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

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. 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. The Hanfu genome had a total of 39,617 genes, and we predicted the function for 38,816 (98.0%) of these. 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. 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.