Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 440743
Title Pyrosequencing as a tool for the detection of Phytophthora species: error rate and risk of false Molecular Operational Taxonomic Units
Author(s) Vettraino, A.M.; Bonants, P.J.M.; Tomassini, A.; Bruni, N.; Vannini, A.
Source Letters in Applied Microbiology 55 (2012)5. - ISSN 0266-8254 - p. 390 - 396.
DOI https://doi.org/10.1111/j.1472-765x.2012.03310.x
Department(s) Bioint Moleculair Phytopathology
Publication type Refereed Article in a scientific journal
Publication year 2012
Keyword(s) fungal communities - identification - phylogeny - diversity - sequences - reveals
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.
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