A quick and efficient method for DNA isolation from freshwater ostracods

Abstract

Freshwater ostracods are ecologically and evolutionarily important small free-living crustaceans occurring in lakes, rivers and small water bodies. However, despite their importance, only a few genetic studies have been conducted so far in ostracoda due to isolation of insufficient amounts of DNA. We present a simple, efficient and cost-effective total DNA extraction protocol from freshwater ostracods for PCR amplification. Total DNA was extracted from four freshwater ostracods; Heterocypris incongruens, Cypridopsis vidua, Eucypris virens and Herpetocypris chevreuxi. We also compared the performance of our protocol with two manual DNA extraction protocols (HotSHOT, Chelex-100) and a commercial kit (Highpure PCR template preparation kit-Roche). The success of the isolation protocol was tested by PCR and sequencing of 18S rRNA and COI regions. Although our technique, Roche and HotSHOT methods resulted in acceptable DNA concentrations and showed an amplifiable band of expected size, both our protocol and Roche generally gave better results than HotSHOT, whereas the poor results were obtained from Chelex protocol. Therefore, we suggest that filter-based DNA isolation is more reproducible than other protocols. Our protocol requires no hazardous organic solvents and adaptable to 0.5 mL 8-strip PCR tubes format facilitating DNA extraction from a large number of samples. © Published by Central Fisheries Research Institute (CFRI) Trabzon, Turkey.