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

被引：38
作者：
Mao, Jianxin [1 ]
Wang, Yan [1 ]
Wang, Baotian [1 ]
Li, Jiqi [1 ]
Zhang, Chao [1 ]
Zhang, Wenshuo [3 ]
Li, Xue [1 ]
Li, Jie [1 ]
Zhang, Junxiang [1 ,2 ]
Li, He [1 ,2 ]
Zhang, Zhihong [1 ,2 ]
机构：
[1] Shenyang Agr Univ, Coll Hort, Liaoning Key Lab Strawberry Breeding & Cultivat, 120 Dongling Rd, Shenyang 110866, Peoples R China
[2] Shenyang Agr Univ, Lab Protected Hort, Minist Educ, Shenyang 110866, Peoples R China
[3] ShanghaiTech Univ, Sch Informat Sci & Technol, 393 Middle Huaxia Rd, Shanghai 201210, Peoples R China
来源：
HORTICULTURE RESEARCH | 2023年 / 10卷 / 01期
基金：
中国国家自然科学基金;
关键词：
COMMON WHEAT; CHROMOSOME; IDENTIFICATION; GENES; REARRANGEMENTS; PREDICTION; ANCESTRY; ACCURATE; PROVIDES; PROGRAM;
D O I：
10.1093/hr/uhad002
中图分类号：
Q94 [植物学];
学科分类号：
071001 ;
摘要：
Cultivated strawberry (Fragaria x 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 similar to 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. x ananassa genome. In summary, we obtained a high-quality haplotype-resolved genome assembly of F. x ananassa, which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.
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页数：12
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