Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species

PLoS ONE

Volumn 5, Issue 1, 2010, Pages

  Chen, Shilin ^a   Yao, Hui ^a   Han, Jianping ^a   Liu, Chang ^b   Song, Jingyuan ^a   Shi, Linchun ^a   Zhu, Yingjie ^a   Ma, Xinye ^a   Gao, Ting ^a   Pang, Xiaohui ^a   Luo, Kun ^c   Li, Ying ^a   Li, Xiwen ^a   Jia, Xiaocheng ^a   Lin, Yulin ^a   Leon, Christine ^d  

^a INSTITUTE OF MEDICINAL PLANT DEVELOPMENT   (China)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

^c HUBEI UNIVERSITY OF CHINESE MEDICINE   (China)

^d ROYAL BOTANIC GARDENS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

ARTICLE; CONTROLLED STUDY; DNA BARCODING; GENE LOCUS; ITS GENE; ITS2 GENE; MATK GENE; MEDICINAL PLANT; NONHUMAN; PLANT GENE; PLANT IDENTIFICATION; POLYMERASE CHAIN REACTION; PSBA TMH GENE; RBCL GENE; RPOC1 GENE; YCF5 GENE; GENETICS; INFORMATION PROCESSING; VALIDATION STUDY;

AUTOMATIC DATA PROCESSING; DNA, PLANT; PLANTS, MEDICINAL; POLYMERASE CHAIN REACTION;

EID: 77649108109     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008613     Document Type: Article

References (42)

1. Hebert PDN, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Biol Sci SerB 270: S96-S99.
2. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Biol Sci SerB 270: 313-321.
3. Blaxter M (2003) Molecular systematics: counting angels with DNA. Nature 421: 122-124.
4. Gregory TR (2005) DNA barcoding does not compete with taxonomy. Nature 434: 1067-1067.
5. Schindel DE, Miller SE (2005) DNA barcoding a useful tool for taxonomists. Nature 435: 17.
6. Miller SE (2007) DNA barcoding and the renaissance of taxonomy. Proc Natl Acad Sci USA 104: 4775-4776.
7. Marshall E (2005) Will DNA bar codes breathe life into classification? Science 307: 1037.
8. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci USA 103: 968-971.
9. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102: 8369-8374.
10. Seifert KA, Samson RA, Dewaard JR, Houbraken J, Lévesque CA, et al. (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci USA 104: 3901-3906.
11. Min XJ, Hickey DA (2007) Assessing the effect of varying sequence length on DNA barcoding of fungi. Mol Ecol Notes 7: 365-373.
12. Ross HA, Murugan S, Li WLS (2008) Testing the reliability of genetic methods of species identification via simulation. Syst Biol 57: 216-230.
13. Pennisi E (2007) Wanted: a barcode for plants. Science 318: 190-191.
14. Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, et al. (2005) Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc Lond B Biol Sci 360: 1889-1895.
15. Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, et al. (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE 3: e2802.
16. Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madriñán S, et al. (2007) A proposal for a standardised protocol to barcode all land plants. Taxon 56: 295-299.
17. Sass C, Little DP, Stevenson DW, Specht CD (2007) DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of Cycads. PLoS ONE 2: e1154.
18. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, et al. (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci USA 105: 2923-2928.
19. Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J (2008) Testing candidate plant barcode regions in the Myristicaceae. Mol Ecol Res 8: 480-490.
20. Newmaster SG, Fazekas AJ, Ragupathy S (2006) DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Can J Bot 84: 335-341.
21. Kress WJ, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2: e508.
22. Hollingsworth PM (2008) DNA barcoding plants in biodiversity hot spots: progress and outstanding questions. Heredity 101: 1-2.
23. Hollingsworth ML, Clark AA, Forrest LL, Richardson J, Pennington RT, et al. (2009) Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Mol Ecol Res 9: 439-457.
24. Kress WJ, Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proc Natl Acad Sci USA 105: 2761-2762.
25. Chiou SJ, Yen JH, Fang CL, Chen HL, Lin TY (2007) Authentication of medicinal herbs using PCR-amplified ITS2 with specific primers. Planta Med 73: 1421-1426.
26. Schultz J, Maisel S, Gerlach D, Müller T, Wolf M (2005) A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 11: 361-364.
27. Coleman AW (2003) ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends in Genetics 19: 370-375.
28. Miao M, Warren A, Song WB, Wang S, Shang HM, et al. (2008) Analysis of the internal transcribed spacer 2 (ITS2) region of Scuticociliates and related taxa (Ciliophora, Oligohymenophorea) to infer their evolution and phylogeny. Protist 159: 519-533.
29. Coleman AW (2007) Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucl Acids Res 35: 3322-3329.
30. Schultz J, Wolf M (2009) ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. Mol Phylogenet Evol 52: 520-523.
31. Sucher NJ, Carles MC (2008) Genome-based approaches to the authentication of medicinal plants. Planta Med 74: 603-623.
32. Yao H, Song JY, Ma XY, Liu C, Li Y, et al. (2009) Identification of Dendrobium species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region. Planta Med 75: 667-669.
33. Song JY, Yao H, Li Y, Li XW, Lin YL, et al. (2009) Authentication of the family Polygonaceae in Chinese pharmacopoeia by DNA barcoding technique. J Ethnopharm 124: 434-439.
34. Shaw D, Leon C, Kolev S, Murray V (1997) Traditional remedies and food supplements: a 5-year toxicological study (1991-1995). Drug Saf 17: 342-356.
35. Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3: 2229-2238.
36. Meier R, Zhang GY, Ali F (2008) The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification. Syst Biol 57: 809-813.
37. Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. PLoS Biol 2: e354.
38. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics 23: 167-172.
39. Müller T, Philippi N, Dandekar T, Schultz J, Wolf M (2007) Distinguishing species. RNA 13: 1469-1472.
40. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106: 12794-12797.
41. Thomas C (2009) Plant bar code soon to become reality. Science 325: 526.
42. Keller A, Schleicher T, Schultz J, Müller T, Dandekar T, et al. (2009) 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 430: 50-57.