Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry

文献类型： 外文期刊

第一作者： Jin, Xin

作者： Jin, Xin;Du, Haiyuan;Zhu, Chumeng;Liu, Fang;Zhu, Andan;Jin, Xin;Du, Haiyuan;Zhu, Chumeng;Wan, Hong;Ruan, Jiwei;Mower, Jeffrey P.;Mower, Jeffrey P.

作者机构：

期刊名称：NATURE PLANTS （ 影响因子：18.0； 五年影响因子：18.6 ）

ISSN： 2055-026X

年卷期： 2023 年 9 卷 8 期

页码：

收录情况： SCI

摘要： Strawberry is an emerging model for studying polyploid genome evolution and rapid domestication of fruit crops. Here we report haplotype-resolved genomes of two wild octoploids (Fragaria chiloensis and Fragaria virginiana), the progenitor species of cultivated strawberry. Substantial variation is identified between species and between haplotypes. We redefine the four subgenomes and track the genetic contributions of diploid species by additional sequencing of the diploid F. nipponica genome. We provide multiple lines of evidence that F. vesca and F. iinumae, rather than other described extant species, are the closest living relatives of these wild and cultivated octoploids. In response to coexistence with quadruplicate gene copies, the octoploid strawberries have experienced subgenome dominance, homoeologous exchanges and coordinated expression of homoeologous genes. However, some homoeologues have substantially altered expression bias after speciation and during domestication. These findings enhance our understanding of the origin, genome evolution and domestication of strawberries. This study reports haplotype-resolved genomes for Fragaria chiloensis and Fragaria virginiana, the progenitor species of cultivated strawberries. These high-quality genomes reveal the origin and genomic diversifications of octoploid strawberries.

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