Beyond Morphology: COI-Based Molecular Identification of Sea Urchins from Kumu Beach, North Sulawesi

Abstract

Sea urchins (Echinoidea) play important ecological and economic roles in coastal ecosystems, but morphological identification is often unreliable due to overlapping diagnostic traits among closely related taxa. This study used DNA barcoding of the mitochondrial COI gene to identify a sea urchin specimen from Kumu Beach, North Sulawesi, and determine its phylogenetic relationship with GenBank reference sequences. DNA was extracted from gonad tissue, amplified via PCR using the BK-COI-AntF&AntR primers, sequenced, and analyzed through BLAST, MUSCLE alignment, and Maximum Likelihood phylogenetic reconstruction (Kimura 2 Parameter model, 1000 bootstrap replications). PCR yielded a clear ~709 bp fragment, producing a 658 bp COI consensus sequence (A+T content: 56.84%). BLAST analysis showed 100% query cover and identity with multiple Tripneustes gratilla reference sequences, and phylogenetic analysis placed the specimen within the Tripneustes clade, closely nested among T. gratilla sequences. These results confirm the specimen as T. gratilla and support COI based DNA barcoding as a reliable method for sea urchin species identification.