title: Unraveling the sequence information in COI barcode to achieve higher taxon assignment based on Indian freshwater fishes.
abstract: Efficacy of cytochrome c oxidase subunit I (COI) DNA barcode in higher taxon assignment is still under debate in spite of several attempts, using the conventional DNA barcoding methods, to assign higher taxa. Here we try to understand whether nucleotide and amino acid sequence in COI gene carry sufficient information to assign species to their higher taxonomic rank, using 160 species of Indian freshwater fishes. Our results reveal that with increase in the taxonomic rank, sequence conservation decreases for both nucleotides and amino acids. Order level exhibits lowest conservation with 50% of the nucleotides and amino acids being conserved. Among the variable sites, 30-50% were found to carry high information content within an order, while it was 70-80% within a family and 80-99% within a genus. High information content shows sites with almost conserved sequence but varying at one or two locations, which can be due to variations at species or population level. Thus, the potential of COI gene in higher taxon assignment is revealed with validation of ample inherent signals latent in the gene.
authors.affiliation: Department of Biotechnology, Assam University , Silchar, Assam , India.
authors.forename: Mohua
authors.initials: M
authors.lastname: Chakraborty
authors.forename: Sankar Kumar
authors.initials: SK
authors.lastname: Ghosh
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D058893:DNA Barcoding, Taxonomic; D003576:Electron Transport Complex IV / Q000235:genetics*; D005399:Fishes / Q000145:classification* / Q000235:genetics*; D050259:Genes, Mitochondrial
chemical_list: D003576:Electron Transport Complex IV
keywords: BOLD; COI gene; DNA barcode; Genbank; Indian freshwater fishes; Rseq; higher taxon assignment; sequence conservation