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 

机构地区：[1]Key Laboratory of Biology and Genetic improvement of Horticultural Crops,Ministry of Agriculture,Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences,Beijing 100081,China [2]College of Horticulture,Jinling Institute of Technology,Nanjing 210038,China [3]Institute of Vegetables Research,Zhejiang Academy of Agricultural Sciences,Hangzhou 310021,China [4]Berry Genomics Corporation,Beijing 100015,China

出　　处：《Molecular Plant》2021年第12期2032-2055,共24页分子植物（英文版）

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).

摘　　要：Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear mechanisms.Raphanus is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and introgres-sion.Here,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 America.Divergence 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)blocks.Extensive gene flow occurred between wild,weedy,and domesticated radishes.High fre-quencies of genome reshuffling,biased retention,and large-fragment translocation have shaped the genomic diversity.Most variety-specific gene-rich blocks showed large structural variations.Extensive translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich islands.Disease resistance genes mostly resided on specific and dispensable loci.Variations causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive evolution.This 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.

关 键 词：RAPHANUS pan-genomes post-polyploid diploidization gene flow speciation 

分 类 号：S631.1[农业科学—蔬菜学]