Next generation sequencing evaluation for detection of potential threats or emerging forest pest, entry point from spore and insect traps.
Bilodeau, G. J., É. D. Tremblay, and J. A. Bérubé. 2016. Next generation sequencing evaluation for detection of potential threats or emerging forest pest, entry point from spore and insect traps. In American Phytopathology Annual Meeting. July 30 - August 3, 2016, Tampa, FL, USA: Phytopathology.
International trade promotes the spread of exotic plant pathogens (fungi, oomycetes) that can act as entry points. Their spores that spread by wind, rain and through vectors (insects) can cause the introduction of exotic diseases responsible for the devastation of various plant species. Since it is difficult to trap and conduct investigations to these organisms, new technologies such as qPCR and metagenomics therefore can now be an option to detect without having to grow them. The DNA is extracted for metagenomics of spore trapping filters and insect traps conservation liquid collected in 2013-2014 and then sequenced with the Ion Torrent platform using fusion primers which we designed in order to three multiplex genic regions (350-400bp amplicons from ribosomal DNA region ITS1 for fungi and oomycetes and the mitochondrial DNA region ATP9-NAD9 for Phytophthora sp) and then deciphered sequences. Bioinformatic analyzes pipelines for analysis of millions of sequences are also made and compared with qPCR testing for multiple targets. Comparing the Next Generation Sequencing consistent qPCR for the detection of forest pathogens species and allowed to find several species related targets of Phytophthora and related Fungi. Based on the results obtained, it was possible to identify potential sources of entry, get access to contents abundancy, biodiversity and phylogeny in order and so accelerate identification process of current risk to these species for biosurveillance.