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Research Article

volume 53 issue 2 (february 2019) : 181-186,   Doi: 10.18805/ijar.B-3476

Molecular characterization of an indigenous barb Pethia manipurensis (Cyprinidae: Barbinae) from Manipur, India and its relationship with other cyprinid fishes inferring from mitochondrial cox1 gene sequences

N
N. Sobita
C
Ch. Basudha
S
S.K. Sharma
1ICAR Research Complex for NEH Region Manipur Centre Lamphelpat, Imphal-795 004, Manipur, India.
Cite article:- Sobita N., Basudha Ch., Sharma S.K. (2018). Molecular characterization of an indigenous barb Pethia manipurensis (Cyprinidae: Barbinae) from Manipur, India and its relationship with other cyprinid fishes inferring from mitochondrial cox1 gene sequences. Indian Journal of Animal Research. 53(2): 181-186. doi: 10.18805/ijar.B-3476.

ABSTRACT

Manipur is one of the north eastern states of India and it is rich in freshwater fish diversity. Among the small indigenous fishes of Manipur, Pethia manipurensis is an economically important fish having both food and ornamental value. For the taxonomic placement of this species among the cyprinid fishes, molecular characterization is conducted by using mitochondrial cox1 gene sequences. Partial sequences of mito. cox1 gene of thirty seven cyprinid species were down loaded from NCBI Genbank and the nucleotide sequence  602 bp were generated from two species i.e. Pethia manipurensis and Puntius sophore for present analysis. Here total 628 characters, 144, 459, 267 and 192 were conserved, variable, parsimony informative and singleton respectively. The average nucleotide frequencies are 26.4% (A), 29% (T), 26.4% (C), and 18.2% (G). The dendogram constructed by both Neighbour-Joining and Maximum Likelihood trees resulted in similar topologies with five clusters with eight sub-clusters which can indicate the taxonomic positions of Pethia manipurensis. 

REFERENCES

  1. Ball, S. L. and Armstrong, K. F. (2006). DNA barcodes for insect pest identification: a test case with tussock moths (Lepidopteran: Lymantriidae). Can. J. For. Res., 36: 337–350.
  2. Cavender, T. and Coburn, M. M. (1992). Phylogenetic relationships of North American Cyprinidea. In: Systematics, historical ecology and North American freshwater fishes. [Ed by Mayden, R. L.] Stanford University Press. Stanford. pp. 293–327.
  3. Chan, Y. C., Roos, C., Inoue-Murayama, M., Inoue, E. Shih, C. C., Pei, K. J. and Vigilant, L. (2010). Mitochondrial genome sequences effectively receal the phylogeny of Hylobates gibbons. PLoS One 5: e14419.
  4. Chen, X., Yue, P. and Lin, R. (1984). Major group within the family Cyprinidae and their phylogenetic relationships. Acta Zootaxon Sin. 9: 424-440.
  5. Collins, R. A., Armstrong, K. F., Meier, R., Yi, Y., Brown, S. D. J., Cruickshank, R. H., Keeling, S. and Johnston, C. (2012). Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS One 7 (1) : e28381. doi:10.1371/journal.pone. 0028381.
  6. FAO. (2003). Yearbook of fisheries statistic summary table. Available at: htt://ftp.fao.org/FI/STAT/summary/default.htm.
  7. Floyd, R., Abebe ,E., Papert, A. and Blaxter, M. (2002). Molecular barcodes for soil nematode identification. Molecular Ecology 11 (4): 839–850. DOI: 10.1046/j.1365- 294X.2002.01485.x
  8. Gilles, A., Lecointre, G., Miquelis, A., Loerstche,r M., Chappaz R. and Brun, G. (2001). Partial combination applied to phylogeny of European cyprinids using the mitochondrial control region. Mol. Phylogenet. Evol. 19 : 22-33.
  9. Gosline, W. A. (1978). Unbranched dorsal-fin rays and subfamily classification of the fish family Cyprinidae. Occas. Pap. Mus. Zool Univ. Mich. 684: 1-21.
  10. Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W. and Hebert, P. D. N. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl. Acad. Sci. USA. 103: 968–971.
  11. Herbet, P. D. N., Cywinska, A., Ball, S. L. and Waard, J. R. (2003a). Biological identifications through DNA barcodes. Proc. R. Soc. Lond., 270: 313-322.
  12. Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D .H. and Hallwachs, W. (2004a). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Asteraptes fulferator. Proc. Natl. Acad. of Sci. U.S.A. 101: 14812-14817.
  13. Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S. and Francis, C .M. ( 2004b). Identification of birds through DNA Barcodes. PLos Biology 2 e321.
  14. Hogg, I. D. and Hebert, P. D. N. (2004). Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes. Can. Zoo. 82(5): 749- 754. 
  15. Howes, G. (1991). Systermatics and biogeography: an overview. In: Win I., Nelson J., (Eds). Cyprinids fishes: systematic biology and exploitation. New York: Chapman and Hall, pp. 1-54.
  16. Hora, S. L. and Mukerji, D. D. (1934). Notes on fishes in Indian Museum. XXIII. On a collection of fish from the S.Shan States, Burma. Records of the Indian Museum, Calcutta 36(3): 353-370. 
  17. Hudson, R., Boos, D. D. and Kaplan, N. L. (1992). A statistical test for detecting population subdivision. Mol Biol Evol. 9:138-151. 
  18. Kottelat, M. (1999). Nomenclature of the genera Barbodes, Cyclocheilichthys, Rasbora and Chonerhinos (Teleostei: Cyprinidae and Tetraodontidae), with comments on the definition of the first reviser. The Raffles Bulletin of Zoology 47:591-600.
  19. Kullander, S. O. (2008). Five new species of Puntius from Myanmar (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters 19: 59-84. 
  20. Kullander, S. O. and Fang, F. (2005). Two new species of Puntius from northern Myanmar (Teleostei: Cyprinidae). Copeia 2005(2): 290- 302.
  21. Li, Y., Ren, Z., Shedlockm, A.M., Wu, J. Sang, L. and Tersing, T. (2013). High altitude adaptation of the Schizothoracine fishes (cyprinidae) revealed by the mitochondrial genome analysis. Gene 517:169-178.
  22. Liu, H .Z. and Chen, Y. J. (2003). Phylogeny of the East Asian cyprinids inferred from sequences of the mitochondrial DNA control region. Can. J. Zool. 81 : 1938-1946.
  23. Menon, A. G. K., Rema, D. K. and Vishwanath, W. (2000). A new species of Puntius (Cyprinidae: Ctprininae) from Manipur, India. J.Bombay Nat. His. Soc., 97(2): Aug.pp 263-268. 
  24. Myers, G. S. (1960). The mormyrid genera Hippopotamyrus and Cyphomyrus. Stanford ichthyol. Bull. 7(4). 123-125.
  25. Nelson, J. S. ( 2006). Fishes of the World. 4th ed. Hoboken (New Jersey, USA): John Wiley & Sons. xix+601 p.
  26. Rosenberg, M. S., Subramanian, S. and Kumar, S. (2003). Patterns of transitional mutation biases within and among mammalian genomes. Mol bio evo . 20(6):988-993. 
  27. Saitoh , K., Sado, T., Mayden, R. L., Hanzawa, N., Nakamura, K., Nishida, M. and Miya , M. (2006). Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J. Mol. Evol. 63: 826-841.
  28. Sobita, N. and Basudha, Ch. (2017). Molecular phylogeny of Barbin fishes of North-East India based on mitochondrial 16SrRNA gene sequences. Indian Journal of Animal Sciences, 51(6):1062-1065
  29. Smith, M. A., Woodley, N. E. Janzen, D. H., Hallwachs, W. and Hebert, P. D. N. (2006). DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae) Proc. Natl. Acad. Sci. USA. 103: 3657–3662. 
  30. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood evolutionary distance and maximum parsimony methods. Mol bio evo. 28(10):2731-2739. 
  31. Topal, M. D. and Fresco, J. R. (1976). Complementary base pairing and the origin of substitution mutations. Nature 263:285-293. 
  32. Vences, M., Thomas, Bonett, R. M. and Vieites, D. R. (2005). Deciphering amphibian diversity through DNA barcoding: chances and challenges. Phil. Trans. R. Soc. Lond. 360: 1859-1868.
  33. Vishwanath, W. (2014). Fishes of North East India : Workshop Manual National Workshop on Freshwater Fish Taxonomy, Manipur University and National Bureau of Fish Genetic Resources, Lucknow, India.
  34. Ward, R. D., Zemlak, T. S., H., Last P. R. and Hebert, P. D. N. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society Part B: Biological Sciences 360 (1462): 1847–1857. DOI: 10.1098/rstb.2005.1716
  35. Ward, R. D., Hanner, R. and Hebert, P. D. N. (2009). The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology 74 (2): 329–356. DOI: 10.1111/j.1095-8649.2008.02080. 
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    Research Article

    volume 53 issue 2 (february 2019) : 181-186,   Doi: 10.18805/ijar.B-3476

    Molecular characterization of an indigenous barb Pethia manipurensis (Cyprinidae: Barbinae) from Manipur, India and its relationship with other cyprinid fishes inferring from mitochondrial cox1 gene sequences

    N
    N. Sobita
    C
    Ch. Basudha
    S
    S.K. Sharma
    1ICAR Research Complex for NEH Region Manipur Centre Lamphelpat, Imphal-795 004, Manipur, India.
    Cite article:- Sobita N., Basudha Ch., Sharma S.K. (2018). Molecular characterization of an indigenous barb Pethia manipurensis (Cyprinidae: Barbinae) from Manipur, India and its relationship with other cyprinid fishes inferring from mitochondrial cox1 gene sequences. Indian Journal of Animal Research. 53(2): 181-186. doi: 10.18805/ijar.B-3476.

    ABSTRACT

    Manipur is one of the north eastern states of India and it is rich in freshwater fish diversity. Among the small indigenous fishes of Manipur, Pethia manipurensis is an economically important fish having both food and ornamental value. For the taxonomic placement of this species among the cyprinid fishes, molecular characterization is conducted by using mitochondrial cox1 gene sequences. Partial sequences of mito. cox1 gene of thirty seven cyprinid species were down loaded from NCBI Genbank and the nucleotide sequence  602 bp were generated from two species i.e. Pethia manipurensis and Puntius sophore for present analysis. Here total 628 characters, 144, 459, 267 and 192 were conserved, variable, parsimony informative and singleton respectively. The average nucleotide frequencies are 26.4% (A), 29% (T), 26.4% (C), and 18.2% (G). The dendogram constructed by both Neighbour-Joining and Maximum Likelihood trees resulted in similar topologies with five clusters with eight sub-clusters which can indicate the taxonomic positions of Pethia manipurensis. 

    REFERENCES

    1. Ball, S. L. and Armstrong, K. F. (2006). DNA barcodes for insect pest identification: a test case with tussock moths (Lepidopteran: Lymantriidae). Can. J. For. Res., 36: 337–350.
    2. Cavender, T. and Coburn, M. M. (1992). Phylogenetic relationships of North American Cyprinidea. In: Systematics, historical ecology and North American freshwater fishes. [Ed by Mayden, R. L.] Stanford University Press. Stanford. pp. 293–327.
    3. Chan, Y. C., Roos, C., Inoue-Murayama, M., Inoue, E. Shih, C. C., Pei, K. J. and Vigilant, L. (2010). Mitochondrial genome sequences effectively receal the phylogeny of Hylobates gibbons. PLoS One 5: e14419.
    4. Chen, X., Yue, P. and Lin, R. (1984). Major group within the family Cyprinidae and their phylogenetic relationships. Acta Zootaxon Sin. 9: 424-440.
    5. Collins, R. A., Armstrong, K. F., Meier, R., Yi, Y., Brown, S. D. J., Cruickshank, R. H., Keeling, S. and Johnston, C. (2012). Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS One 7 (1) : e28381. doi:10.1371/journal.pone. 0028381.
    6. FAO. (2003). Yearbook of fisheries statistic summary table. Available at: htt://ftp.fao.org/FI/STAT/summary/default.htm.
    7. Floyd, R., Abebe ,E., Papert, A. and Blaxter, M. (2002). Molecular barcodes for soil nematode identification. Molecular Ecology 11 (4): 839–850. DOI: 10.1046/j.1365- 294X.2002.01485.x
    8. Gilles, A., Lecointre, G., Miquelis, A., Loerstche,r M., Chappaz R. and Brun, G. (2001). Partial combination applied to phylogeny of European cyprinids using the mitochondrial control region. Mol. Phylogenet. Evol. 19 : 22-33.
    9. Gosline, W. A. (1978). Unbranched dorsal-fin rays and subfamily classification of the fish family Cyprinidae. Occas. Pap. Mus. Zool Univ. Mich. 684: 1-21.
    10. Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W. and Hebert, P. D. N. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl. Acad. Sci. USA. 103: 968–971.
    11. Herbet, P. D. N., Cywinska, A., Ball, S. L. and Waard, J. R. (2003a). Biological identifications through DNA barcodes. Proc. R. Soc. Lond., 270: 313-322.
    12. Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D .H. and Hallwachs, W. (2004a). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Asteraptes fulferator. Proc. Natl. Acad. of Sci. U.S.A. 101: 14812-14817.
    13. Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S. and Francis, C .M. ( 2004b). Identification of birds through DNA Barcodes. PLos Biology 2 e321.
    14. Hogg, I. D. and Hebert, P. D. N. (2004). Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes. Can. Zoo. 82(5): 749- 754. 
    15. Howes, G. (1991). Systermatics and biogeography: an overview. In: Win I., Nelson J., (Eds). Cyprinids fishes: systematic biology and exploitation. New York: Chapman and Hall, pp. 1-54.
    16. Hora, S. L. and Mukerji, D. D. (1934). Notes on fishes in Indian Museum. XXIII. On a collection of fish from the S.Shan States, Burma. Records of the Indian Museum, Calcutta 36(3): 353-370. 
    17. Hudson, R., Boos, D. D. and Kaplan, N. L. (1992). A statistical test for detecting population subdivision. Mol Biol Evol. 9:138-151. 
    18. Kottelat, M. (1999). Nomenclature of the genera Barbodes, Cyclocheilichthys, Rasbora and Chonerhinos (Teleostei: Cyprinidae and Tetraodontidae), with comments on the definition of the first reviser. The Raffles Bulletin of Zoology 47:591-600.
    19. Kullander, S. O. (2008). Five new species of Puntius from Myanmar (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters 19: 59-84. 
    20. Kullander, S. O. and Fang, F. (2005). Two new species of Puntius from northern Myanmar (Teleostei: Cyprinidae). Copeia 2005(2): 290- 302.
    21. Li, Y., Ren, Z., Shedlockm, A.M., Wu, J. Sang, L. and Tersing, T. (2013). High altitude adaptation of the Schizothoracine fishes (cyprinidae) revealed by the mitochondrial genome analysis. Gene 517:169-178.
    22. Liu, H .Z. and Chen, Y. J. (2003). Phylogeny of the East Asian cyprinids inferred from sequences of the mitochondrial DNA control region. Can. J. Zool. 81 : 1938-1946.
    23. Menon, A. G. K., Rema, D. K. and Vishwanath, W. (2000). A new species of Puntius (Cyprinidae: Ctprininae) from Manipur, India. J.Bombay Nat. His. Soc., 97(2): Aug.pp 263-268. 
    24. Myers, G. S. (1960). The mormyrid genera Hippopotamyrus and Cyphomyrus. Stanford ichthyol. Bull. 7(4). 123-125.
    25. Nelson, J. S. ( 2006). Fishes of the World. 4th ed. Hoboken (New Jersey, USA): John Wiley & Sons. xix+601 p.
    26. Rosenberg, M. S., Subramanian, S. and Kumar, S. (2003). Patterns of transitional mutation biases within and among mammalian genomes. Mol bio evo . 20(6):988-993. 
    27. Saitoh , K., Sado, T., Mayden, R. L., Hanzawa, N., Nakamura, K., Nishida, M. and Miya , M. (2006). Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J. Mol. Evol. 63: 826-841.
    28. Sobita, N. and Basudha, Ch. (2017). Molecular phylogeny of Barbin fishes of North-East India based on mitochondrial 16SrRNA gene sequences. Indian Journal of Animal Sciences, 51(6):1062-1065
    29. Smith, M. A., Woodley, N. E. Janzen, D. H., Hallwachs, W. and Hebert, P. D. N. (2006). DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae) Proc. Natl. Acad. Sci. USA. 103: 3657–3662. 
    30. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood evolutionary distance and maximum parsimony methods. Mol bio evo. 28(10):2731-2739. 
    31. Topal, M. D. and Fresco, J. R. (1976). Complementary base pairing and the origin of substitution mutations. Nature 263:285-293. 
    32. Vences, M., Thomas, Bonett, R. M. and Vieites, D. R. (2005). Deciphering amphibian diversity through DNA barcoding: chances and challenges. Phil. Trans. R. Soc. Lond. 360: 1859-1868.
    33. Vishwanath, W. (2014). Fishes of North East India : Workshop Manual National Workshop on Freshwater Fish Taxonomy, Manipur University and National Bureau of Fish Genetic Resources, Lucknow, India.
    34. Ward, R. D., Zemlak, T. S., H., Last P. R. and Hebert, P. D. N. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society Part B: Biological Sciences 360 (1462): 1847–1857. DOI: 10.1098/rstb.2005.1716
    35. Ward, R. D., Hanner, R. and Hebert, P. D. N. (2009). The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology 74 (2): 329–356. DOI: 10.1111/j.1095-8649.2008.02080. 
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