Suitability of DNA sampled from Nile tilapia skin mucus swabs as a template for ddRAD-based studies
2017 | 2016
Khanam, Taslima | Taggart, John | Wehner, Stefanie | McAndrew, Brendan | Penman, David | University of Stirling | Institute of Aquaculture | Institute of Aquaculture | Institute of Aquaculture | Institute of Aquaculture | 0000-0002-3843-9663 | 0000-0002-3632-2584 | 0000-0001-7384-5133 | 0000-0001-8608-6631
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.
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