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.

• BOLD
• COI gene
• DNA barcode
• Genbank
• higher taxon assignment
• Indian freshwater fishes
• R_seq
• sequence conservation

Declarations of interest

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article. Our humble acknowledgement goes to the Department of Biotechnology, Government of India for providing infrastructure facilities (BT/HRD/01/002/2007).

Supplementary material available online

Supplementary material