DNA barcoding using Cytochrome c oxidase gene marker of Marine Sharks and Ray fish of Bangladesh

Abstract

Objective: The Lack of proper identification of various sharks and ray species has been a far cry among scientists. Cytochrome c oxidase gene-based DNA barcoding is used in various species identification not only because of pinpoint accuracy but how it can be used only a small amount of sample which doesn’t have proper morphological identification scope. So a need for a strong database of these sharks and rays identifying marker Cytochrome c oxidase gene is needed to crosscheck, regulate and update for current use and future reference. Methods: Collection of samples were done from the southern region of Bangladesh in the Bay of Bengal at various points and times. To identify the species a partial portion of it was collected, in general an approximate 650bp sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene is taken in consideration for this study. Since cytochrome c oxidase gene is easy to multiply in numbers with specified primers, a good number of outcomes are taken into consideration via Sanger-Sequencing method. The raw sequences were then trimmed according to match value and uploaded to NCBI database from where a cross match is done to verify the sequences. Further analysis was done using both offline and online resources of bioinformatics tools. Results: Our study concluded results that the K2P percentage of intra species of sharks and rays cluster around a close range of 1% to 6.5% in intra species and the range is spread from 11% to a maximum of 64% between species which gives us a genetic gap of 4.5%. For sharks, the GC1, GC2, and GC3 codons were 52.52 ± 0.23, 42.89 ± 0.04, and 20.38 ± 0.31, respectively with an average GC percentage being 38.59 ± 0.12 in the 8 species of sharks. For the rays, the GC1, GC2, and GC3 codons were 53.96 ± 0.36, 43.48 ± 0.19, and 33.59 ± 0.44, respectively with an average GC percentage being 43.67 ± 0.28 among 10 species of rays. Amino acid profiling showed clear similarities among the percentage of amino acid translated from the mitochondrial COI gene of same species and a significant difference between intra and inter species which makes it a good second marker apart from the GC percentage via DNA barcoding method. Conclusion: This study proved that COI gene-based DNA barcoding is a sound technique for rapid and accurate identification of sharks and rays also amino acid profiling can also be set as possible additional identification marker.