Applying plant DNA barcodes for Rosaceae species identification

Cladistics

Volumn 27, Issue 2, 2011, Pages 165-170

  Pang, Xiaohui ^a   Song, Jingyuan ^a   Zhu, Yingjie ^a   Xu, Hongxi ^b   Huang, Linfang ^a   Chen, Shilin ^a  

^a INSTITUTE OF MEDICINAL PLANT DEVELOPMENT   (China)

^b Hong Kong Jockey Club Institute of Chinese Medicine   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DICOTYLEDON; GENETIC ANALYSIS; IDENTIFICATION METHOD; POLYMERASE CHAIN REACTION; TAXONOMY;

ROSACEAE;

EID: 79952401316     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2010.00328.x     Document Type: Article

References (41)

1. Alvarez, I., Wendel, J.F., 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29, 417-434.
2. CBOL Plant Working Group, 2009. A DNA barcode for land plants. Proc. Natl Acad. Sci. USA 106, 12794-12797.
3. Chen, S.L., Yao, H., Han, J.P., Liu, C., Song, J.Y., Shi, L.C., Zhu, Y.J., Ma, X.Y., Gao, T., Pang, X.H., Luo, K., Li, Y., Li, X.W., Jia, X.C., Lin, Y.L., Leon, C., 2010. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE 5, e8613.
4. Chiou, S.J., Yen, J.H., Fang, C.L., Chen, H.L., Lin, T.Y., 2007. Authentication of medicinal herbs using PCR-amplified ITS2 with specific primers. Planta Med. 73, 1421-1426.
5. Coleman, A.W., 2007. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res. 35, 3322-3329.
6. Desalle, R., Amato, G., 2004. The expansion of conservation genetics. Nat. Rev. Genet. 5, 702-712.
7. Ebach, M.C., Holdrege, C., 2005. More taxonomy, not DNA barcoding. Bioscience 55, 823-824.
8. Feliner, G.N., Rosselló, J.A., 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol. Phylogenet. Evol. 44, 911-919.
9. Gehrke, B., Brauchler, C., Romoleroux, K., Lundberg, M., Heubl, G., Eriksson, T., 2008. Molecular phylogenetics of Alchemilla, Aphanes and Lachemilla (Rosaceae) inferred from plastid and nuclear intron and spacer DNA sequences, with comments on generic classification. Mol. Phylogenet. Evol. 47, 1030-1044.
10. Hajibabaei, M., Janzen, D.H., Burns, J.M., Hallwachs, W., Hebert, P.D.N., 2006. DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl Acad. Sci. USA 103, 968-971.
11. Hajibabaei, M., Singer, G.A.C., Clare, E.L., Hebert, P.D.N., 2007. Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biol. 5, 24.
12. Hebert, P.D.N., Cywinska, A., Ball, S.L., de Waard, J.R., 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270, 313-321.
13. Hebert, P.D.N., Stoeckle, M.Y., Zemlak, T.S., Francis, C.M., 2004. Identification of birds through DNA barcodes. PLoS Biol. 2, e312.
14. Kress, W.J., Erickson, D.L., 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.
15. Lahaye, R., van der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., 2008. DNA barcoding the floras of biodiversity hotspots. Proc. Natl Acad. Sci. USA 105, 2923-2928.
16. Lee, S., Wen, J., 2001. A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA. Am. J. Bot. 88, 150-160.
17. Matsumoto, S., Kouchi, M., Yabuki, J., Kusunoki, M., Ueda, Y., Fukui, H., 1998. Phylogenetic analyses of the genus Rosa using the matK sequence: molecular evidence for the narrow genetic background of modern roses. Sci. Hortic. 77, 73-82.
18. Meier, R., Zhang, G.Y., 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.
19. Meyer, C.P., Paulay, G., 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biol. 3, 2229-2238.
20. Miao, M., Warren, A., Song, W., Wang, S., Shang, H., Chen, Z., 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.
21. Morgan, D.R., Soltis, D.E., Robertson, K.R., 1994. Systematic and evolutionary implications of rbcL sequence variation in Rosaceae. Am. J. Bot. 81, 890-903.
22. Moritz, C., Cicero, C., 2004. DNA barcoding: promise and pitfalls. PLoS Biol. 2, 279-354.
23. Newmaster, S.G., Fazekas, A.J., Ragupathy, S., 2006. DNA barcoding in the land plants: evaluation of rbcL in a multigene tiered approach. Can. J. Bot. 84, 335-341.
24. Potter, D., 2003. Molecular phylogenetic studies in Rosaceae. In: Sharma, A.K., Sharma, A. (Eds.), Plant Genome: Biodiversity and Evolution. Science Publishers, New Hampshire, pp. 319-351.
25. Potter, D., Eriksson, T., Evans, R.C., Oh, S., Smedmark, J.E.E., Morgan, D.R., Kerr, M., Robertson, K.R., Arsenault, M., Dickinson, T.A., Campbell, C.S., 2007a. Phylogeny and classification of Rosaceae. Plant Syst. Evol. 266, 5-43.
26. Potter, D., Still, S.M., Grebenc, T., Ballian, D., Bozic, G., Franjia, J., Kraigher, H., 2007b. Phylogenetic relationships in tribe Spiraeeae (Rosaceae) inferred from nucleotide sequence data. Plant Syst. Evol. 266, 105-118.
27. Ross, H.A., Murugan, S., Li, W.L.S., 2008. Testing the reliability of genetic methods of species identification via simulation. Syst. Biol. 57, 216-230.
28. Sass, C., Little, D.P., Stevenson, D.W., Specht, C.D., 2007. DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of Cycads. PLoS ONE 2, e1154.
29. Savolainen, V., Cowan, R.S., Vogler, A.P., Roderick, G.K., Lane, R., 2005. Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360, 1811-1850.
30. 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.
31. Schulze-Menz, G.K., 1964. Rosaceae. In: Melchior, H. (Ed.), Engler's Syllabus der Pflanzenfamilien. Gebrüder Borntraeger, Berlin, pp. 209-218.
32. Song, J.Y., Yao, H., Li, Y., Li, X.W., Lin, Y.L., Liu, C., Han, J.P., Xie, C.X., Chen, S.L., 2009. Authentication of the family Polygonaceae in Chinese pharmacopoeia by DNA barcoding technique. J. Ethnopharmacol. 124, 434-439.
33. Starr, J., Bruneau, A., 2002. Phylogeny of Rosa L. (Rosaceae) based on trnL-F intron and spacer sequences. Abstract Botany 2002, 1. ASPT Colloquium: Rosaceae phylogeny: current knowledge, problems, and prospects. [].
34. Stoeckle, M., 2003. Taxonomy, DNA and the bar code of life. Bioscience 53, 2-3.
35. Takhtajan, A., 1997. Diversity and Classification of Flowering Plants. Columbia University Press, New York.
36. Tamura, K., Dudley, J., Nei, M., Kumar, S., 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599.
37. Ward, R.D., Zemlak, T.S., Innes, B.H., Last, P.R., Hebert, P.D.N., 2005. DNA barcoding Australia's fish species. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360, 1847-1857.
38. Will, K.W., Rubinoff, D., 2004. Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20, 47-55.
39. Will, K.W., Mishler, B., Wheeler, Q., 2005. The perils of DNA barcoding and the need for integrative taxonomy. Syst. Biol. 54, 844-851.
40. Wissemann, V., 2003. Conventional taxonomy of wild roses. In: Roberts, A., Debener, T., Gudin, S. (Eds.), Encyclopedia of Rose Science. Elsevier Science, London, pp. 111-117.
41. Wissemann, V., Ritz, C.M., 2005. The genus Rosa (Rosoideae, Rosaceae) revisited: molecular analysis of nrITS-1 and atpB-rbcL intergenic spacer (IGS) versus conventional taxonomy. Bot. J. Linn. Soc. 147, 275-290.