Abstract
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.
Highlights
Most molecularly characterized plant resistance genes (R genes) belong to the nucleotide-binding-site-leucinerich-repeat (NLR) receptor family and are prone to duplication and transposition with high sequence diversity
Architecture of the genomic region spanning Vat genes in cucurbits We obtained 300–350 kb containing several Vat homologs in seven melon lines: PI 161375, Anso[77], Doublon, Payzawat and HS, DHL92, and Harukei-3
We investigated in several cucurbits the R gene cluster spanning the Vat gene belonging to the NLR gene family
Summary
Most molecularly characterized plant resistance genes (R genes) belong to the nucleotide-binding-site-leucinerich-repeat (NLR) receptor family and are prone to duplication and transposition with high sequence diversity. In eudicots, for instance, on average 63% of these genes clustered[1], with diversity observed in terms of so-called copy number variation (CNV). This diversity within R gene clusters among crops and their wild relatives could be a major source of resistance to diseases and pests, but their introgression in cultivars is. Cisgenesis with Vat-1, isolated from the melon line PI 161375, showed it controlled the resistance to A. gossypii and to potyviruses when plants were inoculated by this aphid species[4]. The genomic region spanning these genes is called the Vat cluster[6]
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