Haplotype-resolved chromosomal-level genome assembly of Prunus mahaleb

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.