Development of a panel of SNP loci in the emblematic southern damselfly (Coenagrion mercuriale) using a hybrid method: Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species

Genomic markers are essential tools for studying species of conservation concern, yet non-model species often lack a reference genome. Here we describe a methodology for identifying and genotyping thousands of SNP loci in the southern damselfly (Coenagrion mercuriale), a bioindicator of freshwater stream quality classified as near-threatened, with locally declining populations. We used a hybrid approach combining reduced representation sequencing and target enrichment. First, we identified putative SNP loci using ddRADseq and de novo assembly. Then, single primer enrichment technology targeted 6,000 of these SNPs across 1,920 individuals. Challenges encountered included sequence recapture failure, coverage depth discrepancies, and aberrant FIS values. We provide recommendations to address such issues. After multiple filtering steps, 2,092 SNPs were retained and used to analyse the genetic structure of 131 individuals belonging to 11 populations in France, comparing central and marginal ..., , , # Development of a panel of SNP loci in the emblematic southern damselfly (Coenagrion mercuriale) using a hybrid method: Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species

[https://doi.org/10.5061/dryad.vq83bk446](https://doi.org/10.5061/dryad.vq83bk446)

## Description of the data and file structure

### Files and variables

#### File: SNP\_genotypes\_131indv.txt

**Description:** this file contains for each population sample: the name of the geographical location where population was sampled (Population), the name of the collected individual (Individual), the geographical coordinates of each sampled population (xcoord_WGS84.EPSG4326, ycoord_WGS84.EPSG4326), the individual genotypes at the 2092 SNPs loci using a genind genotype format. Each individual sample is represented by a row, and each biallelic locus is encoded by two columns indicating the variant, with integers indicating the number of each allele, and summing up to the individuals' ...