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

Belinchon-Moreno, Javier; Berard, Aurelie; Canaguier, Aurelie; Chovelon, Véronique; Cruaud, Corinne; Engelen, Stéfan; Feriche-Linares, Rafael; Le-Clainche, Isabelle; Marande, William; Rittener-Ruff, Vincent; Lagnel, Jacques; Hinsinger, Damien; Boissot, Nathalie; Faivre Rampant, Patricia

doi:10.1101/2023.12.20.572599

Cited by 2 publications

(1 citation statement)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…PacBio IsoSeq; Yu et al 2023 ) and the adaptive sampling approach of full NLR genes (e.g. Oxford Nanopore Technologies; Belinchon-Moreno et al 2023 ) seem promising avenues.…”

Section: Discussionmentioning

confidence: 99%

Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome

Woudstra,

Tumas,

van Ghelder

et al. 2024

Genome Biology and Evolution

View full text Add to dashboard Cite

Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis) but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae and other gymnosperms were scanned for NLR genes using existing and customised pipelines. Discovered genes were mapped across chromosomes and linkage groups and analysed phylogenetically for evolutionary history. Conifer genomes are characterised by dense clusters of NLR genes, highly localised on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and non-coniferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plant’s resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding.

show abstract

“…PacBio IsoSeq; Yu et al 2023 ) and the adaptive sampling approach of full NLR genes (e.g. Oxford Nanopore Technologies; Belinchon-Moreno et al 2023 ) seem promising avenues.…”

Section: Discussionmentioning

confidence: 99%

Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome

Woudstra,

Tumas,

van Ghelder

et al. 2024

Genome Biology and Evolution

View full text Add to dashboard Cite

show abstract

Nuclear and organelle genome assemblies of fiveCucumis meloL. accessions, Ananas, Canton, PI 414723, Vedrantais and Zhimali, belonging to diverse botanical groups

Belinchon-Moreno,

Berard,

Canaguier

et al. 2024

Preprint

View full text Add to dashboard Cite

The construction of accurate whole genome sequences is pivotal for characterizing the genetic diversity of plant species, identifying genes controlling important traits, or understanding their evolutionary dynamics. Here, we generated the nuclear, mitochondrial and chloroplast high-quality assemblies of five melon (Cucumis melo L.) accessions representing five diverse botanical groups, using the Oxford Nanopore sequencing technology. The accessions here studied included varied origins, fruit shapes, sizes, and resistance traits, providing a holistic view of melon genomic diversity. The final chromosome-level genome assemblies ranged in size from 359 to 365 Mb, with approximately 25x coverage for four of them multiplexed in half of a PromethION flowcell, and 48x coverage for the fifth, sequenced individually in another half of a PromethION flowcell. Contigs N50 ranged from seven to 15 Mb for all the assemblies, and very long contigs reaching sizes of 20-25 Mb, almost compatible with complete chromosomes, were assembled in all the accessions. Quality assessment through BUSCO and Mercury indicated the high completeness and accuracy of the assemblies, with BUSCO values exceeding 96% for all accessions, and Mercury QV values ranging between 32 and 47. We focused on the complex NLR resistance gene clusters to validate the accuracy of the assemblies in highly complex and repetitive regions. Through Nanopore adaptive sampling, we generated accurate targeted assemblies of these regions with a significantly higher coverage, enabling the comparison to our whole genome assemblies. Overall, these chromosome-level assembled genomes constitute a valuable resource for research focused on melon diversity, disease resistance, evolution, and breeding applications.

show abstract

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

Cited by 2 publications

References 63 publications

Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome

Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome

Nuclear and organelle genome assemblies of fiveCucumis meloL. accessions, Ananas, Canton, PI 414723, Vedrantais and Zhimali, belonging to diverse botanical groups

Contact Info

Product

Resources

About