Special Interest Group Meeting

The use of membrane-based oligonucleotide arrays as diagnostic tool for the detection and identification of fungal species, including oomycetes

W. Chen and C.A. Levesque, Agriculture and Agri-Food Canada, n/a, Canada

Classical identification of fungi involves culturing and detailed examination of morphology. This is often time consuming, labour intensive and require experienced mycologists. Modern molecular technologies, such as sequencing and microarrays, facilitate rapid and reliable identification or detection of fungal species by researchers with limited taxonomic backgrounds. For identification of pure cultures the sequencing of a DNA barcode is better than using array hybridization. However, for mixed environmental samples, DNA array hybridization is faster and cheaper. In this technique, an array of short (18-40bp) and specific oligonucleotides derived from the marker regions that are amplified and labeled from the environmental sample with universal primers are used for hybridization. These allow rapid and massive scans of suspected species in complex environmental samples without isolation or culturing. Membrane-based oligonucleotide arrays are affordable, sensitive and reusable. Bioinformatics tools are available to design arrays for genera from comprehensive databases of markers, the more variability or indels these markers have, the better specificity the array will have. This technology has been used both for research and commercial applications to test broad ranges of samples including clinically important pathogens. New commercial array platforms can provide final results with a processing time of less than 3 hours.