Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species

Abstract

Hybridization capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. A cross-species approach makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for non-model organisms, for which often no a priori knowledge exists regarding these loci. Here, we have adopted cross-species capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a non-model organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). In this manner, we were able to survey intraspecific variation at hundreds of nuclear loci across the European range of L. lynx. A large set of bi-allelic candidate SNPs was then tested in a high throughput SNP-genotyping platform (Fluidigm), which we reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with additional samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (incl. the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.

Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels

“…The evaluation of tests during the development of the rSP relied on the genotyping of high-and low-DNA reference sample sets (Table 1). For these reference individuals, we assumed the genotypes generated from high-DNA extracts (60 ng/µl) as true genotypes (compare Foerster et al, 2017). Throughout the testing scheme, corresponding low-DNA and noninvasive samples of reference individuals were replicated between runs and compared to the high-DNA genotypes.…”

From STRs to SNPs via ddRAD‐seq: Geographic assignment of confiscated tortoises at reduced costs

“…Custom species‐specific SNP panels, including high‐ranking loci, have been shown to be highly informative for assignment studies (Förster et al, 2018; Jenkins et al, 2019; Kleinman‐Ruiz et al, 2017) and prove to be an important resource for identifying the geographic origin of species in a conservation and forensic perspective.…”

“…Nowadays, custom species‐specific SNP panels are being developed for several wild species providing insights into diverse topics including conservation genomics (Eriksson et al, 2020; Feutry et al, 2020; Henriques et al, 2018; Meek et al, 2016). Small panels of SNPs (<100) have already been used for the identification of distinct genetic populations to delineate biologically accurate management units and for the identification of individuals, including the assignment of individuals to their source population (Förster et al, 2018; Henriques et al, 2018; Kleinman‐Ruiz et al, 2017).…”

From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

“…Custom species-specific SNP panels, including high-ranking loci, have been shown to be highly informative for assignment studies (Förster et al, 2018; Jenkins, Ellis, Triantafyllidis, & Stevens, 2019; Kleinman-Ruiz et al, 2017) and prove to be an important resource for identifying the geographic origin of species in a conservation and forensic perspective.…”

“…Nowadays, custom species-specific SNP panels are being developed for several wild species providing insights into diverse topics including conservation genomics (e.g., Eriksson, Ruprecht, & Levi, 2020;Feutry et al, 2020;Henriques et al, 2018;Meek et al, 2016). Small panels of SNPs (<100) have already been used for the identification of distinct genetic populations to delineate biologically accurate management units and for the identification of individuals, including the assignment of individuals to their source population (Förster et al, 2018;Henriques et al, 2018;Kleinman-Ruiz et al, 2017). This approach can be described in four steps.…”