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<p><i>Prunus mahaleb</i> is widely utilized as rootstock for cherries in Central Asia due to its exceptional resistance to environmental stressors. In this study, we generated a haplotype-resolved, chromosome-scale genome assembly for <i>P. mahaleb</i> using PacBio HiFi long reads and Hi-C technology. The resulting assembly comprises two haplotypes with sizes of 272.64 Mb (contig N50 = 26.60 Mb) and 271.76 Mb (contig N50 = 30.26 Mb), respectively. We identified 27,965 protein-coding genes (27,627 functionally annotated) and 27,931 protein-coding genes (27,607 functionally annotated) in the two haplotypes, respectively. Additionally, we annotated 145.64 Mb repetitive elements, 2,263 rRNAs, 430 tRNAs, and 780 other non-coding RNAs in haplotype A, and 144.04 Mb repetitive elements, 1,999 rRNAs, 442 tRNAs, and 734 other non-coding RNAs in haplotype B. Further analysis indicated that these haplotypes diverged approximately 2.67 million years ago. This high-quality genome assembly lays a solid groundwork for future initiatives in molecular breeding and functional genomics research for <i>P. mahaleb</i>.</p>

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Haplotype-resolved chromosomal-level genome assembly of Prunus mahaleb

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年5月17日

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  • Chenlong Fu,
  • Meng Li,
  • Zhuang Zhao,
  • Lixia Yu,
  • Xianrong Wang,
  • Zhuangwei Hou,
  • Zefu Wang

摘要

Prunus mahaleb is widely utilized as rootstock for cherries in Central Asia due to its exceptional resistance to environmental stressors. In this study, we generated a haplotype-resolved, chromosome-scale genome assembly for P. mahaleb using PacBio HiFi long reads and Hi-C technology. The resulting assembly comprises two haplotypes with sizes of 272.64 Mb (contig N50 = 26.60 Mb) and 271.76 Mb (contig N50 = 30.26 Mb), respectively. We identified 27,965 protein-coding genes (27,627 functionally annotated) and 27,931 protein-coding genes (27,607 functionally annotated) in the two haplotypes, respectively. Additionally, we annotated 145.64 Mb repetitive elements, 2,263 rRNAs, 430 tRNAs, and 780 other non-coding RNAs in haplotype A, and 144.04 Mb repetitive elements, 1,999 rRNAs, 442 tRNAs, and 734 other non-coding RNAs in haplotype B. Further analysis indicated that these haplotypes diverged approximately 2.67 million years ago. This high-quality genome assembly lays a solid groundwork for future initiatives in molecular breeding and functional genomics research for P. mahaleb.