Nanopore adaptive sampling to identify the NLR-gene family in melon (Cucumis meloL.)

Abstract

AbstractBackgroundNanopore Adaptive Sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Herein, we design and validate an experiment to enrich a set of resistance genes in several melon cultivars as a proof of concept.ResultsWe showed that each of the 15 regions we identified in two newly assembled melon genomes (subspeciesmelo) were successfully and accurately reconstructed as well as in a third cultivar from theagrestissubspecies. We obtained a fourfold enrichment, independently from the samples, but with some variations according to the enriched regions. In theagrestiscultivar, we further confirmed our assembly by PCR. We discussed parameters that can influence enrichment and accuracy of assemblies generated through NAS.ConclusionsAltogether, we demonstrated NAS as a simple and efficient approach to explore complex genomic regions. This approach finally unlocks the characterization of resistance genes for a large number of individuals, as required for breeding new cultivars responding to the agroecological transition.