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 ...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.展开更多
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).
文摘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.
