Fecal DNA Isolation and Degradation in Clam Cyclina sinensis: Noninvasive DNA Isolation for Conservation and Genetic Assessment

Abstract

Background To avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA.Results The clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor.Conclusions The clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.

Development of a new faecal DNA extraction method (HV-CTAB-PCI) for amplification of mitochondrial and nuclear markers used in genetic analyses of dugongs (Dugong dugon)

“…11.762, p < 0.001) techniques(Fig 4A). Total DNA concentrations, yielded using the scrape-only technique, were significantly higher than that of swabbing (Tukey-HSD: T 14 = 3.401, p = 0.011).…”

“…The use of faecal DNA for genetic studies of marine species is even more restricted due to degradation and contamination in seawater [10]. Furthermore, the age of faecal samples may impact retrieval of target DNA, i.e., higher yield and quality of target DNA may be extracted from fresh compared to old scats [11].…”

“…Although various extraction methods have been used to retrieve host DNA from faecal samples, there is no ‘one-size-fits-all’ approach that works optimally for all species. Some widely used extraction techniques include the QIAamp Fast DNA Stool Mini Kit (hereafter referred to as QIAamp) [7, 15], phenol-chloroform-isoamyl alcohol (PCI) [11, 16] and cetyltrimethyl ammonium bromide (CTAB) [17]. Interestingly, the 2CTAB/PCI protocol has demonstrated success in extracting DNA from herbivore faeces [18].…”