18Feb 2017

DNA Barcoding and Phylogenetic analysis of South Indian Curcuma species using chloroplast matK gene.

  • Interuniversity centre for Plant Biotechnology, Department of Botany, University of Calicut, Kerala-673635, India.
Crossref Cited-by Linking logo
  • Abstract
  • Keywords
  • References
  • Cite This Article as
  • Corresponding Author

The interspecific relationship between twenty one different Curcuma species was studied using MaturaseK gene (matK). Various Curcuma species are widely exploited for its medicinal, ornamental and other purpose. Floral plasticity in vegetative characters and developmental portion of inflorescence is widely utilized in morphology based classification which leads to erroneous conclusions makes DNA barcoding an essential tool for deciphering the correct identify and pohylogenetic relationship between the species. The sequence of matK gene of Curcuma sp with no barcode gaps were cloned, sequenced and submitted in the Genbank and used for the phylogenetic study. The intra and interspecfic divergence between the species assessed by using K2P of MEGA 6.0.The sequence alignments were performed using Clustal W,transition/transversion rates were predicted and phylogenetic tree was constructed using MEGA 6.Phylogenetic tree was designed to identify the ideal regions of Curcuma species for defining inter and intra-species relationships. The phylogenetic analysis using MEGA 6.0 provided two groups with the second group having two subclades. The study revealed the potential of matK gene as a good candidate gene for phylogenetic analysis of the genus Curcuma.

  1. Amalraj, V.A., Velayudhan,K.C.,Muralidharan,V.K., 1999. Curcuma karnatakensis sp.Nov. (Zingiberaceae)- Anew species from Uttar kannada District of Karnataka State. Journal of Economic and Taxonomic Botany 15(2):490-492.
  2. Aoki, S., Ito,M., 2000. Molecular phylogeny of Nicotiana (Solanaceae) based on the nucleotide sequences of the matK gene. Plant Biology 2: 253–378.
  3. Bakhuizen van den Brink Jr, R.C,. Zingiberaceae [M] // Baker C.A., 1968. Bakhuizen van den Brink Jr. RC. Flora of Java: Vol 3. Groningen: Wolters-Noordhoff N.V.,: 69-72.
  4. Burtt, L.B. 1972. Key species in the taxonomic history of Zingiberaceae.Notes from the Royal Botanic GardenEdinburgh31: 224-227.
  5. Cameron, K.M., Chase,M.W., Anderson,W.R., Hills,H.G.,2001. Molecular systematics of Malpighiaceae: evidence from plastid rbcL and matK sequences. American Journal of Botany 88: 1847–1862.
  6. Chen, J., Xia, N.H., 2010. Chromosome cytology, leaf epidermal morphology and palynology of Curcuma rubrobracteata(Zingiberaceae). Nordic Journal of Botany, 28, 212–215.
  7. Chen, Z.Y., Chen, S.J., Huang, S.F., 1984. Accounts of chromosomal number of Zingiberaceae (2) Guihaia 4: 13-18.
  8. Doyle, J.J., Doyle J.L., 1987. A rapid DNA isolation procedure from small quantities of fresh leaf tissue.Phytochemical Bulletin. 19: 1-15.
  9. Fazekas, A.J., Burgess, K.S., Kesanakurti, P.Ret al., Multiple multilocus DNA barcodesfrom the plastid genome discriminate plant species equally well. PLoS ONE, 3, 2802.
  10. Ford, C.S., Ayres, K.L., Toomey, N.et al.,Selection of candidate coding DNA barcodingregions for use on land plants.Botanical Journal of the Linnean Society, 159, 1–11.
  11. Futuyma, J. D., 2005. Evolution.Sinauer Associates Inc., Sunderland, MA.
  12. Goldman, D.H., Freudenstein,J.V., Kores,P.J.,Molvray,M., Jarrell,D.C., Whitten,W.M., Cameron,K.M., Jansen, R.K., Chase,M.W.,2001.Phylogenetics of Arethuseae (Orchidaceae) based on plastid matK and rbcL sequences. Systematic Botany 26: 670–695.
  13. Hebert, P.D.N., Cywinska, A., Ball,S.L., DeWaard, J.R., 2003a.Biological identifications through DNA barcodes.Proceedings of the Royal Society B Biological Sciences 270: 313–321.
  14. Hollingsworth, M.L., Clark, A., Forrest, L.L et al., Selecting barcod-ing loci for plants:evaluation of seven candidate loci with species level sampling in three divergent groupsof land plants. Molecular Ecology Resources, 9, 439–457.
  15. Holmquist, R., 1983. Transitions and transversion in evolutionary descent: an approach to understanding. Journal of Molecular Evolution 19:134–144.
  16. Hilu, K.W., Borsch,T., Muller,K., Soltis,D.E., Soltis,P.S., Savolainen,V., Chase,M.W., Powell,M., Alice,L.A., Evans,R.C., Sauquet,H., Neinhuis,C.,Slotta,T.A., Rohwer,J.G., Campbell,C.S.,Chatrou,L.,2003. Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: 1758–1776.
  17. Johnson, L.S., Soltis, D.E., 1995. Phylogenetic inference in Saxifragaceaesensustricto and Gilia (Polemoniaceae) using matK sequences. Annals of the Missouri Botanical Garden 82:149–175.
  18. Kress, W.J., Prince, L.M.,Williams, K.J., The phylogeny and a new classification of the gingers (Zingiberaceae): Evidence from molecular data. American Journal of Botany.89: 1682–1696.
  19. Kress, W.J., Erickson, D.L., 2007. A two-locus global DNA barcode for land plants, the codingrbcLgene complements the non-coding trnH-psbAspacer region. PLoS ONE, 2, 508.
  20. Lake, J.A., 1987. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Molecular Biology and Evolution 4:167–191.
  21. Larsen, K., Lock, J.M., Maas, H.et al., 1998.Zingiberaceae. In: The Families and Genera of Vascular Plants (ed. Kubitzki K), pp. 474–495. Vol. 4. Springer-Verlag, Berlin.
  22. Leong- Skornickova, J., S?da, O., Jarol?mova, V.et al., 2007. Chromosome numbers and genome size variation in Indian species of Curcuma (Zingiberaceae). Annals of Botany, 100, 505–526.
  23. Liang, H.P., Hilu, K.W., 1996. Application of the matK gene sequences to grass systematics. Canadian Journal of Botany 74: 125–134.
  24. Ngamriabsakul, C., Newman, M.,Cronk, Q.B.C., The phylogeny of tribe Zingibereae (Zingiberaceae) based on ITS (nr DNA) and trnL-F (cp DNA) sequences. Edinburgh Journal o. Botany.60: 483–507.
  25. Notredame, C., 2000. Journal of Molecular Biology, 205: 217.
  26. Pazos, F., Valencia, A., 2001.Similarity of phylogenetic trees as indicator of protein-protein interaction.Protein Engineering. 14:609–614.
  27. Quicke, D.L.J., 1993.Principle and techniques of contemporary taxonomy.Chapman & Hall, Glasgow.
  28. Rajesh Kumar T., Santhoshkumar R. Yusuf A (2016) Morphological characters and random amplified polymorphic DNA based genetic diversity analysis of curcuma species (zingiberaceae) from india. International Journal of Plant Animal and Environmental Sciences 6:37-52
  29. Sabu, M., 2006.Zingiberaceae and Costaceae of South India.Association for Angiosperm Taxonomy. Page: 126-186.
  30. Sass, C., Little, D.P., Stevenson, D.W.et al.,DNA barcoding in the cycadales, testing thepotential of proposed barcoding markers for species identification of Cycads.PLoS ONE,2, e1154.
  31. Salazar, G.A., Chase,M.W., Arenas,M.A.S., Ingrouille,M.,2003.Phylogenetics of Cranichideae with emphasis on Spiranthinae (Orchidaceae, Orchidoideae): evidence from plastid and nuclear DNA sequences. American Journal of Botany 90: 777–795.
  32. Savolainen, V., Chase, M.W., Hoot,S.B., Morton, C.M., Soltis,D.E., Bayer,C., Fay,M.F., De Bruijn,A.Y., Sullivan,S.,Qiu, Y.L.,2000a. Phylogenetics of flowering plants based upon a combined analysis of plastidatpB and rbcL gene sequences. Systematic Biology 49: 306-362.
  33. Škorni?ková, J.,Taxonomic studies in Indian Curcuma L. Dissertation,Charles University, Prague, Czech Republic.
  34. Soltis, D.E., Soltis, P.S., 1998.Choosing an approach and an appropriate gene for phylogenetic analysis. In: Soltis DE, Soltis PS, Doyle JJ (eds) Molecular systematics of plants II: DNA sequencing. Kluwer, Dordrecht, pp 21–24.
  35. Tajima, F.,Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism.Genetics123:585-595.
  36. Vijayan, K., Tsou, C.H., 2010. DNA barcoding in plants: taxonomy in a new perspective. CurrentScience 99(11):1530–1541.
  37. Webb, C.O., Ackerly, D.D.,McPeek, M.A., Donoghue, M.J., 2002. Phylogenies and community ecology.Annual Review Ecology and Systematics33, 475–505.
  38. Wolfe, K., 1987. Proceedings of the National Academy of Science, 9054: 9058.
  39. Wolfe, K.H., 1991. Protein-coding genes in chloroplast DNA: compilation of nucleotide sequences, data base entries and rates of molecular evolution. In K. Vasil [ed.], Cell culture and somatic cell genetics of plants, 7 BI, 467–482. Academic Press, San Diego, California, USA.
  40. Wolfe, K.H., Morden,C.W., Palmer,J.D., 1992. Function and evolution of a minimal plastid genome from nonphotosynthetic parasitic plants. Proceedings of the National Academy of Sciences, USA 89: 10648–10652.
  41. Wu, D.L., Larsen, K., 2000. Zingiberaceae In: Flora of China, vol. 24 (eds Wu ZY & Raven P), pp. 322–377. Science Press, Beijing and Missouri Botanical Garden Press, St. Louis, MO
  42. Xiang, Q.Y.,Soltis,D.E., Soltis,P.S.,1998. Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences. American Journal of Botany 85: 285–297.
  43. Xiao, X.H., Liu, F.Q., Shi, C.H.et al., 2000.RAPD polymorphism and authentication of medicinal plants from Turmeric (Curcuma ) in China [J].Chinese Traditional Herbal Drugs 31: 209-212.
  44. Ye, X.B., Chen, J., Liu, N., 2008.Curcuma nankunshanensis (Zingiberaceae), a new species from China. Journal of Tropical and Subtropical Botany, 16, 472–476.
  45. Zheng, M.L., Xia, Y.M., 2010.A investigation on the phylogeny of tribe Zingibereae (Zingiberaceae) based on nrDNA ITS and cpDNAmatK sequence data. Journal of Yunnan University 32(S1): 426-432.
  46. Záveská, E., Fér, T., Šída, O.et al., Phylogeny of Curcuma (Zingiberaceae) based on plastid and nuclear sequences: Proposal of the new subgenus Ecomata. Taxon, 61,741-743.

[Santhosh Kumar R. and Yusuf A. (2017); DNA Barcoding and Phylogenetic analysis of South Indian Curcuma species using chloroplast matK gene. Int. J. of Adv. Res. 5 (Feb). 615-621] (ISSN 2320-5407). www.journalijar.com

Yusuf A
Interuniversity centre for Plant Biotechnology, Department of Botany, University of Calicut, Kerala-673635, India

DOI:

Article DOI: 10.21474/IJAR01/3192      
DOI URL: http://dx.doi.org/10.21474/IJAR01/3192

Download Full Paper

Download PDF No. of Downloads: 148 | No. of Views: 371