DNA barcoding in plants: Taxonomy in a new perspective

Current Science

Volumn 99, Issue 11, 2010, Pages 1530-1541

  Vijayan, K ^a,b   Tsou, C H ^a  

^a INSTITUTE OF PLANT AND MICROBIAL BIOLOGY   (Taiwan)

^b CENTRAL SILK BOARD   (India)

Author keywords

Barcoding; DNA sequence; Locus; Plants; Taxonomy

Indexed keywords

ANIMALIA;

EID: 78650450988     PISSN: 00113891     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (104)

1. Hebert, P. D. N., Cywinska, A., Ball, S. L. and deWaard, J. R., Biological identifications through DNA barcodes. Proc. R. Soc. London, Ser. B, 2003, 270, 313-321.
2. Hebert, P. D. N. and Gregory, T. R., The promise of DNA barcoding for taxonomy. Syst. Biol., 2005, 54, 852-859.
3. Taberlet, P. et al., Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res., 2007, 35, e14.
4. Kress, J. W., Wurdack, K. J., Zimmer, E. A., Weigt, L. A. and Janzen, D. H., Use of DNA barcodes to identify flowering plants. Proc. Natl. Acad. Sci. USA, 2005, 102, 8369-8374.
5. CBOL-Plant Working Group, A DNA barcode for land plants. Proc. Natl. Acad. Sci. USA, 2009, 106, 12794-12797.
6. Ratnasingham, S. and Hebert, P. D. N., BOLD: The Barcode of Life Data System (www.barcodinglife.org). Mol. Ecol. Notes, 2007, 7, 355-364.
7. Blaxter, M., Counting angels with DNA. Nature, 2003, 42, 122-124.
8. Schindel, D. E. and Miller, S. E., DNA barcoding a useful tool for taxonomists. Nature, 2005, 435, 177.
9. Lahaye, R. et al., DNA barcoding the floras of biodiversity hotspots. Proc. Natl. Acad. Sci. USA, 2008, 105, 2923-2928.
10. Ebach, M. C. and Holrege, C., DNA barcoding is no substitute for taxonomy. Nature, 2005, 434, 697.
11. Gregory, T. R., DNA barcoding does not compete with taxonomy. Nature, 2005, 434, 1067.
12. Pennisi, E., Taxonomy. Wanted: A barcode for plants. Science, 2007, 318,190-191.
13. Wolfe, K. H., Li, W. H. and Sharp, P. M., Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc. Natl. Acad. Sci. USA, 1987, 84, 9054-9058.
14. Chase, M. W. et al., A proposal for a standardized protocol to barcode all land plants. Taxon, 2007, 56, 295-299.
15. Sass, C., Little, D. P., Stevenson, D. W. and Specht, C. D., DNA barcoding in the Cucadales: testing the potential of proposed barcoding markers for species indentification of cycades. PLoS ONE, 2007, 2, e1154.
16. Appels., R. and Honeycutt, R. L., rDNA: evolution over a billion years. In DNA Systematics Vol. II. Plants (ed. Dutta S. K.), CRC Press, Boca Raton, FL, 1986, pp. 81-135.
17. Hemleben, V., Ganal, M., Gerstner, J., Schiebel, K. and Torres, R. A., Organization and length heterogeneity of plant ribosomal RNA genes. In Architecture of Eukaryotic Genes (ed. Kahl, G.), VCH, Weinhein, Germany, 1988, pp. 371-383.
18. Hershkovitz, M. A. and Zimmer, E. A., Conservation pattern in angiosperm rDNA-ITS2 sequences. Nucleic Acids Res., 1996, 24, 2857-2867.
19. Brown, D., Wensink, P. C. and Jordan, E., Comparison of the ribosomal DNA's of Xenopus laecis and Xenopus muller: the evolution of tandem genes. J. Mol. Biol., 1972, 63, 57-73.
20. Hood, L., Campbell, J. H. and Elgin, S. C. R., The organization, expression and evolution of antibody genes and other multigene families. Annu. Rev. Genet., 1975, 9, 305-353.
21. Zimmer, E. A., Martin, S. L., Beverley, S. M., Kan, Y. W. and Wilson, A. C., Rapid duplication and loss of genes coding for the alpha chains of hemoglobin. Proc. Natl. Acad. Sci. USA, 1980, 77, 2158-2162.
22. Baldwin, B. G., Sanderson, M. J., Porter, J. M., Wojciechowski, M. F., Campbell, C. S. and Donoghue, M. J., The ITS regions of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Mo. Bot. Gard., 1995, 82, 247-277.
23. Alvarez, I. and Wendel, J. F., Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol., 2003, 29, 417-434.
24. Rogers, S. O. and Bendich, A. J., Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol. Biol., 1987, 6, 339-345.
25. Bailey, C. D., Carr, T. G., Harris, S. A. and Hughes, C. E., Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Mol. Phylogenet. Evol., 2003, 29, 435-455.
26. Buckler, E. S., Ipplito, S. A. and Holtsford, T. P., The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics, 1997, 145, 111-125.
27. Campbell, C. S., Wojciechowski, M. F., Baldwin, B. G., Alice, L. A. and Donoghue, M. J., Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Mol. Biol. Evol., 1997, 14, 81-90.
28. Feliner, G. N. and Rosselló, J. A., Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol. Phylogenet. Evol., 2007, 44, 911-919.
29. Vijayan, K., Zhang, W. J. and Tsou, C. H., Molecular taxonomy of Camellia (Theaceae) as inferred from nrITS sequences. Am. J. Bot., 2009, 96, 1348-1360.
30. Muir, G., Fleming, C. C. and Schlötterer, C., Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L. Mol. Biol. Evol., 2001, 18, 112-119.
31. Wendel, J. F., Schnabel, A. and Seelanan, T., Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA, 1995, 92, 280-284.
32. Hollingsworth, M. L. et al., Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Mol. Ecol. Res., 2009, 9, 439-457.
33. Okuyama, Y. and Kato, M., Unveiling cryptic species diversity of flowering plants: successful biological species identification of Asian Mitella using nuclear ribosomal DNA sequences. BMC Evol. Biol., 2009, 9, 105.
34. Chen, S. et al., Validation of the ITS2 region as a model DNA barcode for identifying medicinal plants species. PLoS ONE, 2010, 5, e8613.
35. Ledford, H., Botanical identities: DNA barcoding for plants comes a step closer. Nature, 2008, 451, 616.
36. Shinozaki, K. et al., The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J., 1986, 5, 2043-2049.
37. Zurawski, G., Perrot, B., Bottomley, W. and Whitefield, P. R., The structure of the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase from spinach chloroplast DNA. Nucleic Acids Res., 1981, 9, 3251-3270.
38. Newmaster, S. G., Fazekas, A. J. and Ragupathy, S., DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Can. J. Bot., 2006, 84, 335-341.
39. Albert, V. A., Backlund, A., Bremer, K., Chase, M. W., Manhart, J. R., Mishler, B. D. and Nixon, K. C., Functional constraints and rbcL evidence for land plant phylogeny. Ann. Mo. Bot. Gard., 1994, 81, 534-567.
40. Soltis, D. E. and Soltis, P. S., Choosing an approach and an appropriate gene for phylogenetic analysis. In Molecular Systematics of Plants II: DNA Sequencing (eds Soltis, D. E., Soltis, P. S. and Doyle, J. J.), Kluwer, Dordrecht, 1998, pp. 21-24.
41. Kress, W. J. and Erickson, D. L., A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE, 2007, 2, e508.
42. Fay, M. F., Swensen, S. M. and Chase, M. W., Taxonomic affinities of Medusagyne oppositifolia (Medusagynaceae). Kew Bull., 1997, 52, 111-120.
43. Wolfe, K. H., Protein-coding genes in chloroplast DNA: compilation of nucleotide sequences, data base entries and rates of molecular evolution. In Cell Culture and Somatic Cell Genetics of Plants (ed. Vasil, K.), Academic Press, San Diego, 1991, vol 7BI, pp. 467-482.
44. Neuhaus, H. and Link, G., The chloroplast tRNA(UUU) gene from mustard (Sinapsis alba) contains a class II intron potentially coding for a maturase-related polypeptide. Curr. Genet., 1987, 11, 251-257.
45. Hilu, K. W. and Liang, H., The matK gene: sequence variation and application in plant systematics. Am. J. Bot., 1997, 84, 830-839.
46. Kelchner, S. A., The evolution of noncoding chloroplast DNA and its application in plant systematics. Ann. Mo. Bot. Gard., 2000, 87, 482-498.
47. Cuénoud, P., Savolainen, V., Chatrou, L. W., Powell, M., Grayer, R. J. and Chase, M. W., Molecular phylogenetics of caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. Am. J. Bot., 2002, 89, 132-144.
48. Schmitz-Linneweber, C., Maier, R. M., Alcaraz J. P., Cottet, A., Herrmann, R. G. and Mache, R., The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol., 2001, 45, 307-315.
49. Johnson, L. S. and Soltis, D. E., Phylogenetic inference in Saxifragaceae sensu strict and Gilia (Polemoniaceae) using matK sequences. Ann. Mo. Bot. Gard., 1995, 82, 149-175.
50. Ford, C. S. et al., Selection of candidate coding DNA barcoding regions for use on land plants. Bot. Linn. Soc., 2009, 159, 1-11.
51. Starr, J. R., Naczi, R. F. C. and Chouinard, B. N., Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae). Mol. Ecol. Resour., 2009, 9(Suppl. 1), 151-163.
52. Serino, G. and Maliga, P., RNA polymerase subunits encoded by the plastid rpo genes are not shared with the nucleus-encoded plastid enzyme. Plant Physiol., 1998, 117, 1165-1170.
53. Guisinger, M. M., Kuehl, J. V., Boore, J. L. and Jansen, R. K., Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions. Proc. Natl. Acad. Sci. USA, 2008, 105, 18424-18429.
54. Tsumura, Y., Kawahara, T., Wickneswari, R. and Yoshimura, K., Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes. Theor. Appl. Genet., 1996, 93, 22-29.
55. Adekambi, T., Drancourt, M. and Raoult, D., The rpoB gene as a tool for clinical microbiologists. Trends Microbiol., 2008, 17, 37-46.
56. Logacheva, M. D., Penin, A. A., Samigullin, T. H., Vallejo-Roman, C. M. and Antonov, A. S., Phylogeny of flowering plants by the chloroplast genome sequences: in search of a 'Lucky Gene'. Biochemistry, 2007, 72, 1324-1329.
57. Fazekas, A. J. et al., Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE. 2008, 3, e2802.
58. Liu, Y., Yan, H. F., Cao, T. and Ge, X. J., Evaluation of 10 plant barcodes in bryophyte (mosses). J. Syst. Evol., 2010, 48, 36-46.
59. Hajdukiewicz, P. T. J., Allison, L. A. and Maliga, P., The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J., 1997, 16, 4041-4048.
60. Yasui, Y. and Ohnishi, O., Interspecific relationships in Fagopyrum (Polygonaceae) revealed by the nucleotide sequences of the rbcL and accD genes and their intergenic region. Am. J. Bot., 1998, 85, 1134-1142.
61. Devey, D. S., Chase, M. W. and Clarkson, J. J., A stuttering start to plant DNA barcoding: microsatellites present a previously overlooked problem in non-coding plastid regions. Taxon, 2009, 58, 7-15.
62. Wakasugi, T., Tsudzuki, T. and Sugiura, M., The genomic of plant chloroplasts: gene content and alteration of genomic information by RNA editing. Photosyn. Res., 2001, 70, 107-118.
63. Tsuruya, K., Suzuki, M., Plader, W., Sugita, C. and Sugita, M., Chloroplast transformation reveals that tobacco ycf 5 is involved in photosynthesis. Acta Physiol. Plant., 2006, 28, 365-371.
64. Ohyama, K. et al., Chloroplast gene organisation deduced from complete sequence analysis of liverwort Marchantia polymorpha chloroplast DNA. Nature, 1986, 322, 572-574.
65. Burrows, P. A., Sazanov, L. A., Svab, Z., Maliga, P. and Nixon, P. J., Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes. EMBO J., 1998, 17, 868-876.
66. Nakazono, M. and Hirai, A., Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice. Mol. Gen. Genet., 1993, 236, 341-346.
67. Yamagishi, H., Terachi, T., Ozaki, A. and Ishibashi, A., Inter-and intraspecific sequence variations of the chloroplast genome in wild and cultivated Raphanus. Plant Breed., 2009, 128, 172-177.
68. Wakasugi, T., Tsudzuki, J., Ito, S., Nakashima, K., Sudzuki, T. and Sugiura, M., Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc. Natl. Acad. Sci. USA, 1994, 91, 9794-9798.
69. Haberhausen, G. and Zetsche, K., Functional loss of all ndh genes in an otherwise relatively unaltered plastid genome of the holo-parasitic flowering plant Cuscuta reflexa. Plant Mol. Biol., 1994, 24, 217-222.
70. Braukmann, T. W. A., Kuzmina, M. and Stefanović, S., Loss of all plastid ndh genes in Gnetales and conifers: Extent and evolutionary significance for the seed plant phylogeny. Curr. Genet., 2009, 55, 323-337.
71. Drager, R. G. and Hallick, R. B., A novel Euglena gracilis chloroplast operon encoding 4 ATP synthase subunits and 2 ribosomal-proteins contains 17 Introns. Curr. Genet., 1993, 23, 271-280.
72. Lahaye, R., Savolainen, V., Duthoit, S., Maurin, O. and van der Bank, M., A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park as a model system (South Africa). Nature Proc., 2008; hdl: 10101/npre.1896.1
73. Shaw, J. et al., The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot., 2005, 92, 142-166.
74. Lee, H. L., Yi, D. K., Kim, J. S. and Kim, K. J., Development of plant DNA barcoding markers from the variable noncoding regions of chloroplast genome. In Abstract presented at the Second International Barcode of Life Conference, Academia Sinica, Taipei, Taiwan, September 2007, pp. 18-20; http://www.bolin-fonet.org/conferences/assets/files/confrence_abstract_book.pdf
75. Chang, C. C. et al., The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol. Biol. Evol., 2006, 23, 279-291.
76. Devey, D. S., Chase, M. W. and Clarkson, J. J., A stuttering start to plant DNA barcoding: Microsatellites present a previously overlooked problem in non-coding plastid regions. Taxon, 2009, 58, 7-15.
77. Newmaster, S. G., Fazekas, A. J., Steeves, R. A. D. and Janovec, J., Testing candidate plant barcode regions in the Myristicaceae. Mol. Ecol. Notes, 2008, 8, 480-490.
78. Erickson, D. L., Spouge, J., Resch, A., Weigt, L. A. and Kress, J. W., DNA barcoding in land plants: Developing standards to quantify and maximize success. Taxon, 2008, 57, 1304-1316.
79. van de Wiel, C. C. M., van der Schoot, J., van Valkenburg, J. L., Duistermaat, C. H. and Smulders, M. J. M., DNA barcoding discriminates the noxious invasive plant species, floating pennywort (Hydrocotyle ranunculoides L.f.), from non-invasive relatives. Mol. Ecol. Resour., 2009, 9, 1086-1091.
80. Meng, B. Y., Wakasugi, T. and Sugiura, M., Two promoters within the psbK-psbl-trnG gene-cluster in tobacco chloroplast DNA. Curr. Genet., 1991, 20, 259-264.
81. Knauf, U. and Hachtel, W., The genes encoding subunits of ATP synthase are conserved in the reduced plastid genome of the heterotrophic alga Prototheca wickerhamii. Mol. Genet. Genome, 2002, 267, 492-497.
82. McNeal, J. R., Kuehl, J. V., Boore, J. L. and de Pamphilis, C. W., Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biol., 2007, 7.
83. Taberlet, P., Gielly, L., Pautou, G. and Bouvet, J., Universal primers for amplification of three non-coding regions of the chloroplast DNA. Plant Mol. Biol., 1991, 17, 1105-1109.
84. Besendahl, A., Qiu, Y.-L., Lee, J., Palmer, J. D. and Bhattacharya, D., The cyanobacterial origin and vertical transmission of the plastid tRNALeu group-I-intron. Curr. Genet., 2000, 37, 12-23.
85. Simon, D., Fewer, D., Friedl, T. and Bhattacharya, D., Phylogeny and self-splicing ability of the plastid tRNA-Leu group I intron. J. Mol. Evol., 2003, 57, 710-720.
86. Quandt, D. and Stech, M., Molecular systematics of bryophytes in context of land plant phylogeny. In Plant Genome Phanerogams (eds Sharma, A. K. and Sharma, A.), Oxford and IBH Publishing, New Delhi, 2003, vol. 1, pp. 267-295.
87. Quandt, D., Müller, K., Stech, M., Frahm, J. P., Frey, W., Hilu, K. W. and Borsch, T., Molecular evolution of the chloroplast trnL-F region in land plants. Monogr. Syst. Bot. Mo. Bot. Gard., 2004, 98, 13-37.
88. Jurado-Rivera, J. A., Vogler, A. P., Reid, C. A. M., Petitpierre, E. and Gomez-Zurita, J., DNA barcoding insect-host plant association. Proc. R. Soc. Biol. Sci. Ser. B, 2009, 276, 639-648.
89. Little, D. P. and Stevenson, D. W., A comparison of algorithms for the identification of specimens using DNA barcodes: Examples from gymnosperms. Cladistics, 2007, 23, 1-21.
90. Spooner, D. M., DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. Am. J. Bot., 2009, 96, 1177-1189.
91. Shi, S., Jin, H., Zhong, Y., He, X., Huang, Y., Tan, F. and Bouf-ford, D. E., Phylogenetic relationships of the Magnoliaceae inferred from cpDNA matK sequences. Theor. Appl. Genet., 2000, 101, 925-930.
92. Rohwer, J. G., Towards a phylogenetic classification of the Lau-raceae: Evidence from matK sequences. Syst. Bot., 2000, 25, 60-71.
93. Soltis, D. E., Soltis, P. S. and Milligan, B. G., Intraspecific chloroplast DNA variation: systematic and phylogenetic implications. In Molecular Systematics of Plants (eds Soltis, P. S., Soltis, D. E. and Doyle, J. J.), Chapman and Hall, New York, USA, 1992, pp. 117-150.
94. Okuyama, Y. et al., Nonuniform concerted evolution and chloroplast capture: Heterogeneity of observed introgression patterns in three molecular data partition phylogenies of Asian Mitella (Saxi-fragaceae). Mol. Biol. Evol., 2005, 22, 285-296.
95. Raghupathy, S., Newmaster, S. G., Murugesan, M. and Bala-subramaniam, V., DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India. Mol. Ecol. Resources, 2009, 9 (Suppl. 1), pp. 164-171.
96. Newmaster, S. G. and Raghupathy, S., Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Mol. Ecol. Res., 2009, 9 (Suppl. 1), 172-180.
97. Durbin, R., Eddy, S., Krogh, A. and Mitchison, G., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, UK, 1998.
98. White, T. J., Bruns, T., Lee, S. and Taylor, J. W., Amplification and direct sequencing of fungal ribosomal RNA genes for phy-logenetics. In PCR Protocols: A Guide to Methods and Applications (eds Innis, M. A. et al.), Academic Press, New York, 1990, pp. 315-322.
99. Urbatsch, L. E., Baldwin, B. G. and Donoghue, M. J., Phylogeny of the coneflowers and relatives (Heliantheae: Asteraceae) based on nuclear rDNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction site data. Syst. Bot., 2000, 25, 539-565.
100. Gardes, M. and Bruns, T. D., ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol. Ecol., 1993, 2, 113-118.
101. Wang, X., Tsumura, Y., Yoshimaru, H., Nagasaka, K. and Szmidt, A. E., Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20-rps18 spacer, and trnV intron sequences. Am. J. Bot., 1999, 86, 1742-1753.
102. Tate, J. A. and Simpson, B. B., Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Syst. Bot., 2003, 28, 723-737.
103. Sang, T., Crawford, D. J. and Stuessy, T. F., Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Am. J. Bot., 1997, 84, 1120-1136.
104. Hamilton, M. B., Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol. Ecol., 1999, 8, 513-525.