Evaluation of eight protocols for genomic DNA extraction of Hypostomus commersoni (Valenciennes, 1836), Siluriformes: Loricariidae

The principle and techniques applied in DNA extraction play a pivotal role in the obtention of a considerable and purified yield of genetic material. In this work, we evaluate the efficiency of seven protocols chosen from literature for the DNA extraction of Hypostomus commersoni (Valenciennes, 1836), an important component of South American freshwater ichthyofauna. We also proposed and evaluate an improved protocol, based on the combination of variables from the selected methodologies that demonstrated higher potential for extracting H. commersoni DNA. The quality of samples was assessed through spectrophotometry, gel electrophoresis and PCR-RAPD amplification. The efficiency of DNA extraction was influenced both by the method applied and target-tissue of choice. Higher concentrations and yield of DNA were obtained from ocular tissue, with a positive spectrum of incubation in lysis buffer for up to 36 hours after sample collection, without maceration, using fresh tissues and in the presence of high concentration of Proteinase K. In these conditions, samples were successfully amplified using a set of primers from Operon Technologies. To date, there is no record of description for the parameters analyzed in this work, neither the description of RAPD markers for H. commersoni , evidencing the importance of our findings.