Suitability of DNA sampled from Nile tilapia skin mucus swabs as a template for ddRAD-based studies

Citation

Khanam T, Taggart J, Wehner S, McAndrew B & Penman D (2017) Suitability of DNA sampled from Nile tilapia skin mucus swabs as a template for ddRAD-based studies. Conservation Genetics Resources, 9 (1), pp. 39-42. https://doi.org/10.1007/s12686-016-0614-z

Abstract
For conservation, ethical and welfare reasons, minimally invasive DNA sampling is becoming increasingly important in animal genetics studies. Skin mucus swabs have been used as a source for fish DNA in PCR-based studies, but their suitability for high-throughput sequencing has not been examined. DNA was extracted from skin mucus, muscle and fin samples of two Nile tilapia and used in double-digest restriction-site associated DNA (ddRAD) sequencing. Approximately 16,000 and 9000 RAD loci were retrieved from de novo and reference-based analyses respectively. The numbers of RAD loci retrieved from three tissue sources were similar, with >83 % being shared among all three samples. Minor bacterial contamination was detected in a single muscle sample (0.07 % of the total RAD loci). The data indicates that DNA derived from skin mucus can be reliably used for ddRADseq and is likely to be applicable in other similar genomic analyses.

Keywords
Oreochromis niloticus; Fish mucus; DNA; ddRADseq

Journal
Conservation Genetics Resources: Volume 9, Issue 1