Pomegranates (Punica granatum L.) are a significant fruit crop globally, gaining traction due to their high nutritional value and many uses outside of consumption. Despite increasing interest, genetic resources for pomegranates lag behind other crops. Developing these resources can enhance breeding efficiency and deepen genomic understanding. To address this, we sequenced the genomes of two cultivars: 'Azadi', known for its robust fruit rot resistance, and 'Peppy Le Pom', a dwarf variety with short juvenility. Using the PacBio Revio Platform, we generated HiFi reads with 30x coverage and employed Hi-C for sequencing. Leveraging hifiasm's Hi-C integrated assembly method, we assembled two haplotypes for the genome of each cultivar. For 'Peppy Le Pom', we utilized 10.03 Gb of PacBio HiFi reads and 30 Gb of Hi-C data and constructed two haplotypes with eight chromosome-length scaffolds each, totaling 304.9 Mb and 318.7 Mb, with a BUSCO score of 90.3% and 92.3%, respectively. For 'Azadi', we utilized 10.08 Gb of Pacbio HiFi reads and 30 Gb of Hi-C data and assembled two haplotypes with eight chromosome-length scaffolds, measuring 305.5 Mb and 318.1 Mb, with a BUSCO score of 91.0% and 92.6%, respectively. Chromosome sizes of these pomegranate cultivars range from 27.1 Mb to 62.4 Mb. Notably, these results closely align with the previously published draft genome of the 'Tunisia' cultivar. These phased, chromosome-scale genomes will facilitate further exploration of traits of interest for pomegranate breeding, such as disease resistance, dwarfing, and short juvenility. The genomic resources established here pave the way for accelerated advancements in pomegranate research and breeding.
