Genome assembly characterizes cold tolerance and rootstock traits in Malus robusta, aiding crop improvement.
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.
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