The chromosome-level genome assembly of Malus robusta (Rosales: Rosaceae)

Malus robusta Rehd. is widely used as an apple rootstock owing to its strong cold tolerance and desirable rootstock traits. Here, we report Haplotype-resolved, chromosome-level genome assemblies of the cultivar M. robusta, generated using an integrated strategy combining PacBio HiFi sequencing, Hi-C data, and Ultra-long ONT data. Two phased assemblies were produced, with HapA spanning 628.38 Mb and a contig N50 of 36.35 Mb, and HapB spanning 664.60 Mb with a contig N50 of 39.05 Mb. Repetitive elements accounted for 65.12% and 66.52% of the HapA and HapB genomes, respectively. A total of 49,268 and 51,070 protein-coding genes were predicted in HapA and HapB. Genome-wide synteny analysis revealed differential collinearity between the two haplotypes of M. robusta and the genomes of M. baccata and M. prunifolia, respectively. These Haplotype-resolved genome assemblies provide a comprehensive genomic resource for studies of cold tolerance-related traits, comparative genomics, and apple rootstock improvement.