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Microcoding: the second step in DNA barcoding Summerbell RC; Levesque CA; Seifert KA; Bovers M; Fell JW; Diaz MR; Boekhout T; de Hoog GS; Stalpers J; Crous PWPhilos Trans R Soc Lond B Biol Sci 2005[Oct]; 360 (1462): 1897-903After 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.|*Biodiversity[MESH]|DNA/*genetics[MESH]|Electronic Data Processing/*methods[MESH]|Flow Cytometry[MESH]|Fungi/*genetics[MESH]|Microarray Analysis/methods[MESH]|Molecular Diagnostic Techniques/*methods[MESH]|Oligonucleotides/genetics[MESH]|Species Specificity[MESH] |
