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Abstract
We explored fish fauna Ganga and Yamuna river in Uttarkashi district of Uttarakhand, to establish the molecular taxonomy database. A total of 133 samples were collected from various sampling sites along the entire stretch of rivers in district Uttarkashi. A region of cytochrome c-oxidase unit I (COI) gene (655 bp) was amplified using PCR and sequenced (DNA Barcoded). All the sequences have been uploaded into the NCBI GenBank (accession number assigned). Analysis of data generated showed that these 133 samples belonged to 22 species of 4 orders, 14 genera and 8 families. The genetic variability (K2P distance) distribution analysis was also carried out. The average mean distance of 22 species is 0.219 with 0.014 standard error. The mean genetic distance between 22 species ranged from 0.010%-0.362% while the mean genetic distance within the species ranged from 0.0006%- 0.0048%. The lowest pairwise genetic distance observed in Schizothorax sinuatus and Schizothorax progastus i.e. 0.010% with 0.003 standard error indicating a closer phylogenetic relationship between Schizothorax sinuatus and Schizothorax progastus than other species which was confirmed by the genetic distance data. Maximum divergence were observed between Danio devario and Channa gachua i.e. 0.362% with 0.028 standard error. The maximum sequence divergence within the species is observed in Barilius bendelisis with 0.0048% while minimum sequence divergence is observed in Tor putitora with 0.0006 of cyprinidae family. Our data suggests that there is high inter-specific sequence divergence as compared to intra-specific sequence divergence and also conclude that COI sequencing (barcoding) was found to be suitable for the identification of fresh water fish species.
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References
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References
Avise, J.C. 2004. Molecular Markers, Natural History and Evolution. 2nd ed., Sinauer Associates, Sunderland.
Billington, N. 2003. Mitochondrial DNA. E. M. Hallerman (Ed.), Population genetics: principles and applications for fisheries scientists. American Fisheries Society, Bethesda, Maryland: 59-100.
DeSalle, R. 2006. Species discovery versus species identification in DNA barcoding efforts: Response to Rubinoff. Cons. Biol. 20, 1545-1547.
DeSalle, R., Egan, M.G., Siddall, M. 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding. Phil. Trans. R. Soc. B 360, 1905-1916.
Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95-98.
Hebert, P.D.N.,Cywinska, A., Ball, S.L. & deWaard, J.R. 2003a. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B 270: 313–321.
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16: 111–120.
Lakra, W S, M S Verma, M Goswami, K K Lal, V Mohindra, P Punia, A Gopalakrishnan, K V Singh, R D Ward and P Hebert 2011. DNA barcoding Indian marine fishes. Molecular Ecology Resources 11(1): 60-71 (DOI: 1.1111/j.1755-0998.201.02894.x).
Park, L.K. and Moran, P. 1995. Developments in molecular genetic techniques in fisheries. G.R. Carvalho, and T.J. Pitcher (Eds.), Molecular Genetics in Fisheries. Chapman and Hall, London: 1-28
Tamura K., Stecher G., Peterson D., Filipski A., and Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6. Molecular Biology and Evolution 30: 2725-2729.
Ward R.D., R. Hanner and P.D.N. Hebert. 2009. The campaign to DNA barcode all fishes. FISH-BOL. Journal of Fish Biology 74:329-356.
Ward, R.D., Zemlak, T.S., Innes, B.H., Last, P.R. and Hebert, P.D.N. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society of London B. doi:1.1098/rstb.2005.1716 Published online.