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Pyrosequencing as a tool for the detection of P hytophthora species: error rate and risk of false M olecular O perational T axonomic U nits
Author(s) -
Vettraino A.M.,
Bonants P.,
Tomassini A.,
Bruni N.,
Vannini A.
Publication year - 2012
Publication title -
letters in applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.698
H-Index - 110
eISSN - 1472-765X
pISSN - 0266-8254
DOI - 10.1111/j.1472-765x.2012.03310.x
Subject(s) - pyrosequencing , biology , phytophthora , amplicon , dna sequencing , pythium , internal transcribed spacer , botany , genetics , polymerase chain reaction , gene , phylogenetic tree
Aims To evaluate the accuracy of pyrosequencing for the description of P hytophthora communities in terms of taxa identification and risk of assignment for false M olecular O perational T axonomic U nits ( MOTU s). Methods and Results Pyrosequencing of I nternal T ranscribed S pacer 1 ( ITS 1) amplicons was used to describe the structure of a DNA mixture comprising eight P hytophthora spp. and P ythium vexans . Pyrosequencing resulted in 16 965 reads, detecting all species in the template DNA mixture. Reducing the ITS 1 sequence identity threshold resulted in a decrease in numbers of unmatched reads but a concomitant increase in the numbers of false MOTU s. The total error rate was 0·63% and comprised mainly mismatches (0·25%) Conclusions Pyrosequencing of ITS 1 region is an efficient and accurate technique for the detection and identification of P hytophthora spp. in environmental samples. However, the risk of allocating false MOTU s, even when demonstrated to be low, may require additional validation with alternative detection methods. Significance and Impact of the Study P hytophthora spp. are considered among the most destructive groups of invasive plant pathogens, affecting thousands of cultivated and wild plants worldwide. Simultaneous early detection of P hytophthora 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.