Faivre Rampant, P. | Search bioRxiv

bioRxiv2026

Development of the 4TREE SNP array, a forest multispecies array to enhance European Breeding and conservation programs in pine, poplar and ash.

Within the framework of the European Adaptive BREEDING for Better FORESTs project (B4EST, https://b4est.eu/), we have developed genotyping tools for Poplar, Ash, and Pine forest tree species. SNP arrays are attractive genotyping tools because of the user-friendly genotype calling system and the robust transferability among laboratories. Here we describe the development of an Axiom SNP array for Pinus pinaster (13,407 SNPs), Pinus pinea (5,671 SNPs), Poplar spp. (13,408 SNPs), and Fraxinus spp. (13,407 SNPs) based on a two-step process. We first assembled a high-density (>100,000 SNPs/species) screening array that served to test a large panel of candidate SNPs on a diversity panel involving at least 120 individual trees per species or species group. In the second step, we selected and combined the most informative SNPs to build the final 50,000 SNP 4TREE array. This approach resulted in high genotyping success rates, including for species lacking previously validated high-quality SNP resources. The 4TREE SNP array provides a valuable and transferable genomic tool to support genomic prediction, breeding, and adaptive management of forest tree species.

genomics↗

bioRxiv2024

Nuclear and organelle genome assemblies of five Cucumis melo L. accessions, Ananas, Canton, PI 414723, Vedrantais and Zhimali, belonging to diverse botanical groups

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. Article SummaryThis study presents high-quality nuclear, mitochondrial, and chloroplast genome assemblies for five diverse melon (Cucumis melo L.) accessions, using Oxford Nanopore sequencing. The assemblies represent a broad spectrum of melon diversity, including differences in origin, fruit morphology, or resistance traits. The genomes, ranging from 359 to 365 Mb, were assembled at a chromosome level with high contiguity, and verified using different validation approaches. This study provides valuable insights for research on melon genetic diversity, disease resistance, and breeding applications. The genome data will be especially valuable for plant geneticists, breeders, and researchers working on crop improvement and resistance traits.

genomics↗

bioRxiv2023

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

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.

genomics↗