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<p><i>Malus robusta</i> 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 <i>M. robusta</i>, 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 <i>M. robusta</i> and the genomes of <i>M. baccata</i> and <i>M. prunifolia</i>, respectively. These Haplotype-resolved genome assemblies provide a comprehensive genomic resource for studies of cold tolerance–related traits, comparative genomics, and apple rootstock improvement.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月25日

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  • Mingxuan Sun,
  • Haibo Wang,
  • Lingtong Kong,
  • Jingyuan Zhang,
  • Jinrong Li,
  • Yi Zheng,
  • Sen Wang

摘要

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.