Molecular analysis of Phytophthora diversity in nursery-grown ornamental and fruit plants

The genetic diversity of Phytophthora spp. was investigated in potted ornamental and fruit tree species. A metabarcodingapproach was used, based on a semi-nested PCR with Phytophthora genus-specific primers targeting theITS1 region of the rDNA. More than 50 ITS1 sequence types representing at least 15 distinct Phytophthora taxa weredetected. Nine had ITS sequences that grouped them in defined taxonomic groups (P. nicotianae, P. citrophthora, P.meadii, P. taxon Pgchlamydo, P. cinnamomi, P. parvispora, P. cambivora, P. niederhauserii and P. lateralis) whereasthree phylotypes were associated to two or more taxa (P. citricola taxon E or III; P. pseudosyringae, P. ilicis or P.nemorosa; and P. cryptogea, P. erythroseptica, P. himalayensis or P. sp. ‘kelmania’) that can be challenging to resolvewith ITS1 sequences alone. Three additional phylotypes were considered as representatives of novel Phytophthora taxaand defined as P. meadii-like, P. cinnamomi-like and P. niederhauserii-like. Furthermore, the analyses highlighted avery complex assemblage of Phytophthora taxa in ornamental nurseries within a limited geographic area and providedsome indications of structure amongst populations of P. nicotianae (the most prevalent taxon) and other taxa. Datarevealed new host–pathogen combinations, evidence of new species previously unreported in Italy (P. lateralis) or Europe(P. meadii) and phylotypes representative of species that remain to be taxonomically defined. Furthermore, theresults reinforced the primary role of plant nurseries in favouring the introduction, dissemination and evolution ofPhytophthora species.