Journal of Environment and Sociobiology

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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Maloyjo J. Bhattacharjee ¹, Boni A. Laskar ¹, Bishal Dhar ¹, Sankar K. Ghosh ¹

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

Abstract

Cytochrome c oxidase (COI) DNA barcode is considered to be universal species identifier for animals based on many superlative features, but none has considered the pattern of characteristic nucleotide variation for their role if any. In this study, 50 COI barcode sequences of 10 species of catfishes were analyzed in two steps. In the first step, accurate delineation of species was confirmed while the second step involves analysis of the nucleotide variability in terms of transition and transversion at the different taxon levels and their subsequent effect on genetic divergence. The analysis revealed that the individuals within all the species exhibit distinct barcode cluster and a straight forward divergence at the congeneric (17.4% ± 1.8%) and conspecific level (0.7% ± 0.3%) allowing their unambiguous identification. Transition was found to be significantly higher (t= 4.85 - 41.12, p<0.0001) than transversion at all the three taxon levels. However, as transversion showed a significant increase (0.47 ± 0.38, 29.65 ± 5.12 and 34.21 ± 5.50) with the increase in taxon comparison (conspecific, congeneric and intergeneric), transition only showed a significant rise (t= 119.6, p<0.00001) between the conspecific (1.64 ± 0.76) and congeneric level (54.96 ± 6.75) and then transition became saturated at the intergeneric level (54.83 ± 6.68). The study importantly revealed that the genetic divergence between the congeners at the partial fragment of COI was highly correlated (Pearson correlation, R= 0.935, P<0.001) with transversional substitution than with transition (R= 0.334, P<0.05). Hence, although transition is more frequent, still transversional substitution within the COI barcode sequence plays the key role in species delineation.

Keywords

COI, DNA Barcode, Nucleotide Substitution, Transition, Transversion.

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Subrata Trivedi ¹, Sankar K. Ghosh ², Amalesh Choudhury ³

Affiliations
1 Department of Biology, University of Tabuk, Ministry of Higher Education, SA
2 Department of Biotechnology, School of Life Science, Assam University, Silchar-788011, Assam, IN
3 S. D. Marine Biological Research Institute, Sagar Island 743373, Sunderbans, West Bengal, IN

Abstract

Genomic DNA of COI region of an Oyster, Saccostrea cucullata, collected from Indian Sunderbans was extracted and amplified through PCR, which produced 678 by PCR amplicon. The purified PCR product was sequenced using automated DNA Sequencer (ABI 7300) and deposited to NCBI with accession number FJ 262984.

Keywords

Cytochrome C Oxidase Subunit 1 (COI), DNA Barcode, Sunderbans, Saccostrea cucullata.

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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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Subrata Trivedi ¹, Sankar K. Ghosh ², Amalesh Choudhury ³

Affiliations
1 Department of Biology, University of Tabuk (Under Ministry of Higher Education), SA
2 Department of Biotechnology, School of Life Science, Assam University, Silchar-788011, Assam, IN
3 S. D. Marine Biological Research Institute, Sagar Island 743373, Sunderbans, West Bengal, IN

Abstract

COI region of the prawn Macrobrachium rosenbergii, collected from Indian part of Sunderbans has been amplified. PCR with extracted DNA produced 642 bp PCR amplicon. The DNA sequence has been deposited to NCBI with accession number FJI71913.

Keywords

Cytochrome C Oxidase Subunit 1 (COI), DNA Barcode, Sunderbans, Macrobrachium rosenbergii.

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Subrata Trivedi ¹, Sankar K. Ghosh ², Amalesh Choudhury ³

Affiliations
1 Department of Biology, University of Tabuk, Ministry of Higher Education, SA
2 Department of Biotechnology, School of Life Science, Assam University, Silchar-788011, Assam, IN
3 S. D. Marine Biological Research Institute, Sagar Island 743373, Sunderbans, West Bengal, IN

Abstract

Mitochondrial DNA of COI region of an oyster, Crassostrea cuttakensis, collected from Indian Sunderbans has been amplified. PCR with extracted DNA produced 675 bp PCR amplicon. The DNA sequence has been deposited to NCBI with accession number FJ 262988.

Keywords

Cytochrome C Oxidase Subunit 1 (COI), Dna Barcode, Sunderbans, Crassostrea Cuttakensis.

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Meghali M. Narjari ¹, Ananya Mazumder ², Raima Das ³, Silistina Narzari ¹, Sankar K. Ghosh ²

Affiliations
1 Bodoland University, Rangalikhata, Deborgaon, Assam-783370, IN
2 Assam University, Silchar, Silchar, Assam-788011, IN
3 InBOL Healthcare Educational Centre, Kolkata-700026, IN

Abstract

The orthopterans (grasshoppers, crickets, etc.) comprise one of the large orders of the class Insecta. As phytophagous some species of this order become important agricultural pests. Due to change in behaviour and appearance many of these insects seldom caused confusion in taxonomic identification of species. These confusions can largely be resolved by molecular characterization and DNA markers of the species. In this background a good number of orthopteran specimens from different localities and habitats of Assam state were selected for DNA barcode sequencing. A total of 1661 barcodes representing 369 species, including samples obtained from Northeast India, were evaluated for species delineation using several genealogical techniques like, Kimura 2-Parameter, Neighbor Joining, and Maximum Likelihood. Herein, we found 70% of the orthopteran species as straightforward instances, whereas 20 species exhibited cryptic diversity with intraspecies distances greater than the computed species delimitation threshold, i.e., 4.36%+ 0.9%. The remaining 90 species displayed interspecific genetic distance that is significantly lower than the estimated threshold, revealing ambiguous diversity. We also explored four putative species. This study has given new inputs to the taxonomic understanding of the Orthoptera by exploration of cryptic species. It points out also to the importance of DNA barcoding and molecular characterization of species, apart from the morphometric characteristics, in developing integrative taxonomy of insect species.

Keywords

Orthoptera, Northeast India, DNA Barcoding, Molecular Taxonomy, Phylogeny, Putative Species.

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