A chromosome-scale genome assembly of Malus domestica, a multi-stress resistant and high-quality apple variety

<b>Background: </b>Hanfu apples have the advantages of cold resistance, drought resistance, and high yield, and they have become the main variety grown in the cool areas of Northeast, Northwest, and North China (40–42° N), which have an average temperature of -12 to -10 ℃ in January.<b></b> <b>Results: </b>Here, we proposed a chromosome-level Hanfu genome assembly using PacBio long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data. The total contig length was 628.99 Mb, and the N50 contig length was 1.25 Mb. The total scaffold length was 631.76 Mb, the N50 scaffold length was 36.18 Mb, and the genome mount rate was 99.18%. The Hanfu genome had a total of 39 617 genes, and we predicted the function for 38 816 (98.0%) of these. Repetitive sequences accounted for 54.29% of the genome. Evolutionary analysis showed that the differentiation time of apples and pears was approximately 8.9 Mya. Whole genome duplication (WGD) analysis revealed a γ event in Hanfu, which was a recent whole genome duplication when the 4dTv value was 0.075. By comparing and analyzing the genomic differences between Hanfu and the homozygous line HFTH1, three variation types were determined: single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variants (SVs). We identified 605 species-specific gene families. Among these, 122 Hanfu gene families (including 814 genes) significantly expanded, while 421 gene families significantly contracted (including 1528 genes), and there are 61 candidate genes subject to positive selection. A significant expansion of genes involved in the MAPK signal transduction pathway, calcium-mediated signal transduction pathway, plant hormone signal transduction pathway, sugar metabolism pathway, and phloem development were found; this may explain the formation of ‘Hanfu’s’ unique phenotype. <b>Conclusions:</b> This high quality genome will help explain the formation mechanism of the unique phenotype of Hanfu. In addition, it can provide reference for the genetic improvement of apples and for breeding more varieties with high resistance and high quality.