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Sequencing of COI gene in four rodent pests for species identification

Rengarajan Rengasamy Lakshminarayanan
  • Corresponding author
  • Center for Pheromone Technology, Department of Animal Science, Bharathidasan University,Tiruchirappalli-620 024, India
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Achiraman Shanmugam
  • Corresponding author
  • Department of Environmental Biotechnology, Bharathidasan University,Tiruchirappalli-620 024, India
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Archunan Govindaraju
  • Corresponding author
  • Center for Pheromone Technology, Department of Animal Science, Bharathidasan University,Tiruchirappalli-620 024, India
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2015-03-30 | DOI: https://doi.org/10.1515/dna-2015-0001


Among mammals, rodents are the most important group since they influence the crop production and protection. Species identification of rodents on morphometric parameters is cumbersome and often misleading. However, DNA based identification would enable accurate species identification. For this purpose, we examined 650 bp of Cytochrome c oxidase subunit1 (COI) in four rodent pest species namely Bandicota indica, Milardia meltada, Rattus rattus and Tatera indica. Our results show the maximum identity for Bandicota indica and Rattus rattus within the species. For T. indica the maximum similarity was observed with gerbillinae species and M. meltada showed the maximum identity with B. indica. The result indicates that COI based identification can serve as an accurate and reliable tool in the identification of rodent pest species.

Keywords : Species identification; COI gene; Rodent pest; DNA Barcode; BLAST


  • [1] Baker R.J., Bradley R.D., Speciation in mammals and the genetic species concept, J. Mammal., 2006, 87, 643-662 CrossrefGoogle Scholar

  • [2] Musser G., Carleton M., Super family Muroidea, In: Wilson D.E., Reeder D.M. (Eds.), Mammal species of the World Vol. 2, John Hopkins University Press, Baltimore, 2005 Google Scholar

  • [3] Advani C.R., Mathur R.P., Experimental reduction of rodent damage to vegetable crops in Indian villages. Agro. Eco. Sys., 1982, 8, 39-45 Google Scholar

  • [4] Parshad V.R., Rodent control in India, Int. Pest. Mgmt. Rev.,1999, 4, 97-126 CrossrefGoogle Scholar

  • [5] Pergams O.R.W., Lawler J.J., Recent and wide spread rapid morphological change in rodents, PLoS ONE., 2009, 4, 1-11 Google Scholar

  • [6] Hebert P.D.N., Cywinska A., Ball S.L., de Ward J.R., Biological identifications through DNA barcodes, Proc. R. Soc. Lond. B., 2003, 270, 313-321 Google Scholar

  • [7] Archunan G., Vertebrate pheromones and their biological importance. J. Exp. Zool. India., 2009, 12, 227-239 Google Scholar

  • [8] Boore J.L., Animal mitochondrial genomes, Nucleic Acids Res., 1999, 27, 1767-1780 CrossrefGoogle Scholar

  • [9] Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., Francis C.M., Identification of Birds through DNA Barcodes, PLoS Biol., 2004, 2, 1657-1663 CrossrefGoogle Scholar

  • [10] Hebert P.D.N., Penton Erin H.., Burns John M., Janzen Daniel H., Hallwachs Winnie., Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl. Acad. Sci. USA., 2004, 101, 14812-14817 CrossrefGoogle Scholar

  • [11] Neelanarayanan P., Nagarajan R., Kanakasabai R., Burrow morphology of field rodents of Cauvery delta, Rodent Newl., 1994, 18, 3-4 Google Scholar

  • [12] Palanivelu K., Investigation of volatile components in urine, faeces and major scent glands of Indian Gebril (Tatera indica H.) with special reference to rodent pest management, PhD thesis, Bharathidasan University, Tiruchirappalli, India, 2004 Google Scholar

  • [13] Flowerdew J.R., Shore R.F., Poulton S.M.C., Sparks T.H., Live trapping to monitor small mammals in Britain, Mammal Rev., 2004, 34, 31-50 CrossrefGoogle Scholar

  • [14] Aplin K.P., Brown P.R., Jacob J., Krebs C.J., Singleton G.R., Field methods for rodent studies in Asia and the Indo-Pacific, ACIAR Monograph 100., Canberra (Australia): Australian Centre for International Agricultural Research, 2003 Google Scholar

  • [15] Sambrook J., Fritsch E.F., Maniatis T., Molecular cloning - a laboratory manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1989 Google Scholar

  • [16] Robins J.H., Hingston M., Smith E.M., Ross H.A., et al., Identifying Rattus species using mitochondrial DNA, Mol Ecol Notes., 2007, 7, 717-729 Web of ScienceCrossrefGoogle Scholar

  • [17] Hall T.A., BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp Ser., 1999, 41, 95-98 Google Scholar

  • [18] Parson W., Pegoraro K., Niederstatter H., Foger M., Steinlechner M., Species identification by means of cytochrome b gene, Int J Legal Med., 2000, 114, 23-28 Web of ScienceCrossrefGoogle Scholar

  • [19] Pradeep Kumar M., Rajavel A.R., Natarajan R., Jambulingam P., DNA Barcodes Can Distinguish Species of Indian Mosquitoes (Diptera: Culicidae), J. Med. Entomol., 2007, 44, 1-7 CrossrefWeb of ScienceGoogle Scholar

  • [20] Callejon R., deRojas M, Ariza C., Ubeda J.M., Guevara D.C., Cutillas C., Cytochrome oxidase subunit 1 and mitochondrial 16S rDNA sequence of Trichuris skrjabini (TricocephalidaTrichuridae), Parasitol Res., 2008, 104, 715-716 Google Scholar

  • [21] Dalton D.L., Kotze A., DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa, Forensic Sci, Int., 2011, 207, e51-e54 Web of ScienceGoogle Scholar

  • [22] Hajibabaei M., Janzen D.H., Burns J.M., Hallwachs W., Hebert P.D.N., DNA barcodes distinguish species of tropical Lepidoptera, Proc. Natl. Acad. Sci, USA., 2006, 103, 968-971 CrossrefGoogle Scholar

  • [23] Shin S., Jung S., Lee H., Lee S., Molecular identification of dipteran pests (Diptera:Sciaroidea) from shiitake mushroom, Mol Ecol Res., 2013, 13, 200–209 CrossrefGoogle Scholar

About the article

Received: 2014-09-16

Accepted: 2014-11-17

Published Online: 2015-03-30

Citation Information: DNA Barcodes, Volume 3, Issue 1, ISSN (Online) 2299-1077, DOI: https://doi.org/10.1515/dna-2015-0001.

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© 2015 Rengarajan Rengasamy Lakshminarayanan et al.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

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