The scientific and commercial interest in pomegranate (Punica granatum L.) cultivation has increased noticeably during the last two decades. Because of the high concentration of bioactive compounds and its nutraceutical properties, pomegranate has been defined as a super food. The consumption of pomegranate juice or arils has been related to several possible benefits on human health. Recent studies have highlighted an antioxidant and anti-inflammatory activity of this fruit which seem to prevent cardiovascular, neoplastic, neurological, metabolic, and intestinal disease. The areas of cultivation of this crop are exposed to current and future challenges like long term-drought conditions and invasive pests and diseases. Increasing the biodiversity of pomegranate has been proposed has the main strategy to reduce the risk of food system vulnerability related to monoculture and the valorization of marginal land. In order to develop advanced genetic tools to improve pomegranate breeding program efficiency we present the de novo sequencing of the ‘Wonderful’ pomegranate genome. DNA isolated from diploid leaf tissues was sequenced using long read sequencing technology (PacBio), while DNA extracted from haploid pollen grains was sequenced using short reads (Illumina). Genomic data from single haploid gamete cells were analyzed using the R package called ‘Hapi’. This allowed to infer chromosomal haplotypes obtaining a higher resolution for DNA variants detection and investigating recombination events in single gametes. Although ‘Wonderful’ represents the industry standard in the United States, several cultivars with desirable traits, such as low acidity and soft seednesses, have been identified in the national germplasm. The results of this study will provide the genomic data required to investigate differences among cultivars and create trait-gene associations. This will allow breeders to facilitate the integration of desired quality traits into new germplasm resources.
