View source for Letters in Applied Microbiology (2012) 55, 390-396

{{Publication
|Publication authors=A.M. Vettraino, P. Bonants, A. Tomassini, N. Bruni and [[Andrea Vannini|A. Vannini]]
|Author Page=Andrea Vannini, Anna Maria Vettraino
|Publication date=2012
|dc:title=Pyrosequencing as a tool for the detection of ''Phytophthora'' species: error rate and risk of false Molecular Operational Taxonomic Units
|Publication journal=Letters in Applied Microbiology
|prism:volume=55 (5)
|prism:startingPage=390
|Last page=396
|DOI=10.1111/j.1472-765x.2012.03310.x
|Publication abstract=<br/>'''Aims<br/>'''To evaluate the accuracy of pyrosequencing for the description of ''Phytophthora'' communities in terms of taxa identification and risk of assignment for false Molecular Operational Taxonomic Units (MOTUs).<br/>'''Methods and Results<br/>'''Pyrosequencing of Internal Transcribed Spacer 1 (ITS1) amplicons was used to describe the structure of a DNA mixture comprising eight ''Phytophthora'' spp. and ''Pythium vexans''. Pyrosequencing resulted in 16 965 reads, detecting all species in the template DNA mixture. Reducing the ITS1 sequence identity threshold resulted in a decrease in numbers of unmatched reads but a concomitant increase in the numbers of false MOTUs. The total error rate was 0·63% and comprised mainly mismatches (0·25%)<br/>'''Conclusions<br/>'''Pyrosequencing of ITS1 region is an efficient and accurate technique for the detection and identification of ''Phytophthora'' spp. in environmental samples. However, the risk of allocating false MOTUs, even when demonstrated to be low, may require additional validation with alternative detection methods.<br/>'''Significance and Impact of the Study'''<br/>''Phytophthora'' spp. are considered among the most destructive groups of invasive plant pathogens, affecting thousands of cultivated and wild plants worldwide. Simultaneous early detection of ''Phytophthora'' complexes in environmental samples offers an unique opportunity for the interception of known and unknown species along pathways of introduction, along with the identification of these organisms in invaded environments.
|AbstractCC=Yes
|AuthorsAbstract=No
|Research topic=identification/taxonomy
|Research2P=surveys/sampling/distribution
|Is book=No
|SelArticle=1
|Image=IPMimage5368388.jpg
}}
{{Pest record
|Pest=Phytophthora (genus)
|Quarantined=No
}}