Mazoyer, C. | Search bioRxiv

bioRxiv2024

Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species: the southern damselflies (Coenagrion mercuriale) as a case study.

Genomic markers are essential tools for studying species of conservation concern, yet non-model species often lack a genome reference. 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, we retained 2,092 SNPs. We used them to characterise rear-edge populations of the southern damselfly in Northern France, a region where populations are sparsely distributed. Previous surveys utilising microsatellite markers allowed comparison of genetic diversity and differentiation estimates. Consistent with prior findings, genetic diversity estimates were similar across the studied populations that showed no sign of inbreeding. SNP markers exhibited greater resolution in detecting fine-scaled genetic structure, identifying two putative hybrids in adjacent populations, a feat unattainable with microsatellite loci. Altogether, this study highlighted the ongoing challenge of large-scale SNP genotyping using target sequencing techniques in non-model species to set conservation guidelines. Nonetheless, these new markers showed greater statistical power in identifying conservation units and offered the promise of greater precision in the identification of admixture events or the estimation of key population parameters such as effective population size.

evolutionary biology↗

bioRxiv2018

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Transposable elements (TEs) have initially been viewed as pure genomic parasites but are now recognized as central genome architects and powerful agents of rapid adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either recent or old insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. TE fragments that have been maintained in both species, i.e. those that are orthologous, tend to be located on average closer to genes than those that are retained in one species only. Moreover, compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing TE insertions when they are close to genes. Overall, our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.

evolutionary biology↗