The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry

Abstract

Fragaria vesca, commonly known as wild or woodland strawberry, is the most widely distributed diploid Fragaria species and is native to Europe and Asia. Because of its small plant size, low heterozygosity, and relative ease of genetic transformation, F. vesca has been a model plant for fruit research since the publication of its Illumina-based genome in 2011. However, its genomic contribution to octoploid cultivated strawberry remains a long-standing question. Here, we de novo assembled and annotated a telomere-to-telomere, gap-free genome of F. vesca ‘Hawaii 4’, with all seven chromosomes assembled into single contigs, providing the highest completeness and assembly quality to date. The gap-free genome is 220 785 082 bp in length and encodes 36 173 protein-coding gene models, including 1153 newly annotated genes. All 14 telomeres and seven centromeres were annotated within the seven chromosomes. Among the three previously recognized wild diploid strawberry ancestors, F. vesca, F. iinumae, and F. viridis, phylogenomic analysis showed that F. vesca and F. viridis are the ancestors of the cultivated octoploid strawberry F. × ananassa, and F. vesca is its closest relative. Three subgenomes of F. × ananassa belong to the F. vesca group, and one is sister to F. viridis. We anticipate that this high-quality, telomere-to-telomere, gap-free F. vesca genome, combined with our phylogenomic inference of the origin of cultivated strawberry, will provide insight into the genomic evolution of Fragaria and facilitate strawberry genetics and molecular breeding.

Acknowledgements

Fei Chen acknowledges funding from the National Natural Science Foundation of China (32172614), a startup fund from Hainan University and a Hainan Province Science and Technology Special Fund (ZDYF2023XDNY050).

Author contributions

Z.C. and F.C. designed and led this project. Y.Z., Z.S., Z.X., and M.J. assembled and annotated the genome. Y.Z., C.D., T.G., P.S., S.H., K.W., and J.X. analyzed the data. Y.Z. and F.C. wrote the draft manuscript. Z.C., J.X., and F.C. discussed and revised the draft. All authors have read and agreed to the published version of the manuscript.

Data availability

All raw sequencing data generated in this project, including HiFi, Hi-C, Illumina, and ONT data, have been deposited at NCBI (https://www.ncbi.nlm.nih.gov/) under BioProject accession number PRJNA905123. The genome assembly and annotation data are available at our GDS database: http://eplant.njau.edu.cn/strawberry/.

Conflict of interest

The authors declare that they have no conflicts of interest.

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