Abstract

An amplicon-metagenomic approach was used to investigate Phytophthora spp. diversity in waterscollected from four Scottish natural habitats, i.e. Invergowrie, Glensaugh Research Station, CairngormsNational Park and Sourhope Research Station. Sequencing of the rDNA ITS1 barcode-region on anIllumina MiSeq platform with genus-specific primers produced around 700,000 sequences that wereclustered into 4,671 OTUs using a 99% similarity threshold. Assigning taxonomy to the representativesequences of the OTUs was done using the BLAST algorithm and a manually curatedOomycetesdatabase. The results showed that majority of the sequences were associated to the genusPhytophthora. Although few OTUs were associated to other Oomycetes, the use of genus-specific ITS1primers allowed understanding well the diversity of Phytophthora population. Moreover, the resultsrevealed a clear site-to-site variation, where the lowest species diversity was found in GSB Glensaughand the highest diversity at Invergowrie. The analysis of ?-diversity, based on Bray Curtis matrices,confirmed differences (P<0.001) in populations associated to the investigated environments, with onlyfew OTUs shared among samples. This approach proved effective in the study of Phytophthora spp.diversity and the use of genus-specific primers contributed to an unprecedented level of accuracy,compared to traditional techniques based on direct isolation, while preserving sensitivity of identificationand relative quantification of Phytophthora species. This study demonstrated that Illumina sequencingof the ITS1 region may serve to study in depth diversity and ecological niches of Phytophthora species.

Autore Pugliese

• Bubici Giovanni Nicola

Tutti gli autori

• Prigigallo M. I.; Abdelfattah A.; Schena L.; Bubici G.; Cooke D. E. L.

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Anno di pubblicazione

2018

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