Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry
文献类型： 外文期刊
作者： Jin, Xin 1 ; Du, Haiyuan 1 ; Zhu, Chumeng 1 ; Wan, Hong 3 ; Liu, Fang 1 ; Ruan, Jiwei 4 ; Mower, Jeffrey P. 5 ; Zhu, Andan 1 ;
作者机构： 1.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Crop Wild Relat Om, Germplasm Bank Wild Species, Kunming, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China
3.Yunnan Acad Agr Sci, Hort Res Inst, Kunming, Peoples R China
4.Yunnan Acad Agr Sci, Flower Res Inst, Kunming, Peoples R China
5.Univ Nebraska, Ctr Plant Sci Innovat, Lincoln, NE 68588 USA
6.Univ Nebraska, Dept Agron & Hort, Lincoln, NE 68588 USA
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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