Application of cytochrome oxidase subunit 1 partial gene for species validation of Macrobrachium sintangense from Lake Lido, West Java

Abstract

Lake Lido is one of the habitats for Sunda river prawn (Macrobrachium sintangense), but the species was reported not to be found in December 2015-May 2017. This prawn has an economic value both alive for consumption and dead for bait. Shrimp identified morphologically as M. sintangense required reinforcement using molecular techniques for species certainty. This study aimed to validate Sunda river prawn (Macrobrachium sintangense) based on a molecular approach using cytochrome oxidase subunit 1 (COI) partial gene markers. Species certainty is important as basic information in management. The specimens (n=15) were obtained from Lido Lake and transported to the laboratory for genetic analysis. The analysis includes DNA extraction, polymerase chain reaction (PCR), electrophoresis, and sequencing. Three samples were successfully aligned using MEGA X software. Based on BLASTn in NCBI, the sequences have high similarity with Macrobrachium sp. sequence by 95%. However, nucleotide bases of M. sintangense were found in a database with access code MF622027.1, but it did not match with the samples. Phylogeny analysis showed the different clade positions with M. sintangense database. The prawn samples have been identified morphologically as M. sintangense but have not been validated as the same species by COI partial gene markers. So, it is necessary to validate using other gene markers to obtain species certainty for management.