Critical factors for assembling a high volume of DNA barcodes

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 360, Issue 1462, 2005, Pages 1959-1967

  Hajibabaei, Mehrdad ^a   DeWaard, Jeremy R ^a   Ivanova, Natalia V ^a   Ratnasingham, Sujeevan ^a   Dooh, Robert T ^a   Kirk, Stephanie L ^a   Mackie, Paula M ^a   Hebert, Paul D N ^a  

^a UNIVERSITY OF GUELPH   (Canada)

Author keywords

Cox1; DNA isolation; Museum specimens; PCR; Species identification; Taxonomy

Indexed keywords

DNA; EUKARYOTE; POLYMERASE CHAIN REACTION; SPECIMEN BANK;

EUKARYOTA;

DNA;

ARTICLE; BIODIVERSITY; COMPARATIVE STUDY; DIAGNOSTIC PROCEDURE; DNA SEQUENCE; GENETIC DATABASE; GENETICS; INFORMATION PROCESSING; INFORMATION SYSTEM; INSTRUMENTATION; LABORATORY DIAGNOSIS; METHODOLOGY; POLYMERASE CHAIN REACTION;

AUTOMATIC DATA PROCESSING; BIODIVERSITY; DATABASES, GENETIC; DNA; INFORMATION MANAGEMENT; MOLECULAR DIAGNOSTIC TECHNIQUES; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SPECIMEN HANDLING;

EID: 32244446837     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2005.1727     Document Type: Article

References (44)

1. Abu Al-Soud, W. & Radstrom, P. 2000 Effects of amplification facilitators on diagnostic PCR in the presence of blood, feces, and meat. J. Clin. Microbiol. 38, 4463-4470.
2. Altschul, S. R, Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. 1990 Basic local alignment search tool. J. Mol. Biol. 215, 403-410. (doi:10.1006/jmbi.1990.9999.)
3. Barrett, R. & Hebert, P. D. N. 2005 Identifying spiders through DNA barcodes. Can. J. Zool. 83, 481-491.
4. Bensasson, D., Zhang, D., Hartl, D. L. & Hewitt, G. M. 2001 Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol. Evol. 16, 314-321. (doi:10.1016/S0169-5347(01)02151-6.)
5. Boom, R., Sol, C. J., Salimans, M. M., Jansen, C. L., Wertheim-van Dillen, P. M. & van der Noordaa, J. 1990 Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495-503.
6. Candrian, U., Furrer, B., Hofelein, C. & Luthy, J. 1991 Use of inosine-containing oligonucleotide primers for enzymatic amplification of different alleles of the gene coding for heat-stable toxin type I of enterotoxigenic Escherichia coli. Appl. Environ. Microbiol. 57, 955-961.
7. Chase, M. W., Salamin, N., Wilkinson, M., Dunwell, J. M., Kesanakurthi, R. P., Haidar, N. & Savolainen, V. 2005 Land plants and DNA barcodes: short-term and long-term goals. Phil. Trans. R. Soc. B 360, 1889-1895. (doi:10.1098/rstb.2005.1720.)
8. Cline, J., Braman, J. C. & Hogrefe, H. H. 1996 PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 24, 3546-3551. (doi:10.1093/nar/24.18.3546.)
9. DeSalle, R. & Amato, G. 2004 The expansion of conservation genetics. Nat. Rev. Genet. 5, 702-712. (doi:10.1038/nrg1425.)
10. Di Bernardo, G., Del Gaudio, S., Cammarota, M., Galderisi, U., Cascino, A. & Cipollaro, M. 2002 Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains. Nucleic Acids Res. 30, e16. (doi:10.1093/nar/30.4.e16.)
11. Eglinton, G. & Logan, G. A. 1991 Molecular preservation. Phil. Trans. R. Soc. B 333, 315-327 discussion 327-328.
12. Elphinstone, M. S., Hinten, G. N., Anderson, M. J. & Nock, C. J. 2003 An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies. Mol. Ecol. Notes 3, 317-320. (doi:10.1046/j.1471-8286.2003.00397.x.)
13. Ewing, B., Hillier, L., Wendl, M. C. & Green, P. 1998 Base-calling of automated sequencer traces using phred I. Accuracy assessment. Genome Res. 8, 175-185.
14. Goldstein, P. Z. & Desalle, R. 2003 Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens. Mol. Ecol 12, 1993-1998. (doi:10.1046/j.1365-294X.2003.01860.x.)
15. Greiner, M., Carter, P., Korn, B. & Zink, D. 2004 New approach to complete automation in sizing and quantitation of DNA and proteins by the Automated Lab-on-a-Chip Platform from Agilent Technologies. Nat. Methods 1, 87-89. (doi:10.1038/nmeth1004-87.)
16. Hammond, P. 1992 Species inventory. In Global biodiversity: status of the earth's living resources (ed. B. Groombridge). London: Chapman & Hall.
17. Hawksworth, D. L. 1995 Global biodiversity assessment. Cambridge: Cambridge University Press.
18. Hebert, P. D., Cywinska, A., Ball, S. L. & deWaard, J. R. 2003 Biological identifications through DNA barcodes. Proc. R. Soc. B 270, 313-321. (doi:10.1098/rspb.2002.2218.)
19. Hebert, P. D., Penton, E. H., Burns, J. M., Janzen, D. H. & Hallwachs, W. 2004a Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl Acad. Sci. USA 101, 14812-14817. (doi:10.1073/pnas.0406166101.)
20. Hebert, P. D., Stoeckle, M. Y., Zemlak, T. S. & Francis, C. M. 2004b Identification of birds through DNA barcodes. PLoS Biol. 2, E312. (doi:10.1371/journal.pbio.0020312.)
21. Hogg, I. D. & Hebert, P. D. N. 2005 Biological identifications of springtails (Hexapoda: Collembola) from the Canadian arctic, using mitochondrial barcodes. Can. J. Zool. 82, 749-754.
22. Janzen, D. H., Hajibabaei, M., Burns, J. M., Hallwachs, W., Remigio, E. & Hebert, P. D. N. 2005 Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Phil. Trans. R. Soc. B 360, 1835-1845. (doi:10.1098/rstb.2005.1715.)
23. Junqueira, A. C., Lessinger, A. C. & Azeredo-Espin, A. M. 2002 Methods for the recovery of mitochondrial DNA sequences from museum specimens of myiasis-causing flies. Med. Vet. Entomol 16, 39-45. (doi:10.1046/j.0269-283x. 2002.00336.x.)
24. Kress, J. W., Wurdack, K. J., Zimmer, E. A. C., Weigt, L. A. & Janzen, D. H. 2005 Use of DNA barcodes to identify flowering plants. Proc. Natl Acad. Sci. USA 102, 8369-8374. (doi:10.1073/pnas.0503123102.)
25. Lindahl, T. 1993 Instability and decay of the primary structure of DNA. Nature 362, 709-715. (doi:10.1038/362709a0.)
26. Marshall, E. 2005 Taxonomy. Will DNA bar codes breathe life into classification? Science 307, 1037. (doi:10.1126/science.307.5712.1037.)
27. May, R. M. 1975 Patterns of species abundance and diversity. In Ecology and evolution of communities (ed. M. Cody & J. Diamond), pp. 81-120. Cambridge: Belknap Press of Harvard University Press.
28. Mitchell, D., Willerslev, E. & Hansen, A. 2005 Damage and repair of ancient DNA. Mutat. Res. 571, 265-276.
29. Prendini, L., Hanner, R. & DeSalle, R. 2002 Obtaining, storing and archiving specimens and tissue samples for use in molecular studies. In Techniques in molecular evolution and systematics (ed. R. DeSalle, G. Giribet & W. C. Wheeler), pp. 176-248. Basel: Birkhaeuser Verlag AG.
30. Rohland, N., Siedel, H. & Hofreiter, M. 2004 Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens. Biotechniques 36, 814-816 see also pp. 818-821.
31. Rose, T. M., Henikoff, J. G. & Henikoff, S. 2003 CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res. 31, 3763-3766. (doi:10.1093/nar/gkg524.)
32. Roselaar, K. 2003 An inventory of major European bird collections. Bull. Br. Ornithol. Clin. 123A, 253-337.
33. Rozen, S. & Skaletsky, H. 2000 Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132, 365-386.
34. Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., Mullis, K. B. & Erlich, H. A. 1988 Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487-491.
35. Saitou, N. & Nei, M. 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
36. Sambrook, J., Fritsch, E. F. & Maniatis, T. 1989 Molecular cloning: a laboratory manual. Cold Spring Harbor: Cold Spring Harbor Press.
37. Schander, C. & Halanych, K. M. 2003 DNA, PCR and formalinized animal tissue-a short review and protocols. Org. Divers. Evol. 3, 195-205.
38. Smith, M. A., Fisher, B. L. & Hebert, P. D. N. 2005 Barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Phil. Trans. R. Soc. B 360, 1825-1834. (doi:10.1098/rstb.2005.1714. )
39. Sorenson, M. D., Ast, J. C., Dimcheff, D. E., Yuri, T. & Mindell, D. P. 1999 Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 12, 105-114. (doi:10.1006/mpev.1998.0602.)
40. Spiess, A. N., Mueller, N. & Ivell, R. 2004 Trehalose is a potent PCR enhancer: lowering of DNA melting temperature and thermal stabilization of taq polymerase by the disaccharide trehalose. Clin. Chem. 50, 1256-1259. (doi:10.1373/clinchem.2004.031336.)
41. Su, B., Wang, Y. X., Lan, H., Wang, W. & Zhang, Y. 1999 Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples. Mol. Phylogenet. Evol. 12, 241-249. (doi:10.1006/mpev.l999.0616.)
42. Walsh, P. S., Metzger, D. A. & Higuchi, R. 1991 Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10, 506-513.
43. Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R. & Hebert, P. D. N. 2005 DNA barcoding Australia's fish species. Phil. Trans. R. Soc. B 360, 1847-1857. (doi:10.1098/rstb.2005.1716.)
44. White, H. W. & Wu, M. 2001 Factors affecting quantitation of DNA bands in gels using a charge-coupled device imaging system. Electrophoresis 22, 860-863. (doi:10.1002/1522-2683022:5 〈860::AID-ELPS860〉 3.0.CO;2-D.)