Optimizing DNA extraction and PCR amplification conditions for establishing phylogenetic relationships of bubble corals (family Euphyllidae)


College of Science



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Coral taxonomy traditionally relies on skeletal morphology, a fact, which does not hold true in the case of the family Euphyllidae. Most of the 14 "bubble coral" species under this family are identified in a far more subjective way of visually inspecting their soft tissue features while in their live form. This creates a number of taxonomic issues within the family which may be resolved with information from both molecular techniques and skeletal features. Phylogenetic relationships among species in the family may be clarified in this initial attempt towards applying molecular tools on bubble coral taxonomy particularly on Euphyllia yaeyamaensis ana Euphy/lia ancora. These were initially preserved and kept in Chaotropic buffer solution (CHAOS) upon collection. Viogene Extraction kJt and primer pairs 15 and 255, ITS4 and A18S, previously identified to deliver considerable results in other molecular studies, were tested on the samples. The cost-efficiency of the Viogene Kit is its major advantage over the Phenol chloroform method, which is less likely to yield DNA products after all the tedious and time-consuming steps. Extraction procedure from the Viogene Kit was specifically modified for coral DNA. Gel electrophoresis showed presence of DNA in all the samples. PCR conditions are currently undergoing several modifications to satisfy the requirements that will produce the desired fragments for sequencing.



Marine Biology


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