Journal of Environment and Sociobiology

Prabal Ranjan Ghosh ¹, Pradosh Mahadani ², Rosy Mondal ², Pradip Kumar Das ¹, Sankar Kumar Ghosh ²

Affiliations
1 West Bengal University of Animal and Fishery Sciences, Kolkata-700037, West Bengal, IN
2 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

Poultry biodiversity widely prevails over the world, especially in Indian subcontinent as domestic indigenous fowl. Cross species hybridization of different Gallus species confers ambiguity in proper classification. Molecular approach using DNA barcoding to identify species boundaries is successfully employed to detect hybridization signal of nondescript indigenous fowls. In the present study DNA barcoding region of cytochrome oxidase I (COI) gene collected from geographically distant region of five agroclimatic zones of eastern India is amplified using PCR, sequenced and subsequently deposited in GenBank. Related sequences were retrieved from global databases for phylogenic analysis using bioinformatics. The present study provides for the first time the DNA barcodes of domestic fowls from eastern India and established that the domestic fowls are grouped within the group Gallus gallus. Additional COI sequences within the same and related genus collected from different countries properly discriminate and assign their correct taxonomic positions. Low level of interspecies variation was observed between Gallus gallus and Gallus sonneratii indicating the failure to discriminate them as separate species.

Keywords

DNA Barcoding, Poultry, Gallus Gallus, MtDNA, Cytochrome Oxidase I, Genbank.

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Prabal Ranjan Ghosh ¹, Monika Ahanthem ², Pradosh Mahadani ², Amalesh Choudhury ³, Sankar Kumar Ghosh ²

Affiliations
1 West Bengal University of Animal and Fishery Sciences, Kolkata-700037, West Bengal, IN
2 Department of Biotechnology, Assam University, Silchar-788011, IN
3 S. D. Marine Institute, Sunderban, West Bengal, IN

Abstract

Chicken domestication plays an important role for major supply of animal protein throughout the world. In India, wide diversities of domestic chicken are descended from wild red jungle fowl (RJF) (Gallus gallus), the mother of all fowls of the world. In the present study, DNA barcode sequence and cytochrome c oxidase subunit I (COI) region of wild RJF from northeastern India using PCR are determined, sequenced and subsequently deposited in GenBank (Accession No. JN793568). The study provides for the first time the DNA barcodes of red jungle fowl from northeastern India and subsequent bioinformatics yield that the RJF is grouped within correct taxonomic assignment of other Gallus species proving strong resolving power of DNA barcode in chicken.

Keywords

Cytochrome C Oxidase Subunit I, DNA Barcodes, Red Jungle Fowl, Gallus gallus, Northeastern India.

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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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