High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry

Abstract

Cultivated strawberry (Fragaria × ananassa), a perennial herb belonging to the family Rosaceae, is a complex octoploid with high heterozygosity at most loci. However, there is no research on the haplotype of the octoploid strawberry genome. Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar, “Yanli”, using single molecule real-time sequencing and high-throughput chromosome conformation capture technology. The “Yanli” genome was 823 Mb in size, with a long terminal repeat assembly index of 14.99. The genome was phased into two haplotypes, Hap1 (825 Mb with contig N50 of 26.70 Mb) and Hap2 (808 Mb with contig N50 of 27.51 Mb). Using the combination of Hap1 and Hap2, we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry. We identified a ∼10 Mb inversion and translocation on chromosome 2-1. 104 957 and 102 356 protein-coding genes were annotated in Hap1 and Hap2, respectively. Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F. × ananassa genome. In summary, we obtained a high-quality haplotype-resolved genome assembly of F. × ananassa, which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.

Acknowledgements

We thank Wuhan Onemore-tech Co., Ltd. for their assistance with genome sequencing and analysis. This work was financially supported by National Natural Science Foundation of China (No. 32130092; No. 31872072) and LiaoNing Revitalization Talents Program (No. XLYC1902069).

Author Contributions

Y.W. and Z.Z. conceived and designed the study. Y.W. and J.M. prepared the materials. B.W., J.L., C.Z, W.Z., X.L., J.L., J.Z. and H.L. performed the bioinformatics analysis and prepared the results. J.M. and Y.W. wrote the manuscript. Z.Z. edited and improved the manuscript. All authors approved the final manuscript.

Data availability

The data that support the results are included in this article and its supplementary materials. Other relevant materials are available from the corresponding author upon reasonable request.

Conflict of interest

The authors declare no competing interests.

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