A chromosome-level reference-quality genome of Punica granatum L.

Pomegranate (Punica granatum L.) is one of the most ancient edible fruit tree species. Here we reported a new chromosome-level genome assembly and annotation of sour pomegranate. We assembled the genome with a size of 331.47 Mb and used BUSCO to estimate the completeness of the assembly as 98.8%. More than 97.40% of sequences in the final assembly were anchored to 8 pseudochromosomes, higher than the corresponding percentages for the existing reference genomes Tunisia (92.62%). Using a combination of de novo prediction, protein homology and RNA-seq annotation, 29,326 protein-coding genes were predicted. We re-annotated the protein-coding genes of five other published pomegranate genomes using the same annotation method. We constructed the pan-genome of pomegranate using protein-coding genes, integrating data from our newly assembled genome and five other published genomes. The pan-genome was composed of 28,314 gene families, of which 68.96% were core genes, 30.00% were dispensable genes, and 1.04% were private genes. The chromosome-level reference genome of sour pomegranate would be valuable resource for research and molecular breeding of pomegranate.