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Environmental Analysis

Fungal DNA barcode sequence identification [M110]

Published: July 8th, 2009

Revised: April 9th, 2011

This test provides a low-level identification of a single fungal isolate by sequencing of portions of the nuclear ribosomal gene, specifically the internal transcribed spacer (ITS) region. DNA-based sequence identification is the gold-standard for microbial identification, since it is capable of identifying rare or atypical fungal isolates irrespective of their responses to diagnostic culture media or biochemical tests.

In this test, we carefully cultivate the fungal isolate in a broth medium, typically Modified Leonian’s Broth (MLB). Log-phase cultures are harvested by centrifugation and DNA is isolated from cells using standard procedures. The nuclear ribosomal ITS is amplified by PCR and sequenced in both directions. A consensus sequence of both forward and reverse strands is constructed, and this sequence is used to query one or more fungal DNA sequence database tools. This approach to fungal identification is unmatched in its ability to accurately identify troublesome isolates, or to ascertain the taxonomic position of novel strains.

Results of this test are reported as an identification or series of putative identifications with corresponding confidence measures. A phylogram generated using the UPGMA algorithm indicating the phylogenetic placement of the isolate relative to closely related taxa will is also provided.

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