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

Science Direct 2021
Zhang X. et al

XiaohuiZhang1TongjinLiu12JingleiWang13PengWang1YangQiu1WeiZhao1ShuaiPang4XiaomanLi1HaipingWang1JiangpingSong1WenlinZhang4WenlongYang1YuyanSun13XixiangLi1

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

Abstract

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 introgression. Here, we have sequenced and de novo assembled eleven 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 frequencies 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 elucidates the genomic evolution underlying post-polyploid diploidization and the genetic improvement of radish crops, biological control of weeds and protection of wild species’ germplasms.

Key words

Raphanus
pan-genomes
post-polyploid diploidization
gene flow
speciation

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