Recently, the Strawberry Germplasm Improvement Team of Zhengzhou Fruit Research Institute and Agricultural Genomics Institute at Shenzhen published a paper entitled " Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes " in Horticulture Research . In this paper, we have assembled a haplotype-phased gap-free octoploid genome of ‘Benihoppe’ and revealed the dynamics of gap-free DNA methylation of subgenomes, which allowed us to uncover the sequence, structure, and epigenetic divergences among the subgenomes.
‘Benihoppe’ has become one of the most widely cultivated varieties in our country for its adaptability, shallow dormancy, large fruit size. However, ‘Benihoppe’ is susceptible to powdery mildew and Colletotrichum Spp. pathogen, which seriously restricts the healthy development of the strawberry industry. We assembled a gap-free genome of the cultivated octoploid strawberry ‘Benihoppe’ using PacBio HiFi reads, oxford nanopore technology (ONT) ultra-long reads, and Hi-C technology. We identified 109,320 protein-coding genes of the four subgenomes. Subgenome A, closely related to Fragaria 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. Phylogenomic analyses revealed a close relationship between diploid species Fragaria iinumae and subgenomes B, C, and D. We investigated DNA methylation patterns during fruit ripening at the green, middle, and full stages, and found that subgenome A exhibited lower methylation levels in all contexts compared to the other subgenomes. Transcriptome and DNA methylome analyses revealed subgenome A-biased genes were enriched in fruit development biological processes. Furthermore, subgenome A-biased genes were largely gene body methylated (gbM). 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.
This study was supported by grants from the National Key Research and Development Program, the Major Science and Technology Projects of Henan Province, the Special Fund for Henan Agriculture Research System, and the Agricultural Science and Technology Innovation Program.
Download link: https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhad252/7452862?login="false
The evolutionary patterns and epigenetic dynamics of the gap-free octoploid strawberry
By Yanhong Song
songyanhong@caas.cn