Sains Malaysiana 41(12)(2012): 1527–1533

 

Limit of DNA Barcode in Delineating Penaeus Monodon and in its Developing Stages

(Had Penggunaan Barkod DNA untuk Menentukan Penaeus Monodon dan Peringkat Tumbesarannya)

 

 

C. Prasanna Kumar, S. Ajmal Khan & P.S. Lyla

Centre for Advanced Study in Marine Biology, Faculty of Marine Biology

Annamalai University, Parangipettai – 608502, Tamil Nadu, India

 

B. Akbar John* & K.C.A. Jalal

Department of Biotechnology, Kulliyyah of Science

International Islamic University Malaysia, Jalan Sultan Ahmad Shah

Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia

 

Received: 23 March 2011 / Accepted: 2 August 2012

 

ABSTRACT

Mysis, post larvae and adult specimens of Penaeus monodon were sequenced for Cyctochrome C Oxidase subunit I (COI) gene (DNA barcode) to check the efficiency of DNA barcode in delineating species irrespective of its different life stages. COI gene sequences of different life stages of P. monodon were subjected to pair-wise distance analysis, nucleotide sequence diversity estimation, phylogenetic and BOLD analysis. The pair-wise distance estimation revealed that intra-specific variations within the barcode sequences of P. monodon were low when compared with other species of genus Penaeus spp. The average pair-wise distance within the sequences of different stages of P. monodon was two times lesser than the pair-wise distance of the out-group used. The nucleotide diversity within the barcodes were low (π = 0.324). The constructed phylogram clearly showed that the DNA barcoding using partial COI gene would provide an accurate delineation of species irrespective of their different life stages. The BOLD analysis accurately identified all sequences as belonging to P. monodon.

 

Keywords: COI; DNA barcoding; nucleotide diversity; pair-wise distance; Penaeus monodon

 

ABSTRAK

Sampel mysis, anak pra-matang dan dewasa Peneaus monodon telah dianalisis mengggunakan gen subunit I sitokrom C oksidase (COI) untuk menentukan keupayaan barkod DNA untuk mengenal pasti peringkat tumbesaran Peneaus monodon. Jujukan COI Peneaus monodon pada peringkat yang berbeza telah dianalisis menggunakan kaedah jarak pasangan demi pasangan, kepelbagaian jujukan nukleofida, filogenetik dan BOLD. Analisis jarak pasangan demi pasangan menunjukkan variasi intra-spesifik dalam jujukan barkod Peneaus monodon adalah lebih rendah berbanding spesies Peneaus yang lain. Purata jarak pasangan demi pasangan pada peringkat berbeza Peneaus monodon adalah dua kali lebih rendah berbanding kumpulan luar. Kepelbagaian nukleotida dalam barkod adalah rendah (π= 0.324). Filogram yang dihasilkan menunjukkan barkod DNA yang menggunakan gen COI mampu menentukan tumbesaran spesies mengikut peringkatnya. Analisis BOLD pula menunjukkan bahawa kesemua jujukan yang dihasilkan adalah Peneaus monodon.

 

Kata kunci: Barkod DNA; COI; jarak pasangan demi pasangan;  kepelbagaian jujukan nukleofida; Peneaus monodon

REFERENCES

Ajmal Khan, S., Lyla, P.S., Akbar John, B., Prasanna Kumar, C., Murugan, S. & Jalal, K.C.A. 2010. DNA barcoding of Stolephorus indicus, Stolephorus commersonnii and Terapon jarbua of Parangipettai coastal waters. Biotechnology 9(3): 373-377.

Akbar John, B., Prasanna Kumar, Kamaruzzaman, B.Y. & Jalal, K.C.A. 2011. Revision on the molecular phylogeny of horseshoe crabs - Part 1. In The Living Fossil (Horseshoe Crab)Kamaruzzaman Yunus, Akbar John, Ahmed Jalal Khan Chowdhury & Zaleha Kassim (Eds.) (pp. 251-266). Kuantan: IIUM Press.

Akbar John, B., Prasanna Kumar, Kamaruzzaman, B.Y. & Jalal, K.C.A. 2011. Revision on the molecular phylogeny of horseshoe crabs – Part 2. In: The Living Fossil (Horseshoe Crab). (pp. 267-274).Kamaruzzaman Yunus, Akbar John, Ahmed Jalal Khan Chowdhury & Zaleha Kassim (Eds.). Kuantan:  IIUM Press.

Azinuddin, M.A.M., Nataqain, S.M., Normah, M.N. & Vijay, K. 2011. Isolation and identification of microsatellite repeat motifs from the Epinephelus fuscoguttatus genome. African Journal of Biotechnology 10(43): 8553-8557.

Baldwin, J.D., Bass, A.L., Bowen, B.W. & Clark, W.H. 1998. Molecular phylogeny and phylogeography of marine shrimp Penaeus. Molecular Phylogenetics Evolution 10(3): 399-407.

Benzie, J.A.H. 1998. Penaeid genetics and biotechnology. Aquaculture 164: 23-47.

Boxshall, G.A. 2007. Crustacean classification: On-going controversies and unresolved problems. Zootaxa 1668: 313-325.

Browdy, C.L. 1998. Recent developments in penaeid broodstock and seed production technologies: Improving the outlook of superior captive stocks. Aquaculture 164(1): 3-21.

Browne, W.E., Haddock, S.H. & Martindale, M.Q. 2007. Phylogenetic analysis of lineage relationship among hyperiid amphipods as revealed by examination of the mitochondrial gene, cytochrome oxidase I (COI). Integrative and Comparative Biology 47: 815-830.

Bucklin, A., Frost, B.W. & Allen, L.D. 2003. Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae. Marine Biology 142: 333-343.

Bucklin, A., Wiebe, P.H. & Smolenack, S.B. 2007. DNA barcodes for species identification of euphausiids (Euphausiacea, Crustacea). Journal of Plankton Research 29: 483-493.

Chu, K.H., Ho, H.Y., Li, C.P. & Chan, T.Y. 2003. Molecular phylogenetics of the mitten crab species in Eriocheir, sensu lato (Brachyura, Grapsidae). Journal of Crustacean Biology 23: 738-746.

Clare, E.L., Lim, B.K., Engstrom, M.D., Eger, J.L. & Hebert, P.D.N. 2007. DNA barcoding of Neotropical bats: Species identification and discovery within Guyana. Molecular Ecology Notes 7: 184-190.

Costa, F.O., De-Waard, J.R. & Boutillier, J. 2007. Biological identifications through DNA barcodes: The case of the Crustacea. Canadean Journal of Fisheries and Aquatic Sciences 64: 272-295.

Cunningham, C.W., Blackstone, N.W. & Buss, L.W. 1992. Evolution of king crabs from hermit crab ancestors. Nature 355: 539-542.

Dall, W., Hill, B.J., Rothlisberg, P.W. & Staples, D.J. 1990. The biology of Penaeidae. Advances in Marine Biology 27: 511-523.

Daniels, S.R., Stewart, B.A., Gouws, G., Cunningham, M. & Matthee, C.A. 2002. Phylogenetic relationships of the southern African freshwater crab fauna (Decapda: Potamonautidae; Potamonautes) derived from multiple data sets reveal biogeographical patterning. Molecular Phylogenetics and Evolution 25(3): 511-523.

Ebach, M.C. & Holdrege, C. 2005. More taxonomy, not DNA barcoding. Bioscience 55: 822-823.

Englisch, U., Coleman, C.O. & Wagele, J.W. 2003. First observations on the phylogeny of the families Gammaridae, Crangonyctidae, Melitidae, Niphargidae, Megaluropidae and Oedicerotidae (Amphipoda, Crustacea), using small subunit rRNA gene sequences. Journal of Natural History 37: 2461-2486.

Etter, R.J., Rex, M.A., Chase, M.C. & Quattro, J.M. 1999. A genetic dimension to deep-sea biodiversity. Deep-Sea Research 46: 1095-1099.

Flegel, T.W. 2007. Right to refuse revision in the genus Penaeus. Aquaculture 264(4): 2-8.

Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294-299.

Gusmao, J., Lazoski, C. & Sole-Cava, A.M. 2000. A new species of Penaeus (Crustacea: Penaeidae) revealed by allozyme and cytochrome oxidase I analyses. Marine Biology 137: 435-446.

Hajibabaei, M., Janzen, D.H., Burns, J.M., Hallwachs, W. & Hebert. P.D.N. 2006. DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States of America 103: 968-971.

Haye, P.A., Tam, Y.K. & Kornfield, I. 2002. Molecular phylogenetics of molecrabs (Hippidae: Emerita). Journal of Crustacean Biology 22: 903-915.

Hebert, P.D.N., Cywinska, A., Ball, S.L. & DeWaard, J.R. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270: 313-321.

Hebert, P.D.N., Stoeckle, M.Y., Zemlak, T.S. & Francis, C.M. 2004. Identification of birds through DNA barcodes. PLOS Biology 2: 1657-1663.

Holthuis, L.B. 1980. Shrimps and prawns of the world. An annotated catalogue of species of interest to fisheries. FAO species catalogue. Vol. 1. FAO Fisheries Synopsis, FAO, Roma.

Hou, Z., Fu, J. & Li, S. 2007. A molecular phylogeny of the genus Gammarus (Crustacea: Malacostraca) based on mitochondrial and nuclear gene sequences. Molecular Phylogenetics and Evolution 45: 596-611.

Hubert, N., Delrieu-Trottin, E., Irisson, J-O., Meyer, C. & Planes, S. 2010. Identifying coral reef fish larvae through DNA barcoding: A test case with the families Acanthuridae and Holocentridae. Molecular Phylogenetics and Evolution 55(3): 1195-1203.

Hubert, N., Hanner, R. & Holm, E. 2008. Identifying Canadian freshwater fishes through DNA barcodes. Plos One 3: 1-8.

Khamnamtong, B., Klinbunga, S. & Menasveta, P. 2005. Species identification of five Penaeid shrimps using PCR-RFLP and SSCP analyses of 16S Ribosomal DNA. Journal of Biochemistry and Molecular Biology 38(4): 491-499.

Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120.

Knowlton, N. 1993. Sibling species in the sea. Annual Reviewes Ecological System 24: 189-216.

Knowlton, N. 2000. Molecular genetic analyses of species boundaries in the sea. Hydrobiologia 420: 73-90.

Lavery, S., Chan, T.Y., Tam, Y.K. & Chu, K.H. 2004. Phylogentic relationship and evolutionary history of genus Penaeus s.l. derived from mitochondrial DNA. Molecular Phylogenetics and Evolution 31: 39-49.

Lorenz, J.G., Jackson, W.E., Beck, J.C. & Hanner, R. 2005. The problems and promise of DNA barcodes for species diagnosis of primate biomaterials. Philosophical Transactions of the Royal Society B. Biological Science 360: 1869-1877.

Mokhtar, M.A.A., Normah, M.N., Kumar, S.V. & Baharum, S.N. 2011. Characterization of 10 novel microsatellite loci for the brown marbled grouper, Epinephelus fuscoguttatus (Serranidae). Genetics and Molecular Research 10(2): 885-888.

Pérez-Farfante, I. & Kensley, B. 1997. Penaeoid and Sergestoid Shrimps and Prawns of the World. Editions du Muséum National d’Histoire Naturelle, Paris, France.

Quan, J., Lu, X.M. & Zhuang, Z. 2001. Low genetic variation of Penaeus chinensis as revealed by mitochondrial COI and 16S rRNA gene sequences. Biochemical Genetics 39: 279-284.

Rathnasingham, S. & Hebert, P.D.N. 2007 BOLD: Barcoding of Life Data system (www.barcodinglife.com) Molecular Ecology Notes 7(3):  355-364.

Saitou, N. & Nei, M. 1987. Neighbor joining method: A new method for constructing phylogenetic trees. Molecular Biology Evolution 4: 406-425.

Schander, C. & Willassen, E. 2005. What can biological barcoding do for marine biology? Mar. Biol. Res. 1: 79-83.Tajima, F. 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.

Tamura, K., Dudley, J., Nei, M. & Kumar, S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology Evolution 24: 1596-1599.

Tang, R.W., Yaum, C. & Ng, W.C. 2010. Identification of stomatopod larvae (Crustacea: Stomatopoda) from Hong Kong waters using DNA barcodes. Molecular Ecology Resources 10(3): 439-448.

Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. 1997. The ClustalXwindows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-4882.

Thorpe, J.P., Sole-Cava, A.M. & Watts, P.C. 2000. Exploited marine invertebrates: Genetics and fisheries. In: Marine Genetics Sole-Cava, A. M., Russo, C.A.M. & Thorpe, J. M. (eds) Drodrecth: Kluwer Academic Publisher. pp.165-184.

Vainola, R., Vainio, J.K. & Palo, J.U. 2001. Phylogeography of ‘glacial relict’ Gammaracanthus (Crustacea, Amphipoda) from boreal lakes and the Caspian and White seas. Canadian Journal of Fisheries and Aquatic Sciences 58: 2247-2257.

Ward, R.D., Zemlak, T.S. & Innes, B.H. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions Royal Society of London B 360: 1847-1857.

Webb, K.E., Barnes, D.K.A., Clark, M.S. & Bowden, D.A. 2006. DNA barcoding: A molecular tool to identify Antarctic marine larvae. Deep Sea Research Part II: Topical Studies in Oceanography 53(8-10): 1053-1060.

Will, K.W., Mishler, B.D. & Wheeler, Q.D. 2005. The perils of DNA barcoding and the need for integrative taxonomy. Systems Biology 54: 844-851.

Will, K.W. & Rubinoff, D. 2004. Myth of the molecule: The DNA barcodes for species cannot replace morphology for identification and classification. Cladistics —Int. J. Willi Hennig Soc. 20: 47-55.

Wilson, E.O. 2003. The encyclopedia of life. Trends in Ecology and Evolution 18: 77-80.

 

 

*Corresponding author; email: akbarjohn50@gmail.com