Identifying Single DNA Barcode Regions of Oreochromis niloticus of Shahpura Lake, Bhopal and their Contribution to a Reference Library

Abstract

Background: The present investigation was carried out on the development of a barcode and DNA sequence database of Oreochromis niloticus (Nile Tilapia) of Shahpura Lake, Bhopal, through mitochondrial Cytochrome c Oxidase-I gene (cox1) for public domain use as a reference database for identification, authentication, and variation studies.Materials and Methods: We performed the mitochondrial genomic analyses for molecular studies, for which genomic DNA was extracted from fish tissues using the standard protocol provided by Janarthanan and Vincent (2007). Then, the isolated DNA was introduced to Polymerase Chain Reaction (PCR) using universal primers, after which the electrophoresis of the PCR product was done; subsequently, the DNA bands of interest of the desired molecular weight were obtained on the gel.Results: We generated 02 unique DNA barcodes of morphologically identified fish specimens collected from Shahpura Lake, Bhopal. Considering the ambiguous (0%), Barcode Index Number (BIN) URI (BOLD:AAC9904), Top Hit % (100%), Nearest Member of Neighbor (ANGBF54446-19), Nearest BIN URI (BOLDAET5315), Analysis of Barcode Gap as an average intra-specific (204.14), and Analysis of Cluster Sequences (RESL) (20.583717) was found significant for the development of the DNA barcode of O. niloticus. The overall mean distance among O. niloticus specimens (6A and 6B) was obtained as 1.82, which may be considered good for conservation purposes. RESL in the BOLD systems has a stronger taxonomic performance than that of the Barcode Gap Analysis and thus showed better species identification. During the present investigation, similar results were achieved, which may be related to species identification.

Keywords: DNA barcoding; COX1 gene; Sanger’s DNA sequencing; Barcode Index Number (BIN); Barcode Gap Analysis