Phytopathology (2016) 106, 305-313
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Metabarcoding analysis of Phytophthora diversity using genus-specific primers and 454 pyrosequencing
Phytopathology 106 (3), 305-313
Abstract: A metabarcoding method based on genus-specific primers and 454 pyrosequencing was utilized to investigate the genetic diversity of Phytophthora spp. in soil and root samples of potted plants, from eight nurseries. Pyrosequencing enabled the detection of 25 Phytophthora phylotypes distributed in seven different clades and provided a much higher resolution than a corresponding cloning/Sanger sequencing approach. Eleven of these phylotypes, including P. cactorum, P. citricola s.str., P. palmivora, P. palmivora-like, P. megasperma or P. gonapodyides, P. ramorum, and five putative new Phytophthora species phylogenetically related to clades 1, 2, 4, 6, and 7 were detected only with the 454 pyrosequencing approach. We also found an additional 18 novel records of a phylotype in a particular nursery that were not detected with cloning/Sanger sequencing. Several aspects confirmed the reliability of the method: (i) many identical sequence types were identified independently in different nurseries, (ii) most sequence types identified with 454 pyrosequencing were identical to those from the cloning/Sanger sequencing approach and/or perfectly matched GenBank deposited sequences, and (iii) the divergence noted between sequence types of putative new Phytophthora species and all other detected sequences was sufficient to rule out sequencing errors. The proposed method represents a powerful tool to study Phytophthora diversity providing that particular attention is paid to the analysis of 454 pyrosequencing raw read sequences and to the identification of sequence types.
(The abstract is excluded from the Creative Commons licence and has been copied with permission by the publisher.)
Link to article at publishers website
Database assignments for author(s): Leonardo Schena, Santa O. Cacciola, David E.L. Cooke, Simona M. Sanzani
Research topic(s) for pests/diseases/weeds:
surveys/sampling/distribution
identification/taxonomy
Pest and/or beneficial records:
| Beneficial | Pest/Disease/Weed | Crop/Product | Country | Quarant. |
|---|---|---|---|---|
| Phytophthora palmivora | ||||
| Phytophthora cactorum | ||||
| Phytophthora citricola | ||||
| Phytophthora megasperma | ||||
| Phytophthora gonapodyides | ||||
| Phytophthora ramorum |
