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

Belinchon-Moreno, J.; Berard, A.; Canaguier, A.; Chovelon, V.; Cruaud, C.; Engelen, S.; Feriche-Linares, R.; Le-Clainche, I.; Lagnel, J.; Marande, W.; Rittener-Ruff, V.; Hinsinger, D.; Boissot, N.; Faivre Rampant, P.

doi:10.1101/2023.12.20.572599

bioRxiv · 10.1101/2023.12.20.572599

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

Belinchon-Moreno, J.·Berard, A.·Canaguier, A.·Chovelon, V.·Cruaud, C.·Engelen, S.·Feriche-Linares, R.·Le-Clainche, I.·Lagnel, J.·Marande, W.·Rittener-Ruff, V.·Hinsinger, D.·Boissot, N.·Faivre Rampant, P.

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Abstract

BackgroundNanopore 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 (subspecies melo) were successfully and accurately reconstructed as well as in a third cultivar from the agrestis subspecies. We obtained a fourfold enrichment, independently from the samples, but with some variations according to the enriched regions. In the agrestis cultivar, 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.

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Belinchon-Moreno, J., Berard, A., Canaguier, A., Chovelon, V., Cruaud, C., Engelen, S., Feriche-Linares, R., Le-Clainche, I., Lagnel, J., Marande, W., Rittener-Ruff, V., Hinsinger, D., Boissot, N., Faivre Rampant, P.. 2023-12-21. Nanopore adaptive sampling to identify the NLR-gene family in melon (Cucumis melo L.). https://doi.org/10.1101/2023.12.20.572599

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