Journal of Environment and Sociobiology

Mohua Chakraborty ¹, S. K. Ghosh ¹, Bishal Dhar ¹, Bijoya Khomdram Devi ¹

Affiliations
1 DNA barcode and Genomics Laboratory, Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

Clarias batrachus is a species of freshwater catfish widely used for human consumption. Increasing demand of this species worldwide, coupled with its ability to survive in wide range of environmental conditions, has led to its introduction in many countries. This widespread translocation and distribution of C. batrachus have resulted in the rise of wide variety of haplotypes of this species. Nevertheless, there has been constant decrement in their population density in the last two decades. Thus, to endeavour conservation of the species we employ molecular technique of DNA barcoding in solving the standing problem of crypticism and haplotype sharing of the species. A better knowhow of the genetic makeup of the unique identifier region, that is, the 648 basepair region of COI DNA barcode will help to differentiate among closely related species and identify endemic species. In this study, a comparative analysis of C. batrachus from different regions in India and other parts of world shows presence of distinct haplotypes in different geographical locations. We also present a descriptive study of the various species of Clarias genus that have been barcoded in India till date. Our results also solve the dilemma of considering some species as synonymy of C. batrachus.

Keywords

Clarias batrachus, Cytochrome C Oxidase Subunit I (COI), Genetic Diversity, Kimura's Two Parameter (K2P), Mean Divergence, Neighbour Joining Tree.

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Fazlur Rahman Talukdar ¹, Sankar K. Ghosh ¹, Ruhina S. Laskar ¹, Pradosh Mahadani ¹, Mohua Chakraborty ¹, Bishal Dhar ¹, M. Joyraj Bhattacharjee ¹

Affiliations
1 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

DNA markers (barcode) differentiate species based on their nucleotide sequence diversity among various species. In this study we analyzed the rate and pattern of nucleotide substitution and their consequent influence on the amino acid substitution patterns of the sequences used as barcode mitochondrial COI, cyt b and the exon 1 of nuclear IRBP gene for animals from 15 different species of vertebrates. The analysis shows unlike other codon positions, nucleotide substitution at the third codon position does not show strong correlation with the amino acid substitution, for the three gene sequences. Furthermore, COI gene shows a very low percentage of amino acid variability (15.38%) inspite of high percentage of variation in its nucleotide sequence (40.76%) as well as a significantly (p<0.0001) low level of amino acid sequence divergence than the other gene fragments under study. Interestingly among the compared sequences, a significantly conserved amino acid substitution pattern seems to be a unique feature of barcode region of the COI gene making it a more efficient marker for species identification. Hence, it was concluded that the property of species identification of these sequences is based upon the variable nature of third codon position.

Keywords

Species-Specific Marker, DNA Barcoding, Nucleotide Substitution, Codon Positions, Amino Acid Substitution.

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Mohua Chakraborty ¹, Sankar K. Ghosh ¹

Affiliations
1 Genomics and Bioinformatics Lab., Dept. of Biotechnology, Assam University, Silchar - 788011, Assam, IN

Abstract

Most animal mitochondrial genome exhibit strand asymmetry in nucleotide composition. Crustaceans represent a large diverse group of aquatic arthropods where the pattern of strand asymmetry is often violated with respect to the general pattern that is seen in most of the vertebrates and invertebrates. Most of the crustaceans show an overall strand asymmetry of negative GC skew, but AT skew varies randomly among species. Strand asymmetry in mitochondria is determined by the underlying spectrum of mutations. However, the substitution spectrum involved in crustacean mitogenome remains unclear. We present here a comparative analysis of various mitogenome features of 52 crustaceans' whole mitochondrial genome and elucidate the underlying substitution pattern. The observation reveals various asymmetries among the two strands and variation from the arthropod ground pattern as well. We found that substitution of adenine for guanine acts as the dominant phenomenon in shaping strand asymmetry in crustacean mitogenome. Moreover, the two strands show different bias for substitution pattern. And this phenomenon may have driven the translocation of the four genes (nad1, nad4, nad4l and nad5) in the minor coding strand in crustaceans and other invertebrates, which are otherwise located in the major coding strand in vertebrates. Additionally, the species that show wide variation in gene order from the crustacean ground pattern with a translocation or inversion of the control region seems to have different substitution pattern. Thus, our results demonstrate how the observed substitution pattern shapes various mitogenome features of crustaceans.

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