Microcoding: The second step in DNA barcoding

R. C. Summerbell, C. A. Lévesque, K. A. Seifert, M. Bovers, J. W. Fell, Mara Diaz, T. Boekhout, G. S. De Hoog, J. Stalpers, P. W. Crous

Research output: Contribution to journalArticle

82 Citations (Scopus)

Abstract

After the process of DNA barcoding has become well advanced in a group of organisms, as it has in the economically important fungi, the question then arises as to whether shorter and literally more barcode-like DNA segments should be utilized to facilitate rapid identification and, where applicable, detection. Through appropriate software analysis of typical full-length barcodes (generally over 500 base pairs long), uniquely distinctive oligonucleotide 'microcodes' of less than 25 bp can be found that allow rapid identification of circa 100-200 species on various array-like platforms. Microarrays can in principle fulfill the function of microcode-based species identification but, because of their high cost and low level of reusability, they tend to be less cost-effective. Two alternative platforms in current use in fungal identification are reusable nylon-based macroarrays and the Luminex system of specific, colour-coded DNA detection beads analysed by means of a flow cytometer. When the most efficient means of rapid barcode-based species identification is sought, a choice can be made either for one of these methodologies or for basic high-throughput sequencing, depending on the strategic outlook of the investigator and on current costs. Arrays and functionally similar platforms may have a particular advantage when a biologically complex material such as soil or a human respiratory secretion sample is analysed to give a census of relevant species present.

Original languageEnglish (US)
Pages (from-to)1897-1903
Number of pages7
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Volume360
Issue number1462
DOIs
StatePublished - Oct 29 2005

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barcoding
DNA barcoding
Firmware
DNA
Costs and Cost Analysis
Costs
Nylons
Reusability
cost
Censuses
Microarrays
nylon
oligonucleotides
Fungi
Oligonucleotides
Base Pairing
Soil
Software
Color
Research Personnel

Keywords

  • Barcoding
  • Fungi
  • Macroarrays
  • Species identification

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

Summerbell, R. C., Lévesque, C. A., Seifert, K. A., Bovers, M., Fell, J. W., Diaz, M., ... Crous, P. W. (2005). Microcoding: The second step in DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1897-1903. https://doi.org/10.1098/rstb.2005.1721

Microcoding : The second step in DNA barcoding. / Summerbell, R. C.; Lévesque, C. A.; Seifert, K. A.; Bovers, M.; Fell, J. W.; Diaz, Mara; Boekhout, T.; De Hoog, G. S.; Stalpers, J.; Crous, P. W.

In: Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 360, No. 1462, 29.10.2005, p. 1897-1903.

Research output: Contribution to journalArticle

Summerbell, RC, Lévesque, CA, Seifert, KA, Bovers, M, Fell, JW, Diaz, M, Boekhout, T, De Hoog, GS, Stalpers, J & Crous, PW 2005, 'Microcoding: The second step in DNA barcoding', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 360, no. 1462, pp. 1897-1903. https://doi.org/10.1098/rstb.2005.1721
Summerbell RC, Lévesque CA, Seifert KA, Bovers M, Fell JW, Diaz M et al. Microcoding: The second step in DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences. 2005 Oct 29;360(1462):1897-1903. https://doi.org/10.1098/rstb.2005.1721
Summerbell, R. C. ; Lévesque, C. A. ; Seifert, K. A. ; Bovers, M. ; Fell, J. W. ; Diaz, Mara ; Boekhout, T. ; De Hoog, G. S. ; Stalpers, J. ; Crous, P. W. / Microcoding : The second step in DNA barcoding. In: Philosophical Transactions of the Royal Society B: Biological Sciences. 2005 ; Vol. 360, No. 1462. pp. 1897-1903.
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