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Article|04 Jan 2023|OPEN
High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry
Jianxin Mao1 ,† , Yan Wang1,2 ,† , Baotian Wang1 , Jiqi Li1 , Chao Zhang1 , Wenshuo Zhang3 , Xue Li1 , Jie Li1 , Junxiang Zhang1,2 , He Li1,2 , Zhihong Zhang,1,2 ,
1Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
2Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang 110866, China
3School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
*Corresponding author. E-mail: zhangz@syau.edu.cn
Both authors contributed equally to the study.

Horticulture Research 10,
Article number: uhad002 (2023)
doi: https://doi.org/10.1093/hr/uhad002
Views: 181

Received: 14 Oct 2022
Accepted: 03 Jan 2023
Published online: 04 Jan 2023

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.