YUMNI KHAIRINA GHASSANI, 060810248 (2011) THE APPLICATION OF DNA BARCODING USING CYTOCHROME C OXIDASE I FOR SUMATRAN ELEPHANT (Elephas maximus Sumatrensis). Skripsi thesis, UNIVERSITAS AIRLANGGA.

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Abstract

This study was conducted to develop the molecular genetics identification for Sumatran elephant speciation using mtDNA marker and to do preliminary study for population genetic in captivity. This study was using 11 genomic DNA extracted from whole blood samples. In this study, the conserved of COI and cyt b gene as the molecular genetics marker were used. COI is one of the conserved genes of mtDNA which has very robust universal primers for speciation. The 710-bp fragment of COI gene was amplified using the COI universal primers pair. All of samples showed no sequence divergence compared to the Thai elephant as reference sequence. The Sumatran elephants are clustered together with the Thai elephant in COI gene phylogenetic tree. Cyt b gene is another conserved gene of mtDNA. Its low sequence variation rates at high taxonomic levels compared to other vertebrates makes cyt b a good choice as a marker in speciation, phylogeography and forensic molecular genetics studies. The 376-bp fragment of cyt b gene was amplified using the cyt b universal primers pair. The results showed one SNP in position 14249 where C is substituted by T. Cyt b sequence divergence results showed very high sequence divergence between the samples to the African elephant and very low sequence divergence compared to the Asian elephants. All the samples are clustered together in the cyt b gene phylogenetic tree. From both phylogenetic trees, it can be concluded that COI and cyt b gene can be used for species identification.

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