Phasing of the 'Wonderful' Pomegranate Genome Using Haploid DNA Extracted from Pollen Grains

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 promising nutraceutical properties, pomegranate has been defined as a functional food. In order to develop advanced genomic tools to improve pomegranate breeding program efficiency, we present the chromosome-scale and haplotype-resolved genome assembly of Wonderful, a pomegranate cultivar widely grown around the world. DNA isolated from diploid leaf tissues was sequenced using long read sequencing technology (PacBio and Nanopore), while DNA extracted from haploid pollen grains was sequenced using a short-reads platform (Illumina). Genomic data from 11 single haploid gamete cells were analyzed using the R package called Hapi to phase the genome. The final genome assembly size was of 372.51 Mbp anchored to eight pairs of homologous chromosomes. The present study provides an insight on the adoption of an innovative and efficient approach for the assembly of haplotype-resolved genomes, which enables a higher resolution of DNA variant detection and offers the opportunity to investigate crossover events in single gamete cells during meiosis.