DNA bar-coding of snow trout (Schizothorax plagiostomus) from Neelum and Jhelum rivers of Azad Jammu and Kashmir, Pakistan

Paper Details

Research Paper 01/01/2017
Views (204) Download (77)

DNA bar-coding of snow trout (Schizothorax plagiostomus) from Neelum and Jhelum rivers of Azad Jammu and Kashmir, Pakistan

Tasleem Akhtar, Nuzhat Shafi, Ghazanfar Ali
Int. J. Biosci.10( 1), 302-310, January 2017.
Certificate: IJB 2017 [Generate Certificate]


The mitochondrial Cytochrome oxidase 1 (CO1) gene is used as a standardized, authenticated and reliable genetic marker for a global species-level bio-identification system. The present study was conducted to examine COI gene for Schizothorax plagiostomus, from Azad Jammu and Kashmir, to determine whether barcoding can help accurate species identification in fishes. The overall base composition of Schizothorax species were A, 25.7%; C, 28.0%; T, 28.1% and G 18.1%, A+T content 53.7% and G+C content 46.1%. The Ts/Tv bias (R) was 1.70 and 7 haplotypes were observed. The average value of haplotype diversity was Hd: 0.944±0.07 and the average value of nucleotide diversity (Pi) was 0.0032±0.001. Short fragment (721) was amplified using PCR and sequenced from nine fish samples collected from river Neelum and Jhelum, and identification of species were done in Genbank and BOLD. Two variable characters were parsimony uninformative, and 4 variable characters were parsimony informative. The overall mean intra-specific distance was 0.03±0.001 and mean inter-specific nucleotide sequence divergence was 0.404%. We emphasized that, DNA barcoding is an accurate, reliable and has the great potential for identification of freshwater fish species. The ability to assign species with high precision from DNA samples of different quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity and its sustainability.


Altschul SF, Madden TL, Schaffer AA, Zhang J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.

Asgharian H, Sahafi HH, Ardalan AA, Shekarriz S, Elahi E. 2011. Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species. Molecular Ecology Resources 11, 461-472.

Balkhi MH. 2005. Fish diversity of Jammu and Kashmir and conservation. In: Patloo RA (ed) Kashmir speaks. G. M. Publishers, Kashmir pp. 104-118.

Chen YF, Cao WY. 2000. Schizothoracinae. Fauna Sinica, Osteichthyes, Cypriniformes III. In: Yue P (ed) Science Press, Beijing. pp. 273.335.

Costa FO, deWaard JR, Boutillier JS, Ratnasingham, Dooh RT, Hajibabaei M, Herbert PD. 2007. Biological identifications through DNA barcodes: the case of the Crustacea. Canadian Journal of Fisheries and Aquatic Sciences 64, 272-295.

Elmeer K, Almalki A, Mohran KA, AL-Qahtani KN, Almarri M. 2012. DNA barcoding of Oryx leucoryx using the mitochondrial cytochrome C oxidase gene. Genetics and Molecular Research 11(1), 539-547.

Goel C, Barat A, Pande V, Ali S, Kumar R. 2011. Length-weight relationship of snow trout (Schizothorax richardsonii) based on linear and nonlinear models from hill stream of Uttarakhand, India. World Journal of Fish and Marine Sciences 3(6), 485-488.

Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, Hebert PDN. 2006. A minimalist barcode can identify a specimen whose DNA is degraded. Journal of Molecular Ecological Notes 6, 959-964.

He D, Chen Y. 2006. Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences. Journal of Biogeography 33, 1448-1460.

Hebert PDN, Cywinska A, Ball SL, Waard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London 270, 313-322.

Hebert PDN, Gregory TR. 2005. The promise of DNA barcoding for taxonomy. 254 Systematic Biology 54, 852-859.

Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. 2004. Ten species in one: DNA barcoding reveals cryptic species in the Neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences 101(41), 14812-14817.

Jhingran VG. 1982. Fish and Fisheries of India. Hindustan Publishing Corporation, India.

Jiang Y, Zhang S, Feng S, Sun J, Xu P. 2014. Genome wide identification, phylogeny and expression of zinc transporter genes in common carp. PLoS One 9, e116043.

Kelly RP, Sarkar IN, Eernisse DJ, Desalle R. 2007. DNA barcoding using chitons (genus Mopalia). Molecular Ecological Notes 7, 177-183.

Khan MF, Khattak MNK, He DK, Liang YY, Li C, Dawar F, Chen YF. 2015. The complete mitochondrial genome organization of Schizothorax plagiostomus (Teleostei: Cyprinidae) from Northern Pakistan. Mitochondrial DNA 1-3.

Kullander SO, Fang F, Delling B, Ahlander E. 1999. The fishes of the Kashmir Valley. In: Nyman L (Ed) River Jhelum, Kashmir Valley. Impact on the aquatic environment, Swedmar pp. 99-162.

Mikkelsen NT, Schander C, Willassen E. 2007. Local scale DNA barcoding of bivalves (Mollusca): a case study. Journal of Zoologica Scripta 36(5), 455-463.

Mirza MR. 1991. A contribution to the systematics of the Schizothoracine fishes (Pisces: Cyprinidae) with the description of three new tribes. Pakistan Journal of Zoology 23, 339-341.

Perez-Martin RI, Sotelo CG. 2003. Authenticity of species in meat and seafood products. Eduardo Cabello, Spain: Association International Congress on Authenticity of Species in Meat and Seafood Products. Advances in Animal and Veterinary Sciences 3(6), 334-346.

Qi D, Guo S, Tang J, Zhao X, Liu J. 2007. Mitochondrial DNA phylogeny of two morphologically enigmatic fishes in the subfamily Schizothoracinae (Teleostei: Cyprinidae) in the Qinghai-Tibetan Plateau. Journal of Fish Biology 70, 60-74.

Raina HS, Petr T. 1999. Coldwater fish and fisheries in the Indian Himalayas: lakes and reservoirs. In: Petr T (ed) Fish and fisheries at higher altitude: Asia. FAO Fish. Tech. Pap. No. 385. FAO, Rome pp 64-88.

Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406-425.

Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, New York, p 1659. ISBN. 087969-309-6.

Silas EG. 1960. Fishes from the Kashmir valley. Journal of Bombay Natural History Society 57(1), 66-77.

Sunder S, Bhagat MJ. 1979. A note on the food of Schizothorax plagiostomus (McClelland) in the Chenab drainage of Jammu Province during 1973-74. Journal Inland Fish Society India 11(1), 117-118.

Talwar PK, Jhingran AG. 1991. Inland fishes of India and adjacent countries. Oxford and IBH Publishing, New Delhi.

Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP. 2002. DNA points the way ahead in taxonomy. Nature pp. 418-479.

Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP. 2003. A plea for DNA taxonomy. Trends in Ecology and Evolution 18, 70-74.

Tsigenopoulos CS, Berredi P. 2000. Molecular phylogeny of North Mediterranean freshwater barbs genus Barbus: Cyprinidae) inferred from cytochrome bsequences: biogeographic and systematic implications. Molecular Phylogenetics and Evolution 14, 165-179.

Tzeng CS, Hui CF, Shen SC, Huang PC. 1992. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: Conservation and variations among vertebrates. Nucleic Acids Research 20, 4853-8.

Wheeler QD. 2005. Losing the plot: DNA ‘barcodes’ and taxonomy. Cladistics 21, 405-407.

Wu YF, Wu CZ. 1992. The Fishes of the Qinghai-Xizang Plateau, Chengdu: Sichuan Publishing House of Science and Technology.

Zhang DX, Hewitt GM. 1996. Nuclear integrations: Challenge for mitochondria DNA markers. Trends in Ecology and Evolution 11, 247-251.

Zhu YX, Chen Y, Cheng QQ, Qiao HY, Chen WM. 2012. The complete mitochondrial genome sequence of Schizothorax macropogon (Cypriniformes: Cyprinidae). Mitochondrial DNA 24, 237-9.