Abstract
DNA barcoding was a molecular diagnostic method that provided rapid and accurate species identification. The 650 bp-length cytochrome c oxidase subunit I (COI) gene of 33 species in Irtysh River China was sequenced and analyzed in this study. The average intra-species, -genus, -family, and -order of Kimura two parameter (K2P) distances were 0.003, 0.060, 0.163 and 0.240, respectively. The genetic distance between genus Barbatula and Cobitis was the largest whereas that between genus Hypophthalmichthys and Aristichthys was the smallest. The neighbour-joining tree constructed by all 44 haplotypes was divided into two major clusters: Cypriniformes fishes and other fishes. A cryptic species of Barbatula barbatula was detected according to 2% genetic threshold.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Ren, M.L., Guo, Y., and Zhang, R.M., et al., Fisheries Resources and Fishery of the Ertixhe River in China, Urumqi: Xinjiang Health Science and Technology Publishing House, 2002, pp. 1–8.
Wu, X.W., Yang, G.R., and Le, P.Q., et al., China’s Economic Animals: Freshwater Fishes, Beijing: Science Press, 1963.
Wu, X.W., The Cyprinid Fishes of China, Shanghai: Shanghai Science and Technology Press, 1964.
Li, S.Z., Dai, D.Y., and Zhang, S.Y., et al., Notes on a collection of fishes from north Sinkiang, China, Acta Zool. Sin., 1966, vol. 18, no. 1 pp. 41–56.
Institute of Zoology, Pedology and Desert Research institute of Xinjiang and Xinjiang Bureau of Aquatic Products, Fishes of Xinjiang, Urumqi: Xinjiang People’s Publishing House, 1979.
Hebert, P.D., Cywinska, A., and Ball, S.L., et al., Biological identifications through DNA barcodes, Proc. R. Soc. B, 2003, vol. 270, pp. 313–322.
Shneyer, V.S., DNA barcoding is a new approach in comparative genomics of plants, Russ. J. Genet., 2009, vol. 45, no. 11 pp. 1267–1278.
Waugh, J., DNA barcoding in animal species: progress, potential and pitfalls, BioEssays, 2007, vol. 29, pp. 188–197.
Kwong, S., Srivathsan, A., and Meier, R., An update on DNA barcoding: low species coverage and numerous unidentified sequences, Cladistics, 2012, vol. 28, pp. 639–644.
Sharina, S.N., and Kartavtsev., Y.P., Phylogenetic and taxonomic analysis of flatfish species (Teleostei,Pleuronectiformes) inferred from the primary nucleotide sequence of cytochrome oxidase 1 gene (Co-1), Russ. J. Genet., 2010, vol. 46, no. 3 pp. 401–407.
Andrianov, B. V., Goryacheva, I. I., and Vlasov, S. V., et al., Identification of potentially invasive species of black flies [Diptera: Simuliidae] from Armenia based on an analysis of variability in the mtDNA barcode of the cox1 gene and chromosomal polymorphism, Russ. J. Genet., 2015, vol. 51, no. 3 pp. 351–361.
Miller, S.E., DNA barcoding and the renaissance of taxonomy, Proc. Natl. Acad. Sci., 2007, vol. 104, no. 12 pp. 4775–4776.
Ward, R.D., Hanner, R., and Hebert, P.D., The campaign to DNA barcode all fishes, FISH-BOL, J. Fish Biol., 2009, vol.74, pp. 329–356.
Barmintseva, A.E. and Mugue, N.S., The use of microsatellite loci for identification of sturgeon species (Acipenseridae) and hybrid forms, Russ. J. Genet., 2013, vol. 49, no. 9 pp. 950–961.
Fang, H.H., Zhang, J.L., and Song, N., et al., Population genetic structure and geographical differentiation of burbot (Lota lota) in China, Russ. J. Genet., 2013, vol. 49, no. 10 pp. 1047–1056.
Sakai, H., Iguchi, K., and Yamazaki, Y., et al., Morphological and mtDNA sequence studies on three crucian carps (Carassius: Cyprinidae) including a new stock from the Ob River system, Kazakhstan, J. Fish Biol., 2009, vol. 74, no. 8 pp. 1756–1773.
Alekseev, S.S. and Osinov, A.G., Blunt-snouted lenoks (genus Brachymystax: Salmoniformes, Salmonidae) from the Ob’ basin: new data on morphology and allozyme variation, J. Ichthyol., 2006, vol. 46, no. 7 pp. 500–516.
Zhigileva, O.N., Ozhirel’ev, V.V., and Brol’, I.S., et al., Populational structure of three fish species (Cypriniformes: Cyprinidae) living in rivers of the Ob–Irtysh basin, by the data of isoenzyme analysis, J. Ichthyol., 2010, vol. 50, no. 9 pp. 778–787.
Maniatis, T., Fritsch, E.F., and Sambrook, J., Molecular Cloning: a Laboratory Manual, New York: Cold Spring Harbor Laboratory, 1982.
Ward, R.D., Zemlak, T.S., and Innes, B.H., et al., DNA barcoding Australia’s fish species, Proc. R. Soc. B, 2005, vol. 360, pp. 1847–1857.
Kimura, M., A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences, J. Mol. Evol., 1980, vol. 16, pp. 111–120.
Tamura, K., Stecher, G., and Peterson, D., et al., MEGA6: Molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 2013, vol. 30, no.12, pp. 2725–2729.
Bickford, D., Lohman, D.J., Sodhi, N.S., et al., Cryptic species as a window on diversity and conservation, Trends Ecol. Evol., 2007, vol. 22, no. 3, pp.148–155.
Herbert, P.N., Stoeckle, M.Y., and Zemlak, T.S., et al., Identification of birds through DNA barcodes, PloS Biol., 2004, vol. 2. e312
Hubert, N., Hanner, R., and Holm, E., et al., Identifying Canadian freshwater fishes through DNA barcodes, PLoS One, 2008, vol.3, no. 6. e2490.
Kim, S., Eo, H.S., and Koo, H., et al., DNA barcodebased molecular identification system for fish species, Mol. Cells, 2010, vol. 30, no. 6 pp. 507–512.
Zhu, S.Q., The Loaches of the Subfamily Nemacheilinae in China, Nanjing: Jiangsu Science and Technology Press, 1989, pp. 29–31.
Eschmeyer, W. N. and Fricke, R., Catalog of fishes. Updated internet version as of 30 November 2011, Catalog databases of CAS cited in FishBase, 2011, website.
Chen, Y.Y., Systematic studies on the fishes of the family Homalopteridae of China: 3. Phyletic studies of the homalopterid fishes, Acta Zootaxon. Sin., 1980, vol. 5, no. 2 pp. 200–211.
Zhu, S.Q., The Synopsis of Freshwater Fishes of China, Nanjing: Jiangsu Science and Technology Press, 1995.
Sawada, Y., Phylogeny and zoogeography of the superfamily Cobitoidea (Cyprinoidei, Cypriniformes), Mem. Fac. Fish. Hokkaido Univ., 1982, vol. 28, no. 2 pp. 65–223.
Nelson, J.S., Fishes of the World, New York: Wiley, 1994.
Kottelat, M., Botia kubotai, a new species of loach (Teleostei:Cobitidae) from the Ataran River basin (Myanmar), with comments on botiine nomenclature and diagnosis of a new genus, Zootaxa, 2004, vol. 401, pp. 1–18.
Nalbant, T.T., Sixty million years of evolution: 1. Family Botiidae (Pisces: Ostariophysi: Cobitidae). Trav. Mus. Hist. Nat. “Grigore Antipa”, 2002, vol. 44, pp. 343–379.
Howes, G., Anatomy and phylogeny of the Chinese major carps Ctenopharyngodon Steind., 1866 and Hypophthalmichthys Blkr., 1980, Bull. Br. Mus. (Nat. Hist.), Zool., 1981, vol. 41, pp. 1–52.
Kolar, C.S., Chapman, D.C., Courtenay, W.R., et al., Bigheaded carps, a biological synopsis and environmental risk assessment, American Fisheries Society Special Publication, 2007, p. 33.
Cheng, Q.T. and Zheng, B.S., Systematic Synopsis of Chinese Fishes, Beijing: Science, 1987.
Wu, X.W., Fishes of Cyprinidae in China. Shanghai: Shanghai Scientific Press, 1964.
Li, S.F., Xu, J.W., and Yang, Q.L., et al., A comparison of complete mitochondrial genomes of silver carp Hypophthalmichthys molitrix and bighead carp Hypophthalmichthys nobilis: implications for their taxonomic relationship and phylogeny, J. Fish Biol., 2009, vol. 74, pp. 1787–1803.
Avise, J.C., Phylogeography: the History and Formation of Species, Cambridge: Harvard University Press, 2000.
Brown, W.M., The mitochondrial genome of animals, in Molecular evolutionary genetics, New York: Plenum, 1985, pp. 95–130.
Ward, R.D. and Holmes, B.H., An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes, Mol. Ecol. Notes, 2007, vol. 7, no. 6 pp. 899–907.
Clayton, D.A., Replication of animal mitochondrial DNA, Cell, 1982, vol. 28, no. 4 pp. 693–705.
Grantham, R., Gautier, C., and Gouy, M., et al., Codon catalog usage and the genome hypothesis, Nucleic Acids Res., 1980, vol. 8, no. 1 pp. 49–62.
Knebelsberger, T., Dunz, A.R., and Neumann D., et al., Molecular diversity of Germany’s freshwater fishes and lampreys assessed by DNA barcoding, Mol. Ecol. Resour., 2015, vol. 15, no. 3 pp. 562–572.
Inoue, J., Miya, M., and Tsukamoto, K., et al., Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the’ ancient fish’, Mol. Phylogenet. Evol., 2003, vol. 26, no. 1, pp.110–120.
Zhang, D., Lei, G.C., and Gong, C., et al., Genetic diversity of Neosalanx taihuensis based on mitochondrial COI sequences, J. Lack Sci., 2012, vol. 24, no. 2 pp. 299–306.
Author information
Authors and Affiliations
Corresponding author
Additional information
The article is published in the original.
Rights and permissions
About this article
Cite this article
Yang, T., Meng, W., Zhang, R. et al. DNA barcoding of fishes in Irtysh River China. Russ J Genet 52, 969–976 (2016). https://doi.org/10.1134/S1022795416090167
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S1022795416090167