DNA barcoding bromeliaceae: Achievements and pitfalls

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Maia, Vitor Hugo ^b   da Mata, Camila Souza ^a   Franco, Luciana Ozório ^a   Cardoso, Mônica Aires ^a   Cardoso, Sérgio Ricardo Sodré ^a   Hemerly, Adriana Silva ^b   Ferreira, Paulo Cavalcanti Gomes ^b  

^a INSTITUTO DE PESQUISAS JARDIM BOTÂNICO DO RIO DE JANEIRO   (Brazil)

^b FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

ARTICLE; ASTERACEAE; BROMELIACEAE; CONTROLLED STUDY; DNA BARCODING; DNA EXTRACTION; DNA SEQUENCE; GENE AMPLIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORCHIDACEAE; PHYLOGENY; PLASTID GENOME; RAIN FOREST; SEQUENCE ALIGNMENT; SPECIES IDENTIFICATION; TAXONOMY; CLASSIFICATION; GENETIC DATABASE; GENETICS; METHODOLOGY; PLASTID; POLYMERASE CHAIN REACTION;

ANIMALIA; ASTERACEAE; BROMELIACEAE; EMBRYOPHYTA; ORCHIDACEAE;

BASE SEQUENCE; BROMELIACEAE; DATABASES, GENETIC; DNA BARCODING, TAXONOMIC; PHYLOGENY; PLASTIDS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84855392573     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029877     Document Type: Article

References (31)

1. Vernooy R, Haribabu E, Muller MR, Vogel JH, Hebert PDN, et al. (2010) Barcoding life to conserve biological diversity: beyond the taxonomic imperative. Plos Biol 8: e1000417 doi:10.1371/journal.pbio.1000417.
2. Bradshaw CJA, Sodhi NS, Brook BW, (2009) Tropical turmoil: a biodiversity tragedy in progress. Front Ecol Environ 7: 79-87 doi:10.1890/070193.
3. Malhi Y, Roberts JT, Betts RA, Killeen TJ, Li W, et al. (2008) Climate change, deforestation, and the fate of the Amazon. Science 319: 169-172 doi:10.1126/science.1146961.
4. Savolainen V, Reeves G, (2004) A plea for DNA banking. Science 304: 1445-1445 doi:10.1126/science.304.5676.1445b.
5. Hebert PDN, Cywinska A, Ball SL, deWaard JR, (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270: 313-321 doi:10.1098/rspb.2002.2218.
6. Smith MA, Woodley NE, Janzen DH, Hallwachs W, Hebert PDN, (2006) DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). P Natl Acad Sci Usa 103: 3657-3662 doi:10.1073/pnas.0511318103.
7. Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD, (2007) Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol 7: 135 doi:10.1186/1471-2148-7-135.
8. CBOL Plant Working Group (2009) A DNA barcode for land plants. P Natl Acad Sci Usa 106: 12794-12797 doi:10.1073/pnas.0905845106.
9. Steven GN, Subramanyam R, (2009) Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Molecular Ecology Resources 9 (Suppl s1): 172-180 doi:10.1111/j.1755-0998.2009.02642.x.
10. Dolye JJ, Doyle JL, (1987) A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochemical Bulletin 9: 11-15.
11. Cuénoud P, Savolainen V, Chatrou L, Powell M, Grayer R, et al. (2002) Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. Am J Bot 89: 132-144.
12. Fay M, Cameron K, Prance G, Lledó M, (1997) Familial relationships of Rhabdodendron (Rhabdodendraceae): plastid rbcL sequences indicate a caryophyllid placement. Kew Bulletin 52 (4): 923-932.
13. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32 (5): 1792-97.
14. Arenas-Diaz E, Ochoterena H, Rodriguez-Vazquez K, (2009) Multiple sequence alignment using a genetic algorithm and GLOCSA. Journal of Artificial Evolution and Applications 2009: 963150.
15. Swofford DL, (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusett.
16. Farris JS, Kallersjo M, Kluge AG, Bult C, (1994) Testing Significance of Incongruence. Cladistics 10 (3): 315-319.
17. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol doi:10.1093/molbev/msr121.
18. Nei M, Kumar S, (2000) Molecular evolution and phylogenetics. Oxford University Press, New York, NY, USA.
19. Posada D, (2008) jModelTest: Phylogenetic Model Averaging. Mol Biol Evol 25 (7): 1253-1256.
20. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52 (5): 696-704.
21. Gascuel O, (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14 (7): 685-95.
22. Ebihara A, Nitta JH, Ito M, (2010) Molecular Species Identification with Rich Floristic Sampling: DNA Barcoding the Pteridophyte Flora of Japan. Plos One 5: e15136 doi:10.1371/journal.pone.0015136.
23. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinf 10: 421.
24. Givnish TJ, Barfuss MHJ, Ee BV, Riina R, Schulte K, et al. (2011) Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: Insights from an eight-locus plastid phylogeny. Am J Bot 98: 872-895 doi:10.3732/ajb.1000059.
25. Pang X, Song J, Zhu Y, Xu H, Huang L, et al. (2011) Applying plant DNA barcodes for Rosaceae species identification. Cladistics 27: 165-170 doi:10.1111/j.1096-0031.2010.00328.x.
26. Gao T, Sun Z, Yao H, Song J, Zhu Y, et al. (2011) Identification of Fabaceae plants using the DNA barcode matK. Planta Med 77: 92-94 doi:10.1055/s-0030-1250050.
27. Pang X, Song J, Zhu Y, Xie C, Chen S, (2010) Using DNA barcoding to identify species within Euphorbiaceae. Planta Med 76: 1784-1786 doi:10.1055/s-0030-1249806.
28. Gao T, Yao H, Song J, Zhu Y, Liu C, et al. (2010) Evaluating the feasibility of using candidate DNA barcodes in discriminating species of the large Asteraceae family. BMC Evol Biol 10: 324 doi:10.1186/1471-2148-10-324.
29. Spooner DM, (2009) DNA barcoding will frequently fail in complicated groups: An example in wild potatoes. Am J Bot 96: 1177-1189 doi:10.3732/ajb.0800246.
30. Gonzalez MA, Baraloto C, Engel J, Mori SA, Petronelli P, et al. (2009) Identification of Amazonian Trees with DNA Barcodes. Plos One 4: e7483 doi:10.1371/journal.pone.0007483.
31. Steele PR, Pires JC, (2011) Biodiversity assessment: State-of-the-art techniques in phylogenomics and species identification. Am J Bot 98: 415-425 doi:10.3732/ajb.1000296.