Critical factors for assembling a high volume of DNA barcodes

Large-scale DNA barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. To satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. In this paper we discuss the prospects for establishing high volume DNA barcoding facilities by evaluating key steps in the analytical chain from specimens to barcodes. Alliances with members of the taxonomic community represent the most effective strategy for provisioning the analytical chain with specimens. The optimal protocols for DNA extraction and subsequent PCR amplification of the barcode region depend strongly on their condition, but production targets of 100K barcode records per year are now feasible for facilities working with compliant specimens. The analysis of museum collections is currently challenging, but PCR cocktails that combine polymerases with repair enzyme(s) promise future success. Barcode analysis is already a cost-effective option for species identification in some situations and this will increasingly be the case as reference libraries are assembled and analytical protocols are simplified.

[1]  J. Braman,et al.  PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. , 1996, Nucleic acids research.

[2]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[3]  R Higuchi,et al.  Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. , 2013, BioTechniques.

[4]  Paul D. N. Hebert,et al.  Identifying spiders through DNA barcodes , 2005 .

[5]  U. Galderisi,et al.  Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains. , 2002, Nucleic acids research.

[6]  Rob DeSalle,et al.  Obtaining, Storing and Archiving Specimens and Tissue Samples for Use in Molecular Studies , 2002 .

[7]  J. Lüthy,et al.  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 , 1991, Applied and environmental microbiology.

[8]  Y. Zhang,et al.  Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples. , 1999, Molecular phylogenetics and evolution.

[9]  E. Willerslev,et al.  Damage and repair of ancient DNA. , 2005, Mutation research.

[10]  C. Schander,et al.  DNA, PCR and formalinized animal tissue - a short review and protocols , 2003 .

[11]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[12]  G. Eglinton,et al.  Molecular preservation. Discussion , 1991 .

[13]  Nicolas Salamin,et al.  Land plants and DNA barcodes: short-term and long-term goals , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[14]  G. Hinten,et al.  An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies , 2003 .

[15]  D. Janzen,et al.  Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[16]  P. Rådström,et al.  Effects of Amplification Facilitators on Diagnostic PCR in the Presence of Blood, Feces, and Meat , 2000, Journal of Clinical Microbiology.

[17]  P. Hebert,et al.  Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes , 2004 .

[18]  P. Hebert,et al.  DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[19]  D. Hartl,et al.  Mitochondrial pseudogenes: evolution's misplaced witnesses. , 2001, Trends in ecology & evolution.

[20]  R. DeSalle,et al.  Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens , 2003, Molecular ecology.

[21]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[22]  P. Hebert,et al.  Identification of Birds through DNA Barcodes , 2004, PLoS biology.

[23]  Eliot Marshall,et al.  Will DNA Bar Codes Breathe Life Into Classification? , 2005, Science.

[24]  R. May.  Patterns of species abundance and diversity , 1975 .

[25]  D. Mindell,et al.  Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. , 1999, Molecular phylogenetics and evolution.

[26]  Martin Greiner,et al.  New approach to complete automation in sizing and quantitation of DNA and proteins by the Automated Lab-on-a-Chip Platform from Agilent Technologies , 2004 .

[27]  C. Roselaar.  An inventory of major European bird collections , 2003 .

[28]  R. Ward,et al.  DNA barcoding Australia's fish species , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[29]  H. Sambrook.  Molecular cloning : a laboratory manual. Cold Spring Harbor, NY , 1989 .

[30]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[31]  Andrej-Nikolai Spiess,et al.  Trehalose is a potent PCR enhancer: lowering of DNA melting temperature and thermal stabilization of taq polymerase by the disaccharide trehalose. , 2004, Clinical chemistry.

[32]  D. Janzen,et al.  Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[33]  A. Azeredo-Espin,et al.  Methods for the recovery of mitochondrial DNA sequences from museum specimens of myiasis‐causing flies , 2002, Medical and veterinary entomology.

[34]  B. Groombridge.  Global biodiversity: status of the earth's living resources. , 1992 .

[35]  V. Heywood,et al.  Global Biodiversity Assessment , 1996 .

[36]  Rob DeSalle,et al.  The expansion of conservation genetics , 2004, Nature Reviews Genetics.

[37]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[38]  Timothy Rose,et al.  CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design , 2003, Nucleic Acids Res..

[39]  D. Janzen,et al.  Use of DNA barcodes to identify flowering plants. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[40]  G. Eglinton,et al.  Molecular preservation. , 1991, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[41]  V. Heywood,et al.  Global Biodiversity Assessment , 1996 .

[42]  Michael Hofreiter,et al.  Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens. , 2004, BioTechniques.

[43]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[44]  M. Salimans,et al.  Rapid and simple method for purification of nucleic acids , 1990, Journal of clinical microbiology.

[45]  T. Lindahl.  Instability and decay of the primary structure of DNA , 1993, Nature.