Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2017, Article ID 2734960, 10 pages
https://doi.org/10.1155/2017/2734960
Research Article

Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China

Correspondence should be addressed to Jianping Han; nc.ca.dalpmi@nahpj

Received 8 June 2017; Revised 17 August 2017; Accepted 13 September 2017; Published 17 October 2017

Academic Editor: Chiu-Chung Young

Copyright © 2017 Xiaoyue Wang et al. 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.

Linked References

  1. X. Y. Ding, W. M. Zhang, Z. T. Wang, and L. S. Xu, “Summarization of the studies of taxonomy and pharmacognosy of ethnological materials of Dendrobium,” The Chinese Academic Medical Magazine of Organisms, no. 1, pp. 1–14, 2003. View at Google Scholar
  2. S. Y. Yang, S. G. Wang, H. L. Li, and Z. H. Di, “Research Status of Identification on CAULIS DENDROBII,” Journal of Anhui Agricultural Sciences, vol. 41, pp. 1495–1497, 2013. View at Google Scholar
  3. S. O. Rogers and A. J. Bendich, “Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer,” Plant Molecular Biology, vol. 9, no. 5, pp. 509–520, 1987. View at Publisher · View at Google Scholar · View at Scopus
  4. D. M. Hillis and M. T. Dixon, “Ribosomal DNA: molecular evolution and phylogenetic inference,” The Quarterly Review of Biology, vol. 66, no. 4, pp. 411–453, 1991. View at Publisher · View at Google Scholar · View at Scopus
  5. C. D. Prokopowich, T. R. Gregory, and T. J. Crease, “The correlation between rDNA copy number and genome size in eukaryotes,” Genome, vol. 46, no. 1, pp. 48–50, 2003. View at Publisher · View at Google Scholar · View at Scopus
  6. F. J. Stewart and C. M. Cavanaugh, “Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria,” Journal of Molecular Evolution, vol. 65, no. 1, pp. 44–67, 2007. View at Publisher · View at Google Scholar · View at Scopus
  7. C. Li and R. C. Wilkerson, “Intragenomic rDNA ITS2 variation in the neotropical Anopheles (Nyssorhynchus) albitarsis complex (Diptera: Culicidae),” Journal of Heredity, vol. 98, no. 1, pp. 51–59, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. D. J. Harris and K. A. Crandall, “Intragenomic variation within ITS1 and ITS2 of freshwater crayfishes (Decapoda: Cambaridae): Implications for phylogenetic and microsatellite studies,” Molecular Biology and Evolution, vol. 17, no. 2, pp. 284–291, 2000. View at Publisher · View at Google Scholar · View at Scopus
  9. M. He, L. Huang, J. Shi, and Y. Jiang, “Variability of ribosomal DNA ITS-2 and its utility in detecting genetic relatedness of pearl oyster,” Marine Biotechnology, vol. 7, no. 1, pp. 40–45, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. R. Freire, A. Arias, J. Méndez, and A. Insua, “Sequence variation of the internal transcribed spacer (ITS) region of ribosomal DNA in Cerastoderma species (Bivalvia: Cardiidae),” Journal of Molluscan Studies, vol. 76, no. 1, pp. 77–86, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. Z.-L. Liu, D. Zhang, X.-Q. Wang, X.-F. Ma, and X.-R. Wang, “Intragenomic and interspecific 5S rDNA sequence variation in five Asian pines,” American Journal of Botany, vol. 90, no. 1, pp. 17–24, 2003. View at Publisher · View at Google Scholar · View at Scopus
  12. S. Feng, Y. Jiang, S. Wang et al., “Molecular identification of dendrobium species (Orchidaceae) based on the dna barcode its2 region and its application for phylogenetic study,” International Journal of Molecular Sciences, vol. 16, no. 9, pp. 21975–21988, 2015. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Xu, D. Li, J. Li et al., “Evaluation of the DNA barcodes in dendrobium (Orchidaceae) from mainland Asia,” PLoS ONE, vol. 10, no. 1, Article ID e0115168, 2015. View at Publisher · View at Google Scholar · View at Scopus
  14. X.-Y. Ding, Z.-T. Wang, H. Xu, L.-S. Xu, and K.-Y. Zhou, “Database establishment of the whole rDNA its region of Dendrobium species of “Fengdou” and authentication by analysis of their sequences,” Yaoxue Xuebao, vol. 37, no. 7, pp. 567–573, 2002. View at Google Scholar · View at Scopus
  15. L. Zhang, D. S. Qiu, S. K. Cai, R. Y. Deng, H. M. Luo, and X. J. Liu, “The Genuine and Adulterants Identification of Dendrobium officinaleby rDNA ITS Sequences Analysis,” Journal of Anhui Agricultural Sciences, vol. 4, pp. 2872–2874, 2013. View at Google Scholar
  16. D. Li, J. Z. Li, P. Mao, F. Y. X, Z. Chun, and X. R. Ma, “Phylogenetic Analysis and Identification of Dendrobium Species Based on Ribosomal DNA Internal Transcribed Spacer (ITS) sequence,” Acta Horticulturae Sinica, vol. 39, pp. 1539–1550, 2012. View at Google Scholar
  17. I. Álvarez and J. F. Wendel, “Ribosomal ITS sequences and plant phylogenetic inference,” Molecular Phylogenetics and Evolution, vol. 29, no. 3, pp. 417–434, 2003. View at Publisher · View at Google Scholar · View at Scopus
  18. G. N. Feliner and J. A. Rosselló, “Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants,” Molecular Phylogenetics and Evolution, vol. 44, no. 2, pp. 911–919, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. L.-C. Shi, J. Zhang, J.-P. Han et al., “Testing the potential of proposed DNA barcodes for species identification of Zingiberaceae,” Journal of Systematics and Evolution, vol. 49, no. 3, pp. 261–266, 2011. View at Publisher · View at Google Scholar · View at Scopus
  20. X. Chen, B. Liao, J. Song, X. Pang, J. Han, and S. Chen, “A fast SNP identification and analysis of intraspecific variation in the medicinal Panax species based on DNA barcoding,” Gene, vol. 530, no. 1, pp. 39–43, 2013. View at Publisher · View at Google Scholar · View at Scopus
  21. X. Z. Zhu and T. Gao, “Molecular identification of 17 invasive plant species based on ITS2 sequences,” Pratacultural Science, vol. 31, pp. 1900–1907, 2014. View at Google Scholar
  22. J. M. Guillamön, J. Sabaté, E. Barrio, J. Cano, and A. Querol, “Rapid identification of wine yeast species based on RFLP analysis of the ribosomal internal transcribed spacer (ITS) region,” Archives of Microbiology, vol. 169, no. 5, pp. 387–392, 1998. View at Publisher · View at Google Scholar · View at Scopus
  23. Y. C. Chen, J. D. Eisner, M. M. Kattar et al., “Identification of medically important yeasts using PCR-based detection of DNA sequence polymorphisms in the internal transcribed spacer 2 region of the rRNA genes,” Journal of Clinical Microbiology, vol. 38, no. 6, pp. 2302–2310, 2000. View at Google Scholar · View at Scopus
  24. L. Xiang, J. Song, T. Xin et al., “DNA barcoding the commercial Chinese caterpillar fungus,” FEMS Microbiology Letters, vol. 347, no. 2, pp. 156–162, 2013. View at Publisher · View at Google Scholar · View at Scopus
  25. R. Stouthamer, J. Hu, F. J. P. M. Van Kan, G. R. Platner, and J. D. Pinto, “The utility of internally transcribed spacer 2 DNA sequences of the nuclear ribosomal gene for distinguishing sibling species of Trichogramma,” BioControl, vol. 43, no. 4, pp. 421–440, 1999. View at Publisher · View at Google Scholar · View at Scopus
  26. W. J. Kress, K. J. Wurdack, E. A. Zimmer, L. A. Weigt, and D. H. Janzen, “Use of DNA barcodes to identify flowering plants,” Proceedings of the National Acadamy of Sciences of the United States of America, vol. 102, no. 23, pp. 8369–8374, 2005. View at Publisher · View at Google Scholar · View at Scopus
  27. S. L. Chen, H. Yao, J. P. Han et al., “Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species,” PLoS ONE, vol. 5, no. 1, Article ID e8613, 2010. View at Publisher · View at Google Scholar · View at Scopus
  28. J. Song, L. Shi, D. Li et al., “Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA,” PLoS ONE, vol. 7, no. 8, Article ID e43971, 2012. View at Publisher · View at Google Scholar · View at Scopus
  29. A. Keller, T. Schleicher, J. Schultz, T. Müller, T. Dandekar, and M. Wolf, “5.8S-28S rRNA interaction and HMM-based ITS2 annotation,” Gene, vol. 430, no. 1-2, pp. 50–57, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution, vol. 28, no. 10, pp. 2731–2739, 2011. View at Publisher · View at Google Scholar · View at Scopus
  31. K. Beckingham, “Insect rDNA,” The Cell Nucleus, vol. 10, pp. 205–269, 1982. View at Google Scholar
  32. H. H. Fan, T. C. Li, J. Qiu, Z. P. Li, Y. Lin, and Y. P. Cai, “Studies on genetic diversity of medicinal Dendrobium by SRAP,” Zhongguo Zhong Yao Za Zhi, vol. 33, pp. 6–10, 2008. View at Google Scholar
  33. M. Sharif and Abdul Jawad, “Interacting generalized dark energy and reconstruction of scalar field models,” Modern Physics Letters A, vol. 28, no. 38, Article ID 1350180, 15 pages, 2013. View at Publisher · View at Google Scholar
  34. Y. H. Bao, C. M. Pan, Y. Bai, and Y. N. Yan, “Genetic diversity of germplasm resources of Tiepishihu (Dendrobium officinale) analyzed with SRAP,” Journal of Beijing University of Chinese Medicine, vol. 37, pp. 349–353, 2014. View at Google Scholar
  35. Y. T. Liu, R. K. Chen, S. J. Lin et al., “Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify dendrobium species,” Genetics and Molecular Research, vol. 13, no. 2, pp. 2709–2717, 2014. View at Publisher · View at Google Scholar · View at Scopus
  36. W. L. Zhang, “Page analysis of genetic diversity of Dendrobium germplasm resources,” Northern Horticulture, pp. 104–106, 2014. View at Google Scholar
  37. D. J. Thornhill, T. C. Lajeunesse, and S. R. Santos, “Measuring rDNA diversity in eukaryotic microbial systems: How intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates,” Molecular Ecology, vol. 16, no. 24, pp. 5326–5340, 2007. View at Publisher · View at Google Scholar · View at Scopus
  38. M. Hajibabaei, G. A. C. Singer, P. D. N. Hebert, and D. A. Hickey, “DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics,” Trends in Genetics, vol. 23, no. 4, pp. 167–172, 2007. View at Publisher · View at Google Scholar · View at Scopus
  39. R. M. Caesar, M. Sörensson, and A. I. Cognato, “Integrating DNA data and traditional taxonomy to streamline biodiversity assessment: An example from edaphic beetles in the Klamath ecoregion, California, USA,” Diversity and Distributions, vol. 12, no. 5, pp. 483–489, 2006. View at Publisher · View at Google Scholar · View at Scopus
  40. H. Yao, J. Song, C. Liu et al., “Use of ITS2 region as the universal DNA barcode for plants and animals,” PLoS ONE, vol. 5, no. 10, Article ID e13102, 2010. View at Publisher · View at Google Scholar · View at Scopus
  41. J. Han, Y. Zhu, X. Chen et al., “The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS,” BioMed Research International, vol. 2013, Article ID 741476, 7 pages, 2013. View at Publisher · View at Google Scholar · View at Scopus
  42. J. C. Mai and A. W. Coleman, “The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants,” Journal of Molecular Evolution, vol. 44, no. 3, pp. 258–271, 1997. View at Publisher · View at Google Scholar · View at Scopus
  43. J. Schultz, S. Maisel, D. Gerlach, T. Müller, and M. Wolf, “A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota,” RNA, vol. 11, no. 4, pp. 361–364, 2005. View at Publisher · View at Google Scholar · View at Scopus
  44. T. J. Lott, B. M. Burns, R. Zancope-Oliveira, C. M. Elie, and E. Reiss, “Sequence analysis of the internal transcribed spacer 2 (ITS2) from yeast species within the genus Candida,” Current Microbiology, vol. 36, no. 2, pp. 63–69, 1998. View at Publisher · View at Google Scholar · View at Scopus
  45. H.-E. Lein, C.-F. Dai, and C. C. Wallace, “Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in scleractinian corals,” Zoological Studies, vol. 43, pp. 759–771, 2004. View at Google Scholar
  46. I. Young and A. W. Coleman, “The advantages of the ITS2 region of the nuclear rDNA cistron for analysis of phylogenetic relationships of insects: A Drosophila example,” Molecular Phylogenetics and Evolution, vol. 30, no. 1, pp. 236–242, 2004. View at Publisher · View at Google Scholar · View at Scopus
  47. J. Schultz, T. Müller, M. Achtziger, P. N. Seibel, T. Dandekar, and M. Wolf, “The internal transcribed spacer 2 database - A web server for (not only) low level phylogenetic analyses,” Nucleic Acids Research, vol. 34, pp. W704–W707, 2006. View at Publisher · View at Google Scholar · View at Scopus
  48. G. N. Fritz, J. Conn, A. Cockburn, and J. Seawright, “Sequence analysis of the ribosomal DNA internal transcribed spacer 2 from populations of Anopheles nuneztovari (diptera: culicidae),” Molecular Biology and Evolution, vol. 11, no. 3, pp. 406–416, 1994. View at Google Scholar · View at Scopus
  49. J. Liu, H.-F. Yan, S. G. Newmaster, N. Pei, S. Ragupathy, and X.-J. Ge, “The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China,” Diversity and Distributions, vol. 21, no. 2, pp. 188–199, 2015. View at Publisher · View at Google Scholar · View at Scopus
  50. G. Ding, X.-Y. Ding, J. Shen et al., “Genetic diversity and molecular authentication of wild populations of Dendrobium officinale by RAPD,” Yaoxue Xuebao, vol. 40, no. 11, pp. 1028–1032, 2005. View at Google Scholar · View at Scopus
  51. J. S. Lu, Z. Y. Bu, W. L. Lv, J. M. Su, C. Y. Huang, and C. N. Li, “ISSR analysis on genetic diversity of germplasms resources in Dendrobium SW. from different habitats,” Chinese Traditional and Herbal Drugs44, vol. 44, pp. 96–100, 2013. View at Google Scholar
  52. T. Takamiya, P. Wongsawad, N. Tajima et al., “Identification of Dendrobium species used for herbal medicines based on ribosomal DNA Internal transcribed spacer sequence,” Biological & Pharmaceutical Bulletin, vol. 34, no. 5, pp. 779–782, 2011. View at Publisher · View at Google Scholar · View at Scopus