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

doi:10.1038/s41477-023-01473-2

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	Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry
	Jin,Xin; Du,Haiyuan; Zhu,Chumeng; Wan,Hong; Liu,Fang; Ruan,Jiwei; Mower,Jeffrey P.; Zhu,Andan
	2023
发表期刊	NATURE PLANTS
ISSN	2055-0278
卷号	9 期号:8 页码:1252-+
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.
关键词	FRAGARIA ACCURATE RECONSTRUCTION EVOLUTIONARY ALIGNMENT ORIGIN POPULATIONS ASSEMBLIES ANNOTATION GENERATION
DOI	10.1038/s41477-023-01473-2
收录类别	SCI
WOS记录号	WOS:001042057200004
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75433
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Jin,Xin,Du,Haiyuan,Zhu,Chumeng,et al. Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry[J]. NATURE PLANTS,2023,9(8):1252-+.
APA	Jin,Xin.,Du,Haiyuan.,Zhu,Chumeng.,Wan,Hong.,Liu,Fang.,...&Zhu,Andan.(2023).Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry.NATURE PLANTS,9(8),1252-+.
MLA	Jin,Xin,et al."Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry".NATURE PLANTS 9.8(2023):1252-+.

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