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

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

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The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes(ABCD)in octoploid strawberries(Fragaria × 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.

Yanhong Song、Yanling Peng、Lifeng Liu、Gang Li、Xia Zhao、Xu Wang、Shuo Cao、Aline Muyle、Yongfeng Zhou、Houcheng Zhou

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National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops,Zhengzhou Fruit Research Institute,Chinese Academy of Agricultural Sciences,Zhengzhou,450009,China

National Key Laboratory of Tropical Crop Breeding,Shenzhen Branch,Guangdong Laboratory of Lingnan Modern Agriculture,Key Laboratory of Synthetic Biology,Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen 518120,China

CEFE,University of Montpellier,CNRS,EPHE,IRD,Montpellier 34000,France

National Key Laboratory of Tropical Crop Breeding,Tropical Crops Genetic Resources Institute,Chinese Academy of Tropical Agricultural Sciences,Haikou 570000,China

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国家重点研发计划国家重点研发计划Major Science and Technology Projects of Henan ProvinceSpecial Fund for Henan Agriculture Research SystemAgricultural Science and Technology Innovation Program

2022YFD16007002019YFD1000203221100110400HARS-22-09-G2CAAS-ASTIP-2021-ZFRI

2024

10.1093/hr/uhad252

园艺研究(英文)

园艺研究(英文)

CSTPCD
ISSN：
年,卷(期)：2024.11(1)
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