Approximately half of the trees harvested for commercial purposes are lost because of native or introduced insects or insect-vectored microorganisms. Ophiostomatoid fungi, which are well adapted to dissemination by insects, include ~140 species of saprobes and pathogens. They are present worldwide, have high economical impact and many are subject to quarantine regulation. Thus, it is necessary to quickly and efficiently characterize which fungi are associated with beetles, host trees, and wood products, and to establish the relative degree of damage or quarantine risk associated with these pests. During the past decade, molecular biology approaches have provided diverse DNA-based diagnostic tools that have gradually made their way into forestry and forest products industries. Such tools are typically sensitive, able to detect pests without the need to grow the microorganisms and able to provide quick answers. The new tools are rapidly becoming the new standard for detecting, monitoring and quantifying pests worldwide. In this paper we will review the molecular techniques available, as well as some of our own results, discussing issues like single and multiple gene amplification, sequencing and phylogeny, genetic markers to differentiate species or individual in a species, quantitative PCR and meta-genomic sequencing.

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