Summerbell R C, Lévesque C A, Seifert K A, Bovers M, Fell J W, Diaz M R, Boekhout T, de Hoog G S, Stalpers J, Crous P W
CBS Fungal Biodiversity Centre, Utrecht, The Netherlands.
Philos Trans R Soc Lond B Biol Sci. 2005 Oct 29;360(1462):1897-903. doi: 10.1098/rstb.2005.1721.
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.
在DNA条形码技术在一类生物中取得了长足进展之后，就像在具有经济重要性的真菌中那样，随之而来的问题是，是否应该使用更短且实际上更像条形码的DNA片段来促进快速鉴定，并在适用的情况下进行检测。通过对典型的全长条形码（通常超过500个碱基对长）进行适当的软件分析，可以找到长度小于25 bp的独特的寡核苷酸“微码”，这些微码能够在各种类似阵列的平台上快速鉴定大约100 - 200个物种。微阵列原则上可以实现基于微码的物种鉴定功能，但由于其成本高且可重复使用性低，它们的性价比往往较低。目前在真菌鉴定中使用的两个替代平台是可重复使用的基于尼龙的宏阵列和通过流式细胞仪分析特定的、带有颜色编码的DNA检测珠的Luminex系统。当寻求基于条形码的快速物种鉴定的最有效方法时，可以根据研究者的战略眼光和当前成本，选择这些方法中的一种或基本的高通量测序。当分析诸如土壤或人类呼吸道分泌物样本等生物复杂材料以统计其中存在的相关物种时，阵列和功能类似的平台可能具有特别的优势。
