Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes

文献类型： 外文期刊

第一作者： Song, Yanhong

作者： Song, Yanhong;Liu, Lifeng;Li, Gang;Zhao, Xia;Zhou, Houcheng;Peng, Yanling;Wang, Xu;Cao, Shuo;Zhou, Yongfeng;Muyle, Aline;Zhou, Yongfeng

作者机构： Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Natl Key Lab Germplasm Innovat & Utilizat Hort Cro, Zhengzhou 450009, Peoples R China;Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch,Key Lab Synthet Biol, Natl Key Lab Trop Crop Breeding,Guangdong Lab Lin, Shenzhen 518120, Peoples R China;Univ Montpellier, CEFE, CNRS, EPHE,IRD, F-34000 Montpellier, France;Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, Natl Key Lab Trop Crop Breeding, Haikou 570000, Peoples R China

期刊名称：HORTICULTURE RESEARCH （ 2022影响因子：8.7； 五年影响因子：9.0 ）

ISSN： 2662-6810

年卷期： 2024 年 11 卷 1 期

页码：

收录情况： SCI

摘要： The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria x ananassa) remains poorly understood. In this study, we have assembled a haplotype-phased gap-free octoploid genome for the strawberry, which allowed us to uncover the sequence, structure, and epigenetic divergences among the subgenomes. The diploid progenitors of the octoploid strawberry, apart from subgenome A (Fragaria vesca), have been a subject of public controversy. Phylogenomic analyses revealed a close relationship between diploid species Fragaria iinumae and subgenomes B, C, and D. Subgenome A, closely related to F. vesca, retains the highest number of genes, exhibits the lowest content of transposable elements (TEs), experiences the strongest purifying selection, shows the lowest DNA methylation levels, and displays the highest expression level compared to the other three subgenomes. Transcriptome and DNA methylome analyses revealed that subgenome A-biased genes were enriched in fruit development biological processes. In contrast, although subgenomes B, C, and D contain equivalent amounts of repetitive sequences, they exhibit diverged methylation levels, particularly for TEs located near genes. Taken together, our findings provide valuable insights into the evolutionary patterns of subgenome structure, divergence and epigenetic dynamics in octoploid strawberries, which could be utilized in strawberry genetics and breeding research.

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