The construction and analysis of wax gourd pangenome uncover fruit quality-related and resistance genes

Large-scale resequencing studies in wax gourd have generated a large data resource and mined many selection signals and candidate genes. In this study, we constructed the first pangenome of wax gourd based on rese-quencing data and obtained 316 Mb novel contigs containing 996 novel genes. A pan-genome-wide gene present/ absent variations analysis of 25,188 genes identified 2154 genes as variable genes. Analysis of gene present/ absent variations selection between wild accessions, landraces, and cultivar accessions revealed that many genes, including resistance genes, were lost during the process of domestication and improvement. The 22 resistance gene analogs identified in non-reference contigs are complementary to the 642 resistance gene analogs on the reference genome. Genome-wide association studies of gene present/absent variations with fruit weight, fruit length, fruit diameter, and fruit thickness of wax gourd identified five phenotypic-related candidate genes. Pan-genome-wide identification of NAC, WRKY and HSF gene family identified 7 novel genes. In conclusion, this study provides a more complete sequence and genes of the wax gourd genome and identifies new selected genes as well as phenotypically related candidate genes through a series of analyses, as well as provides an abundant resource and research reference for breeding and gene function studies in the wax gourd.