全文 作　　者：Yongming [1]Chen;Wanjun [1,2]Song;Xiaoming [1]Xie;Zihao [1]Wang;Panfeng [1]Guan;Huiru [1]Peng;Yuannian [3,4]Jiao;Zhongfu [1]Ni;Qixin [1]Sun;Weilong [1]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》索引2020年第13卷第12期,共15页

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(http://gffzz6c7fcf032cb94ff5snwo9k5cufqqu6vc5.ffgz.tsg.suse.edu.cn/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://gffzzaeec8df70e7c4b21hnwo9k5cufqqu6vc5.ffgz.tsg.suse.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

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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

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