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

文献类型： 外文期刊

作者： Zhang, Xiaohui 1 ; Liu, Tongjin 1 ; Wang, Jinglei 1 ; Wang, Peng 1 ; Qiu, Yang 1 ; Zhao, Wei 1 ; Pang, Shuai 4 ; Li, Xiaoman 1 ; Wang, Haiping 1 ; Song, Jiangping 1 ; Zhang, Wenlin 4 ; Yang, Wenlong 1 ; Sun, Yuyan 1 ; Li, Xixiang 1 ;

作者机构： 1.Chinese Acad Agr Sci, Inst Vegetables & Flowers, Key Lab Biol & Genet Improvement Hort Crops, Minist Agr, Beijing 100081, Peoples R China

2.Jinling Inst Technol, Coll Hort, Nanjing 210038, Peoples R China

3.Zhejiang Acad Agr Sci, Inst Vegetables Res, Hangzhou 310021, Peoples R China

4.Berry Genom Corp, Beijing 100015, Peoples R China

关键词： Raphanus; pan-genomes; post-polyploid diploidization; gene flow; speciation

期刊名称：MOLECULAR PLANT （ 影响因子：21.949； 五年影响因子：19.617 ）

ISSN： 1674-2052

年卷期： 2021 年 14 卷 12 期

页码：

收录情况： SCI

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 introgression. 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 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 provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improvement of radish crops, biological control of weeds, and protection of wild species' germplasms.

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