Haplotype‐resolved genome assembly provides new insights into the genomic origin of purple colour in Prunus mume

Summary Prunus mume , an important ornamental woody plant in the Rosaceae family, contains many interspecific hybridizations. Purple colour is a breeding trait of aesthetic value for P. mume , but little is known about the origin and genetic architecture of this trait. Here we address these issues by producing a haplotype‐resolved genome from an interspecific hybrid cultivar of P. mume (M) and P. cerasifera ‘Pissardii’ (C), named P. mume ‘Meiren’, followed by a detailed molecular characterization. The final length of the diploid genome is 499.47 Mb, with 250.66 Mb of haplotype M (HM) and 248.79 Mb of haplotype C (HC). Approximately 95.42% (476.61 Mb) of the phased assembly is further anchored to 16 homologous chromosomes. Based on the genomic variation, we identify a 1.8 Mb large‐fragmented inversion (INV) on chromosome 1b of HC, which co‐segregates with purple colour traits of ‘Meiren’ inherited from its purple C parent ‘Pissardii’. We find that a MYB transcription factor, PmmMYB10.5b , resides at the distal breakpoint of the INV, which displays consistent allele‐specific expression (ASE). By directly binding to the promoter of anthocyanin synthetic alleles, PmmMYB10.5b serves as a co‐activator to promote anthocyanin accumulation in ‘Meiren’ organs. Notably, the INV identified in ‘Meiren’ is generated from ‘Pissardii’ rather than P. cerasifera , which alters the promoter sequence of PmmMYB10.5b , activates its expression and results in the purple colour trait. Results from this study shed light on the evolutionary origin of purple colour in ‘Meiren’ and could potentially provide guidance on the genetic improvement of colour traits in ornamental woody plants.