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Article|01 Apr 2021|OPEN
Building a cluster of NLR genes conferring resistance to pests and pathogens: the story of the Vat gene cluster in cucurbits
Véronique Chovelon1, Rafael Feriche-Linares1, Guillaume Barreau1, Joël Chadoeuf1, Caroline Callot2, Véronique Gautier3, Marie-Christine Le Paslier4, Aurélie Berad4, Patricia Faivre-Rampant4, Jacques Lagnel1 & Nathalie Boissot1,
1 INRAE, GAFL, 84143 Montfavet, France
2INRAE, CNRGV, 31326 Castanet-Tolosan, France
3INRAE, GDEC-Gentyane Plateform, 63000 Clermont-Ferrand, France
4Université Paris-Saclay, INRAE, EPGV, 91000 Evry-Courcouronnes, France

Horticulture Research 8,
Article number: 72 (2021)
doi: 10.1038/hortres.2021.72
Views: 226

Received: 06 Nov 2020
Revised: 15 Jan 2021
Accepted: 06 Feb 2021
Published online: 01 Apr 2021

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.