High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry.
High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry.
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栽培八倍体草莓的高质量单倍体解析基因组组装
DOI：
10.1093/hr/uhad002
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发表时间：
2023-01
影响因子：
8.7
通讯作者：
中科院分区：
文献类型：
--
作者：
栽培草莓（Fragaria × ananassa）是蔷薇科（Rosaceae）多年生草本植物，是一种复杂的二倍体，在大多数位点上具有高度的杂合性。然而，还没有关于四倍体草莓基因组单倍型的研究。本研究旨在利用单分子实时测序技术和高通量染色体构象捕获技术获得高质量的草莓栽培品种“艳丽”基因组。“艳丽”基因组大小为823 Mb，长末端重复序列组装指数为14.99。将基因组分相为两种单倍型，Hap 1（825 Mb，重叠群N50为26.70 Mb）和Hap 2（808 Mb，重叠群N50为27.51 Mb）。利用Hap 1和Hap 2的组合，我们首次获得了栽培草莓的56条染色体的单倍型解析基因组。我们鉴定了2-1号染色体上的~ 10 Mb倒位和易位。在Hap 1和Hap 2中分别注释了104 957和102 356个蛋白质编码基因。花色素苷合成途径相关基因的分析揭示了四倍体F.× ananassa基因组。综上所述，我们获得了高质量的单倍型分辨的F.× ananassa，为研究栽培四倍体草莓基因组的功能和进化奠定了基础。
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.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
3.7
作者：
Alger EI;Platts AE;Deb SK;Luo X;Ou S;Cao Y;Hummer KE;Xiong Z;Knapp SJ;Liu Z;McKain MR;Edger PP
通讯作者：
Edger PP
影响因子：
3
作者：
De Summa S;Malerba G;Pinto R;Mori A;Mijatovic V;Tommasi S
通讯作者：
Tommasi S
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
48
作者：
Cheng H;Concepcion GT;Feng X;Zhang H;Li H
通讯作者：
Li H