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Mitochondrial DNA
The Journal of DNA Mapping, Sequencing, and Analysis
Volume 26, 2015 - Issue 1
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Research Articles

A comparative study of COI and 16 S rRNA genes for DNA barcoding of cultivable carps in India

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Pages 79-87 | Received 07 May 2013, Accepted 04 Jul 2013, Published online: 19 Sep 2013

References

  • Ardura A, Linde AR, Moreira JC, Vazquez EG. (2010). DNA barcoding for conservation and management of Amazonian commercial fish. Biol Consr 143:1438–43
  • Bartlett SE, Davidson WS. (1992). FINS (forensically informative nucleotide sequencing): A procedure for identifying the animal origin of biological specimens. Biotechniques 12:408–11
  • Bej D, Sahoo L, Das SP, Swain S, Jayasankar P, Das PC, Routray P, et al. (2012). Complete mitochondrial genome sequence of Catla catla and its phylogenetic consideration. Mol Biol Rep 39:10347–54
  • Briolay J, Galtier N, Brito RM, Bouvet Y. (1998). Molecular phylogeny of Cyprinidae inferred from cytochrome b DNA sequences. Mol Phylogenet Evol 9:100–8
  • Chauhan T, Rajiv K. (2010). Molecular markers and their applications in fisheries and aquaculture. Adv Biosci Biotechnol 1:281–91
  • Comi G, Iacumin L, Rantsiou K, Cantoni C, Cocolin L. (2005). Molecular methods for the differentiation of species used in production of cod-fish can detect commercial frauds. Food Control 16:37–42
  • Cui Z, Liu Y, Liu J, Luan W. (2010). Molecular identification of Pampus fishes (Perciformes, Stromateidae). Ichthyol Res 57:32–9
  • Di Finizio A, Guerriero G, Russo G, Ciarcia G. (2007). Identification of gadoid species (Pisces, Gadidae) by sequencing and PCRRFLP analysis of mitochondrial 12S and 16S rRNA gene fragments. Eur Food Res Technol 225:337–44
  • Gharrett AJ, Gray AK, Heifetz J. (2001). Identification of rockfish (Sebastes spp.) by restriction site analysis of the mitochondrial ND-3/ND-4 and 12S/16S rRNA gene regions. Fish Bull 99:49–62
  • Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PD. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci USA 103:968–71
  • Hall TA. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41:95–8
  • He S, Mayden RL, Wang X, Wang W, Tang KL, Chen WJ, Chen Y. (2008). Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: Further evidence from a nuclear gene of the systematic chaos in the family. Mol Phylogenet Evol 46:818–29
  • Hebert PD, Cywinska A, Ball SL, Dewaard JR. (2003). Biological identifications through DNA barcodes. Proc Biol Sci 270:313–21
  • Hebert PD, Penton EH, Burns JM, Janzen DH, Hallwachs W. (2004a). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812–17
  • Hebert PD, Stoeckle MY, Zemlak TS, Francis CM. (2004b). Identification of birds through DNA barcodes. PLoS Biol 2:1657--63
  • Hubalkova Z, Kralik P, Tremlova B, Rencova E. (2007). Methods of gadoid fish species identification in food and their economic impact in the Czech Republic: A review. Vet Med 52:273–92
  • Karlsson AO, Holmlund G. (2007). Identification of mammal species using species-specific DNA pyrosequencing. Forensic Sci Int 173:16–20
  • Kimura M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–20
  • Kitano T, Umetsu K, Tian W, Osawa M. (2007). Two universal primer sets for species identification among vertebrates. Int J Legal Med 121:423–7
  • Lakra WS, Goswami M, Gopalakrishnan A. (2009). Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: Perciformes, Sciaenidae) based on 16S rRNA and cytochrome c oxidase subunit I mitochondrial genes. Mol Biol Rep 36:831–9
  • Librado P, Rozas J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–2
  • Linacre A, Tobe SS. (2011). An overview to the investigative approach to species testing in wildlife forensic science. Investig Genet 2:2. doi: 10.1186/2041-2223-2-2
  • Lockley AK, Bardsley RG. (2000). DNA-based methods for food authentication. Trends Food Sci Technol 11:67–77
  • Luca C, Manea A, Luca A, Dinischiotu A, Costache M. (2008). Molecular phylogeny of the Romanian cyprinids from the Danube River. Roumanian Biotechnological Lett 13:3970–5
  • Manna GK, Khuda Bukhsh AR. (1977). Karyomorphology of cyprinid fishes and cytological evaluation of the family. Nucleus 20:119–27
  • Nelson JS. (1994). Fishes of the world. New York: John Wiley and Sons
  • Palumbi SR. (1996). Nucleic acids II: The polymerase chain reaction. In: Hillis DM, Moritz C, Mable BK, editors. Molecular systematics. Sunderland: Sinauer Associates, Inc. p 205--47
  • Persis M, Chandra Sekhar Reddy A, Rao LM, Khedkar GD, Ravinder K, Nasruddin K. (2009). COI (cytochrome oxidase-I) sequence based studies of Carangid fishes from Kakinada coast, India. Mol Biol Rep 36:1733–40
  • Ratnasingham S, Hebert PD. (2007). The barcode of life data system (http://www.barcodinglife.org). Mol Ecol Notes 7:355–64
  • Sambrook J, Fritsch EF, Maniatis T. (1989). Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press
  • Sasaki T, Kartavtsev YP, Chiba SN, Uematsu T, Sviridov VV, Hanzawa N. (2007). Genetic divergence and phylogenetic independence of Far Eastern species in subfamily Leuciscinae (Pisces: Cyprinidae) inferred from mitochondrial DNA analyses. Genes Genet Syst 82:329–40
  • Shirak A, Cohen-Zinder M, Barroso RM, Seroussi E, Ron M, Hulata G. (2009). DNA Barcoding of Israeli Indigenous and Introduced Cichlids. The Israeli J Aquaculture – Bamidgeh 61:83–8
  • Smith MA. (2008). Using DNA barcodes to assessidentity and diversity of Dendropsophus minutus: Failure? Zootaxa 1691:67–8
  • Smith PJ, Mcveagh SM, Steinke D. (2008). DNA barcoding for the identification of smoked fish products. J Fish Biol 72:464–71
  • Spies IB, Gaichas S, Stevenson DE, Orr JW, Canino MF. (2006). DNA-based identification of Alaska skates (Amblyraja, Bathyraja and Raja: Rajidae) using cytochrome c oxidase subunit I (COI) variation. J Fish Biol 69:283–92
  • Talwar PK, Jhingran AG. (1991). Inland fishes of India and adjacent countries. 1st ed. New Delhi: Oxford & IBH Pub. Co
  • Tamura K, Dudley J, Nei M, Kumar S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–9
  • Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–80
  • Vences M, Thomas M, Bonett RM, Vieites DR. (2005a). Deciphering amphibian diversity through DNA barcoding: Chances and challenges. Philos Trans R Soc Lond B Biol Sci 360:1859–68
  • Vences M, Thomas M, Van Der Meijden A, Chiari Y, Vieites DR. (2005b). Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool 2:5(1--12)
  • Ward RD, Holmes BH, Yearsley GK. (2008). DNA barcoding reveals a likely second species of Asian sea bass (barramundi) (Lates calcarifer). J Fish Biol 72:458–63
  • Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. (2005). DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci 360:1847–57
  • Wilson EO. (2003). The encyclopedia of life. Trends Ecol Evol 18:77–80
  • Xia X, Xie Z. (2001). DAMBE: Software package for data analysis in molecular biology and evolution. J Heredity 92:371–3
  • Xia Y, Gu HF, Peng R, Chen Q, Zheng YC, Murphy RW, Zeng XM. (2012). COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae). Mol Ecol Resour 12:48–56
  • Yu C, Song Z, Yue B. (2006). Taxonomic implications from phylogenetic relationships of subspecies of Schizopygopsis malacanthus (Pisces: Cyprinidae) based on sequence analysis of cytochrome b and mitochondrial DNA control region. J Nat Hist 40:2569–76
  • Zardoya R, Economidis PS, Doadrio I. (1999). Phylogenetic relationships of Greek cyprinidae: Molecular evidence for at least two origins of the Greek cyprinid fauna. Mol Phylogenet Evol 13:122–31
  • Zhang SM, Reddy PVGK. (1991). On the comparative karyomorphology of three Indian major carps, Catla catla (Hamilton), Labeo rohita (Hamilton) and Cirrhinus mrigala (Hamilton). Aquaculture 97:7–12

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