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Int. J. Mol. Sci. 2015, 16(9), 21975-21988; doi:10.3390/ijms160921975

Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study

1
Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China
2
College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha 410128, China
3
Zhejiang Institute of Chinese Meteria Medica, Hangzhou 310023, China
*
Authors to whom correspondence should be addressed.
Academic Editor: Marcello Iriti
Received: 1 June 2015 / Revised: 26 August 2015 / Accepted: 27 August 2015 / Published: 11 September 2015
(This article belongs to the Special Issue Plant Molecular Biology)
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Abstract

The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In the present study, we examined the application of the ITS2 region in barcoding and phylogenetic analyses of Dendrobium species (Orchidaceae). For barcoding, ITS2 regions of 43 samples in Dendrobium were amplified. In combination with sequences from GenBank, the sequences were aligned using Clustal W and genetic distances were computed using MEGA V5.1. The success rate of PCR amplification and sequencing was 100%. There was a significant divergence between the inter- and intra-specific genetic distances of ITS2 regions, while the presence of a barcoding gap was obvious. Based on the BLAST1, nearest distance and TaxonGAP methods, our results showed that the ITS2 regions could successfully identify the species of most Dendrobium samples examined; Second, we used ITS2 as a DNA marker to infer phylogenetic relationships of 64 Dendrobium species. The results showed that cluster analysis using the ITS2 region mainly supported the relationship between the species of Dendrobium established by traditional morphological methods and many previous molecular analyses. To sum up, the ITS2 region can not only be used as an efficient barcode to identify Dendrobium species, but also has the potential to contribute to the phylogenetic analysis of the genus Dendrobium. View Full-Text
Keywords: Dendrobium; ITS2; DNA barcode; species identification; genetic relationship Dendrobium; ITS2; DNA barcode; species identification; genetic relationship
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Feng, S.; Jiang, Y.; Wang, S.; Jiang, M.; Chen, Z.; Ying, Q.; Wang, H. Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study. Int. J. Mol. Sci. 2015, 16, 21975-21988.

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