Pan-genome of Raphanus highlights genetic variation and introgression among domesticated,wild,and weedy radishes

作     者：Xiaohui Zhang Tongjin Liu Jinglei Wang Peng Wang Yang Qiu Wei Zhao Shuai Pang Xiaoman Li Haiping Wang Jiangping Song Wenlin Zhang Wenlong Yang Yuyan Sun Xixiang Li Xiaohui Zhang;Tongjin Liu;Jinglei Wang;Peng Wang;Yang Qiu;Wei Zhao;Shuai Pang;Xiaoman Li;Haiping Wang;Jiangping Song;Wenlin Zhang;Wenlong Yang;Yuyan Sun;Xixiang Li

作者机构：Key Laboratory of Biology and Genetic improvement of Horticultural CropsMinistry of AgricultureInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China College of HorticultureJinling Institute of TechnologyNanjing 210038China Institute of Vegetables ResearchZhejiang Academy of Agricultural SciencesHangzhou 310021China Berry Genomics CorporationBeijing 100015China 

出 版 物：《Molecular Plant》 (分子植物（英文版）)

年 卷 期：2021年第14卷第12期

页      面：2032-2055页

核心收录：

学科分类：09[农学] 0902[农学-园艺学] 090202[农学-蔬菜学] 

基　　金：supported by the National Key Research and Development Program of China(2016YFD0100204-02,2013BAD01B04-1) the National Natural Science Foundation of China(31772301,31772303,and 31801858) the Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP-2019-IVFCAAS,CAAS-XTCX2016016-4-4,and CAAS-XTCX2016001-5-2) 

主　　题：Raphanus pan-genomes post-polyploid diploidization gene flow speciation 

摘      要：Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear *** is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and ***,we report the de novo sequence assemblies for 11 genomes covering most of the typical sub-species and varieties of domesticated,wild and weedy radishes from East Asia,South Asia,Europe,and *** among the species,sub-species,and South/East Asian types coincided with Quaternary glaciations.A genus-level pan-genome was constructed with family-based,locus-based,and graph-based methods,and whole-genome comparisons revealed genetic variations ranging from single-nucleotide polymorphisms(SNPs)to inversions and translocations of whole ancestral karyotype(AK)*** gene flow occurred between wild,weedy,and domesticated *** fre-quencies of genome reshuffling,biased retention,and large-fragment translocation have shaped the genomic *** variety-specific gene-rich blocks showed large structural *** translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich *** resistance genes mostly resided on specific and dispensable *** causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive *** study provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improve-ment of radish crops,biological control of weeds,and protection of wild species germplasms.