DNA barcoding of sea urchin species in the bird’s head seascape Papua-Indonesia

Abstract

The DNA barcoding of COI gene has been used for molecular identification of the numerous individuals of sea urchin present in Bird’s Head Seascape (BHS) Papua in Indonesia. We extracted, sequenced, and analysed DNA of a total of 29 individuals collected from Raja Ampat, Rumberpon, Fakfak and Manokwari. The fragment gene of cytochrome oxidase subunit 1, were amplified with polymerase chain reaction by using coif and coitri primers. Total 570 base pairs nucleotide from each sample were analysed with MEGA X. The results of sample sequence homology with the GenBank and BOLD System databases show that some samples can be identified at the species level, and some samples can only be identified at the genus level. The phylogenetic tree results show that all samples are separated into two large clades.