title: Pyrosequencing as a tool for the detection of Phytophthora species: error rate and risk of false Molecular Operational Taxonomic Units.
abstract: OBJECTIVE
  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).
  
  
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, ItalyResearch Institute for Plant Protection (IPO-DLO), Wageningen, The Netherlands.
authors.forename: A M
authors.initials: AM
authors.lastname: Vettraino
authors.affiliation: Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, ItalyResearch Institute for Plant Protection (IPO-DLO), Wageningen, The Netherlands.
authors.forename: P
authors.initials: P
authors.lastname: Bonants
authors.affiliation: Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, ItalyResearch Institute for Plant Protection (IPO-DLO), Wageningen, The Netherlands.
authors.forename: A
authors.initials: A
authors.lastname: Tomassini
authors.affiliation: Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, ItalyResearch Institute for Plant Protection (IPO-DLO), Wageningen, The Netherlands.
authors.forename: N
authors.initials: N
authors.lastname: Bruni
authors.affiliation: Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, ItalyResearch Institute for Plant Protection (IPO-DLO), Wageningen, The Netherlands.
authors.forename: A
authors.initials: A
authors.lastname: Vannini
mesh_terms: D015373:Bacterial Typing Techniques; D001483:Base Sequence; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D025282:Mycelium / Q000254:growth & development; D010838:Phytophthora / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D010935:Plant Diseases / Q000382:microbiology; D010944:Plants / Q000382:microbiology; D011775:Pythium / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D021903:DNA, Ribosomal Spacer
keywords: Phytophthora spp; diagnosis; next‐generation sequencing