Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles

Abstract

AbstractAssociation and genetic mapping studies aimed at linking genotype to phenotype are powerful tools that require large numbers of samples, complicating their use in long-lived species with low fecundity. Shed skins of snakes and other reptiles contain DNA; are a safe and ethical way of non-invasively sampling large numbers of individuals; and provide a simple mechanism by which to involve the public in scientific research. Here we test whether the DNA in dried shed skins mailed to us from citizen scientists is suitable for reduced representation sequencing approaches, specifically genotyping-by-sequencing (GBS). We find that shed skin samples provide DNA of sufficient quality and quantity for GBS, although libraries from shed skin resulted in fewer sequenced reads than libraries from snap-frozen muscle, and contained slightly fewer variants (70,685 SNPs versus 97,724). This issue is a direct result of lower read counts of the shed skin samples, and can be rectified quite simply with deeper sequencing. Skin-derived libraries also have a very slight (but significantly different) profile of transitions and transversions, suggesting that DNA damage occurs but is minimal. We conclude that shed skin-derived DNA is a good source of genomic DNA for a variety of genetic studies, and use it to identify sex-linked scaffolds in the corn snake genome.