Wednesday, 25 March 2015

Testing the utility of the COI and 16S genes as DNA barcode markers in species delineation on two selected animal taxa

An IRRI Seminar

By Ian Kendrich C. Fontanilla
Assistant Professor & Associate Dean for Academic Affairs
College of Science
University of the Philippines, Diliman

26 March  2015
1:15-2:15 p.m.
Havener Auditorium


DNA barcoding is a novel technique for taxonomic identification of different species at the molecular level. Its premise lies on its ability to distinguish species based on interspecific genetic differences, which should be greater than within species variation. The cytochrome c oxidase subunit I (COI) gene has been designated as the barcode marker of choice for animals because it is easy to amplify through polymerase chain reaction (PCR). However, other genes have also been suggested as possible markers for DNA barcoding, particularly the ribosomal RNA genes such as the mitochondrial 16S rRNA. This study aimed to test the utility of COI and 16S rRNA genes on the Muricidae (Mollusca: Gastropoda) and the Dicroglossidae (Chordata: Amphibia), two taxa based on the COI sequences in the GenBank database. For the Muricidae, a total of 1607 COI sequences and 552 16S rRNA sequences were mined from GenBank, and 505 bp of the COI and 445 bp of the 16S rRNA were evaluated. For the Dicroglossidae, 57 COI sequences and 410 16S rRNA sequences were used, and 558 bp of the COI 501 bp of the 16S rRNA were evaluated. Results showed that for the Muricidae, there was minimal overlap between intraspecific and interspecific variations in the COI, with most species being distinguished at 3% K2P genetic distance, whereas greater overlap was seen in the 16S rRNA, particularly at 0-2.5% interval. The COI is therefore more suitable as a DNA barcode marker at this time. For the Dicroglossidae, on the other hand, there was extensive overlap in the COI, whereas the 16S fared better where most species could be distinguished at 3% K2P genetic distance. Overlaps may be due to the presence of cryptic species or incomplete taxon sampling. It is recommended that DNA barcoding should rely on more than just one gene, but this will only be effective if the taxonomic group in question is well sampled.

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