Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species: the southern damselflies (Coenagrion mercuriale) as a case study DOI Creative Commons
Agathe Lévêque, Jean‐François Arnaud,

Vincent Vignon

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 5, 2024

Abstract Genomic markers are essential tools for studying species of conservation concern, yet non-model often lack a genome reference. Here we describe methodology identifying and genotyping thousands SNP loci in the southern damselfly ( Coenagrion mercuriale ), bioindicator freshwater stream quality classified as near-threatened, with locally declining populations. We used hybrid approach combining reduced representation sequencing target enrichment. First, identified putative using ddRADseq de novo assembly. Then, single primer enrichment technology targeted 6,000 these SNPs across 1,920 individuals. Challenges encountered included sequence recapture failure, coverage depth discrepancies, aberrant F IS values. provide recommendations to address such issues. After multiple filtering, retained 2,092 SNPs. them characterise rear-edge populations Northern France, region where sparsely distributed. Previous surveys utilising microsatellite allowed comparison genetic diversity differentiation estimates. Consistent prior findings, estimates were similar studied that showed no sign inbreeding. exhibited greater resolution detecting fine-scaled structure, two hybrids adjacent populations, feat unattainable loci. Altogether, this study highlighted ongoing challenge large-scale techniques set guidelines. Nonetheless, new statistical power units offered promise precision identification admixture events or estimation key population parameters effective size.

Language: Английский

Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species: the southern damselflies (Coenagrion mercuriale) as a case study DOI Creative Commons
Agathe Lévêque, Jean‐François Arnaud,

Vincent Vignon

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 5, 2024

Abstract Genomic markers are essential tools for studying species of conservation concern, yet non-model often lack a genome reference. Here we describe methodology identifying and genotyping thousands SNP loci in the southern damselfly ( Coenagrion mercuriale ), bioindicator freshwater stream quality classified as near-threatened, with locally declining populations. We used hybrid approach combining reduced representation sequencing target enrichment. First, identified putative using ddRADseq de novo assembly. Then, single primer enrichment technology targeted 6,000 these SNPs across 1,920 individuals. Challenges encountered included sequence recapture failure, coverage depth discrepancies, aberrant F IS values. provide recommendations to address such issues. After multiple filtering, retained 2,092 SNPs. them characterise rear-edge populations Northern France, region where sparsely distributed. Previous surveys utilising microsatellite allowed comparison genetic diversity differentiation estimates. Consistent prior findings, estimates were similar studied that showed no sign inbreeding. exhibited greater resolution detecting fine-scaled structure, two hybrids adjacent populations, feat unattainable loci. Altogether, this study highlighted ongoing challenge large-scale techniques set guidelines. Nonetheless, new statistical power units offered promise precision identification admixture events or estimation key population parameters effective size.

Language: Английский

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