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

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

Rapid and accurate species identification for ecological studies and monitoring using CRISPR‐based SHERLOCK

“…Once the specificity, sensitivity and speed of SHERLOCK results were characterized for traditionally extracted tissue, we focused on developing a method for accessing the target species’ DNA with minimal invasiveness and requiring little to no additional upstream procedures prior to commencing the SHERLOCK reaction. Fish mucus, which is abundant and covers all epithelial surfaces, can be swabbed with a brush to obtain DNA samples, and this method has been successfully used for genotyping and high‐throughput sequencing (Taslima, Davie, McAndrew, & Penman, 2016; Taslima, Taggart, Wehner, McAndrew, & Penman, 2017). More generally, mucus swabbing is used for genetic analysis of many other diverse organisms including humans (Clarke et al., 2014), amphibians (Pidancier, Miquel, & Miaud, 2003) and molluscs (Henley, Grobler, & Neves, 2006).…”

“…Fish mucus, which is abundant and covers all epithelial surfaces, can be swabbed with a brush to obtain DNA samples, and this method has been successfully used for genotyping and high-throughput sequencing (Taslima, Davie, McAndrew, & Penman, 2016;Taslima, Taggart, Wehner, McAndrew, & Penman, 2017). More generally, mucus swabbing is used for genetic analysis of many other diverse organisms including humans (Clarke et al, 2014), amphibians (Pidancier, Miquel, & Miaud, 2003) and molluscs (Henley, Grobler, & Neves, 2006).…”

Population Structure and Genetic Diversity of Nile Tilapia (Oreochromis niloticus) Strains Cultured in Tanzania

“…Several studies have applied ddRAD-seq sequencing to generate high-density linkage maps (Brown et al, 2016;Manousaki et al, 2016) and estimate genetic diversity (Antoniou et al, 2017;Hosoya et al, 2018). Furthermore, ddRADseq has been utilized in several tilapia studies for evaluating the suitability of DNA from skin mucus swabs (Taslima et al, 2017), identification of sex determining regions (Wessels et al, 2017), and quantitative trait loci (QTL) analysis (Li et al, 2017).…”

Investigation of genetic sex of GIFT strain of tilapia in Bangladesh using Y‐linked Amh marker

“…Taking into account the genomic DNA quality is essential for reliable results; here, we tested two protocols such as commercial DNA extraction kit and salt‐isopropanol precipitation method. Therefore in this experiment, three GIFT tilapia samples were first used to extract genomic DNA from a commercial DNA extraction kit (Manufacturer's protocol was used, ADDBIO INC.) and compared with the pure extraction protocol named as salt‐isopropanol precipitation method (adapted the protocol from Taslima et al, 2016; Taslima et al, 2017). Three DNA samples from each extraction method was also analysed using 233 bp deletion in exon VII ( Amhy ) marker following the protocol described in Taslima et al, 2020.…”