Fusarium circinatum is an important pathogen of pine trees and its management in the commercial
forestry environment relies largely on early detection, particularly in seedling nurseries. The fact that
the entire genome of this pathogen is available opens new avenues for the development of diagnostic tools
for this fungus. In this study we identified open reading frames (ORFs) unique to F. circinatum and determined
that they were specific to the pathogen. The ORF identification process involved bioinformaticsbased
screening of all the putative F. circinatum ORFs against public databases. This was followed by
functional characterization of ORFs found to be unique to F. circinatum. We used PCR- and hybridization-
based approaches to confirm the presence of selected unique genes in different strains of F. circinatum
and their absence from other Fusarium species for which genome sequence data are not yet available.
These included species that are closely related to F. circinatum as well as those that are commonly encountered
in the forestry environment. Thirty-six ORFs were identified as potentially unique to F. circinatum.
Nineteen of these encode proteins with known domains while the other 17 encode proteins of unknown
function. The results of our PCR analyses and hybridization assays showed that three of the selected genes
were present in all of the strains of F. circinatum tested and absent from the other Fusarium species
screened. These data thus indicate that the selected genes are common and unique to F. circinatum. These
genes thus could be good candidates for use in rapid, in-the-field diagnostic assays specific to F. circinatum.
Our study further demonstrates how genome sequence information can be mined for the identification of
new diagnostic markers for the detection of plant pathogens.