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Article|20 Feb 2023|OPEN
The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry
Yuhan Zhou1,2 ,† , Jinsong Xiong1 ,† , Ziqiang Shu3 , Chao Dong2 , Tingting Gu1 , Pengchuan Sun4 , Shuang He5 , Mian Jiang3 , Zhiqiang Xia1,5,6 and Jiayu Xue1 , Wasi Ullah Khan5 , Fei Chen2,5,6 , , Zong-Ming Cheng,1
1College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
2Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
3Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, China
4Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu 610065, China
5College of Tropical Crops, Hainan University, Haikou 570228, China
6Sanya Nanfan Research Institute from Hainan University, Sanya 572025, China
*Corresponding author. E-mail:
Both authors contributed equally to the study.

Horticulture Research 10,
Article number: uhad027 (2023)
Views: 41

Received: 20 Dec 2022
Accepted: 13 Feb 2023
Published online: 20 Feb 2023


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. vescaF. 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.