Microcoding: the second step in DNA barcoding.
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.
Summerbell
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RC
CBS Fungal Biodiversity Centre, Utrecht, The Netherlands. summerbell@cbs.knaw.nl
Lévesque
C A
CA
Seifert
K A
KA
Bovers
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M
Fell
J W
JW
Diaz
M R
MR
Boekhout
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T
de Hoog
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GS
Stalpers
J
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Crous
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D044822:Biodiversity; D004247:DNA / Q000235:genetics*; D001330:Electronic Data Processing / Q000379:methods*; D005434:Flow Cytometry; D005658:Fungi / Q000235:genetics*; D046228:Microarray Analysis / Q000379:methods; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics; D013045:Species Specificity
D009841:Oligonucleotides; D004247:DNA