Cover Image

The comparison between nuclear ribosomal DNA and chloroplast DNA in molecular systematic study of four sections of genus Dendrobium sw. (orchidaceae)

Maryam Moudi*, Rusea Go


Phylogenetic study of the four sections (Aporum, Crumenata, Strongyle, and Bolbidium) of genus Dendrobium (family Orchidaceae) was conducted using molecular data. Classifications based on morphological characters have not being able to clearly divide these four sections neither do they supported their monophyly origin. Therefore, deeper and detailed analysis especially using molecular data is required to ascertain their status. Molecular evidences were used to clarify their relations either to lump them into one section or reduce them into two. The study has been carried out for the 34 species of Dendrobium using Maximum Parsimony (MP). Three nucleotide sequences data sets from two distinct genomes chloroplast DNA genes (rbcL and matK) and nuclear ribosomal DNA (ITS) were used to construct cladograms. The results that obtained from the Internal Transcribed Spacer (ITS) gene showed that the nuclear genes are reliable marker for the phylogenetic study of Dendrobium compared to chloroplast DNA with low resolution level among sections. 


Dendrobium, phylogeny, ITS, rbcL, matK

Full Text:



Small RL, Cronn RC and Wendel JF, LAS. JOHNSON REVIEW No. 2. Use of nuclear genes for phylogeny reconstruction in plants, Australian systematic Botany, 2004, 17, 145- 170.

Olmstead RG, Palmer JD. Chloroplast DNA systematics: a review of methods and data analysis. American Journal of Botany, 1994, 81, 205–1224.

Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N. Land plants and DNA barcods: short-term and long-term goals. Philosophical Transactions of the Royal Society B, 2005, 360, 1889-1895.

Seidenfaden G, Wood JJ. The Orchids of Peninsular Malaysia and Singapore. Fredensborg: Olsen and Olsen, 1992.

Turner IM. A catalogue of the vascular plants of Malaya. The Gardens’ Bulletin Singapore, 1995, 47 (1): 559-620.

Wang HZ, Fenga SG, Lua JJ, Shia NN, Liub JJ. Phylogenetic study and molecular identification of 31 Dendrobium species using inter-simple sequence repeat (ISSR) markers. Scientia Horticulture, 2009, 122, 440-447.

Asahina H, Shinozaki J, Masuda K, Morimitsu Y, Satake M. Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences. Journal of Natural Medicines, 2010, 64, 133-138.

Kuehnle AR. Chapter 20: Orchids, Dendrobium. In: N.O Anderson (ed.), Flower Breeding and Genetics. Springer, 2007, 539-560.

Yukawa T, Ohba H, Cameron, KM, Chase MW. Chloroplast DNA phylogeny of subtribe Dendrobiinae (Orchidaceae): insights from a combined analysis based on rbcL sequences and restriction site variation. Journal Plant Research, 1996, 109 (2), 169–176.

Wang HZ, Wang YD, Zhou XY, Ying QC, Zheng KL. Analysis of genetic diversity of 14 species of Cymbidium based on RAPDs and AFLPs. Acta Biologiae Exprimetalis Sin, 2004, 37 (6), 482–486.

Hall AT. Bio Edit: a user friendly biological sequence alignment editor and analysis performer windows 95/98/NT. Nucleic Acid Symposium series, Axford Journals, 1999, 41, 95-98.

Swofford DL. PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4b10. Sinauer, Sunderland, Massachusetts, USA, 2002.

Tamura K, Peterson D, Peterson N. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, Advance access: 10.1093/molbev/msr121, 2011.

Farris JS, Källersjö M, Kluge AG, Bult C. Constructing a significance test for incongruence. Systematic Biology, 1995, 44(4), 570-572.

Wendel JF, Schnabel A, Seelanan T. Bi-directional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceeding of the Naionatl Academy Sciences of the USA, 1995, 92, 280-284.

Sanderson MJ, Driskell AC, Ree RH, Eulenstein O, Langley S. Obtaining maximal concatenated phylogenetic datasets from large sequence databaces. Molecular Biology and Evolution, 2003, 20(7), 1036-1042.

Soltis DE, Soltis PS. Molecular systematics of plants II: DNA sequencing. Boston: Kluwer Academic Publishers, 1998.

Cameron KM, Chase MW, Whitten WM, Korse PJ, Jarrell DC, Albert VA. A phylogenetic analysis of the Orchidaceae: Evidence from rbcL nucleotide sequences. American Journal of Botany, 1990, 86(2), 208-224.

Wolf KH, Morden CW, Palmer JD. Function and Evolution of a minimal plastid genome from nonphotosynthetic parasitic plant. Proceeding of the National Academy of Sciences USA, 1992, 89(22), 10648-10652.

Soltis DE, Soltis PS, Chase MW, Mort ME, Albach DC, Zanis M. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Botanical Journal of the Linnean Society, 2000, 133(4), 381-461.

Hilu KW, Borsch T, Müller K, Soltis DE, Soltis PS, Savolainen V. Angiosperm phylogeny based on matK sequence information. American Journal of Botany, 2003, 90, 1758-1776.

Moudi M, Go R. Monophyly of four sections of genus Dendrobium (ORCHIDACEAE): Eidence from nuclear ribosomal DNA Internal Transcribed Spacer (ITS) sequencs. Internatinal journal of Bioassays, 2015, 4(01), 3622-3626.

Kim KJ, Jansen RK. Comparisons of phylogenetic hypotheses among different datasets in dwarf dandelions (Kriga, Asteraceae): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA. Plant Systematic and Evolution, 1994, 190(3-4), 157-185.

Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ. The ITS region of nuclear ribosomal DNA — a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden, 1995, 82, 247–277.

Choi BH, Kim JH. ITS sequences and speciation on far Eastern Indigofera (Leguminosae). Plant Research, 1997, 110, 339-346.

Choi HK, Kim CK, Shin HC. Molecular reexamination of Korean Umbelliferae based on internal transcribed spacer sequences of rDNA: Ligusticum tenuissimum (Nakai) Kitagawa. and Libanotis coreana (Wolf)vKitagawa. Plant Biology, 2000, 43, 136-142.

Koehler K, Stechele M, Hetzel U, Domingo M, Schönian G, Zahner H. Cutaneous leishaniosis in a horse in Southern Germany caused by Leishmania infantum. Veterinary Parasitology, 2002, 109(1-2), 9-17.

Salazar GA, Chase MW, Soto Arenas MA, Ingrouille M. Phylogenetics of Cranichideae with emphasis on Spiranthinae (Orchidaceae: Orchidoideae): Evidence from plastid and nuclear DNA sequences. American Journal of Botany, 2003, 90(5), 777-795.

Van Den Berg C, Goldman DH, Frudenstein JV, Pridgeon AM, Cameron KM, Chase MW. An overview of the phylogenetic relationships within Epidendroideae inferred from multiple DNA regions and recircumscription of Epidendreae and Arethuseae (Orchidaceae). American Journal of Botany, 2005, 92(4), 613-624.

Whitten WM, Blanco MA, Williams NH, Koehler S, Carnevali G, Singer RB. Molecular phylogenetics of Maxillaria and related genera (Orchidaceae: Cymbidieae) based on combined molecular datasets. American Journal of Botany, 2007, 94(11), 1860-1889.

Clements MA. Molecular phylogenetic systematics in the Dendrobiinae (Orchidaceae), with emphasis on Dendrobium section Pedilonum. Telopea, 2003, 10(1), 247-272.

Yukawa T, Kurita S, Nishida M, Hasebe M. Phylogenetic implications of chloroplast DNA restriction site variation in subtribe Dendrobiinae (Orchidacaeae). Lindleyana, 1993, 8, 211–221.

Yukawa T, Kita K, Handa T. DNA phylogeny and morphological diversification of Australian Dendrobium (Orchidaceae). In: Wilson, K.L. and Mossison, D.A. (eds) Monocots: Systematics and Evolution. Melbourne: CSIRO Publishing, 2000, 465-471.

Schuietman A. Dendrobium (Orchidaceae): to split or not split?. Gardens Bulletin Singapore 1and, 2011, 2, 245-257.

Yukawa T. Molecular phylogeny of Dendrobium. In: Nagata, H. and Ichihashi, S. (eds) Proceedings of the seventh Asia Pacific orchid conference (APOC7), 2001.

Lavarack PS, Harris W, Stocker G. Dendrobium and its relatives. Oregon, Portland: Timber Press, 2000.



  • There are currently no refbacks.

Copyright (c) 2016 International Journal of Bioassays

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

International Journal of Bioassays is a member of the Publishers International Linking Association, Inc. (PILA), CROSSREF and CROSSMARK (USA). Digital Object Identifier (DOI) will be assigned to all its published content.