Comparative Evaluation of Different Established Genomic Extraction Methods for Scleractinian Coral

Abstract

Studies on coral genetics have been widely used recently for varied research purposes, including to solve the taxonomical challenge or to understand the physiological-ecological aspects of corals towards climate change. While the information provided by coral genome is crucial for those works, isolation of coral genome is still a difficult preliminary step due to coral's nature. This study aimed to evaluate and to suggest the best application of among four established methods for DNA extraction from scleractinian coral, i.e., Guanidine hydrochloride (GuHCl), Chelex chelating resin, Guanidinium thiocyanate-phenol-chloroform (AGPC), and spin-column methods. Coral samples were grounded and submitted to each extraction method's protocol. Final extracts were checked for their quality and quantity. The final extracts feasibility were tested through PCR (Polymerase Chain Reaction), followed by electrophoresis for amplicon quality screening. The scoring was done for assessment aspects: time efficiency, successful extraction process, extracted DNA quantity and quality, final extract properness, and cost effort per sample. The highest DNA concentration was obtained by spin-column methods, reaching up to 724.31 ng/μl, while other methods can only provide between 264.94±36.453 to 378.19±0 ng/μl of DNA. Among all method tested, the spin-column was able to provide reproducible and feasible quality of final extracts for the amplification. Other methods were failed to provide such consistent and proper results. The results suggest that the spin-column is the most appropriate method for DNA isolation from scleractinian specimen.