Fragaria nipponica KIB CAS Genome v1.0 Assembly & Annotation

Publication:

Xin Jin, Haiyuan Du, Chumeng Zhu, Hong Wan, Fang Liu, Jiwei Ruan, Jeffrey P. Mower, and Andan Zhu. (2023) Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. Nature Plants.

https://www.nature.com/articles/s41477-023-01473-2

Abstract:

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.

Table 1 Summary of genome features and quality evaluation of the three sequenced Fragaria species