Abstract:
AIMS: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). METHODS AND RESULTS: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%) CONCLUSIONS: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. SIGNIFICANCE AND IMPACT OF THE STUDY: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.
journal_name
Lett Appl Microbioljournal_title
Letters in applied microbiologyauthors
Vettraino AM,Bonants P,Tomassini A,Bruni N,Vannini Adoi
10.1111/j.1472-765x.2012.03310.xsubject
Has Abstractpub_date
2012-11-01 00:00:00pages
390-6issue
5eissn
0266-8254issn
1472-765Xjournal_volume
55pub_type
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