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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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Molecular Plant 2020年第12期13卷 1694-1708页

作者： Yongming Chen Wanjun Song Xiaoming Xie Zihao Wang Panfeng Guan Huiru Peng Yuannian Jiao Zhongfu Ni Qixin Sun Weilong Guo Key Laboratory of Crop Heterosis and Utilization State Key Laboratory for AgrobiotechnologyBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Beijing Geek Gene Technology Co Ltd Beijing 100193China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Plant genome sequencing has dramatically increased,and some species even have multiple high-quality reference *** for clade-specific homology inference and analysis have increased in the pangenomic *** we present a novel method,GeneTribe(https://***/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 *** Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops,such as wheat,barley,and *** built Triticeae-GeneTribe(http://***/TGT/),a homology database,by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization *** 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 *** 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 *** 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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