Building a cluster of NLR genes conferring resistance to pests and pathogens: the story of the Vat gene cluster in cucurbits

Most molecularly characterized plant resistance genes(R genes)belong to the nucleotide-binding-site-leucine-rich-repeat(NLR)receptor family and are prone to duplication and transposition with high sequence diversity.In this family,the Vat gene in melon is one of the few R genes known for conferring resistance to insect,i.e.,Aphis gossypii,but it has been misassembled and/or mispredicted in the whole genomes of Cucurbits.We examined 14 genomic regions(about 400 kb)derived from long-read assemblies spanning Vat-related genes in Cucumis melo,Cucumis sativus,Citrullus lanatus,Benincasa hispida,Cucurbita argyrosperma,and Momordica charantia.We built the phylogeny of those genes.Investigating the paleohistory of the Vat gene cluster,we revealed a step by step process beginning from a common ancestry in cucurbits older than 50 my.We highlighted Vat exclusively in the Cucumis genera,which diverged about 20 my ago.We then focused on melon,evaluating a minimum duplication rate of Vat in 80 wild and cultivated melon lines using generalist primers;our results suggested that duplication started before melon domestication.The phylogeny of 44 Vat-CDS obtained from 21 melon lines revealed gain and loss of leucine-rich-repeat domains along diversification.Altogether,we revealed the high putative recognition scale offered in melon based on a combination of SNPs,number of leucine-rich-repeat domains within each homolog and number of homologs within each cluster that might jointly confer resistance to a large pest and pathogen spectrum.Based on our findings,we propose possible avenues for breeding programs.