College of Horticulture, Key Lab of Fruit Quality Development and Regulation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China.
College of Horticulture, Key Lab of Fruit Quality Development and Regulation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China.
Genomics. 2023 May;115(3):110627. doi: 10.1016/j.ygeno.2023.110627. Epub 2023 Apr 14.
Hanfu apple is the main cultivar grown in the cool areas of Northeast, Northwest, and North China. Here, we proposed a chromosome-level Hanfu genome assembly using PacBio, Illumina and Hi-C sequencing data. The total contig length was 628.99 Mb, with scaffold and contig N50 sizes of 36.18 Mb and 1.25 Mb, respectively. The Hanfu genome had a total of 39,617 genes, of which we predicted the function for 38,816. Evolutionary analysis showed that Hanfu may have undergone a γ-event, a recent whole-genome duplication. A comparative analysis was conducted on the genomes of Hanfu and homozygous triploid HFTH1, which were cultured using the anthers of diploid Hanfu apples. Three variants were identified, including 2,155,184 single nucleotide polymorphisms (SNPs), 413,108 insertions/deletions (indels), and 7,587 structural variants (SVs).This high-quality genome will provide a reference for the genetic improvement of apples and the breeding of more varieties with high resistance and high quality.
汉服苹果是中国东北、西北和华北地区冷凉地区的主要栽培品种。在这里，我们使用 PacBio、Illumina 和 Hi-C 测序数据提出了一个汉服苹果的染色体水平基因组组装。总拼接长度为 628.99Mb，支架和拼接 N50 大小分别为 36.18Mb 和 1.25Mb。汉服苹果基因组共有 39617 个基因，其中我们预测了 38816 个基因的功能。进化分析表明，汉服苹果可能经历了γ事件，即最近的全基因组复制。我们还对汉服苹果和同源三倍体 HFTH1 的基因组进行了比较分析，HFTH1 是通过二倍体汉服苹果的花药培养得到的。共鉴定出 3 种变异，包括 2155184 个单核苷酸多态性（SNP）、413108 个插入/缺失（indel）和 7587 个结构变异（SV）。这个高质量的基因组将为苹果的遗传改良和培育更多抗性和高质量的品种提供参考。
