AFLP and phylogenetic analyses of North American and European populations of Phytophthora ramorum

Abstract

The genetic structure within and between USA and European populations of the emerging phytopathogen Phytophthora ramorum was examined. Four primer combinations were used for amplified fragment length polymorphism (AFLP) fingerprinting of 67 USA isolates from California and Oregon, and 18 European isolates from Belgium, Germany, The Netherlands, Spain and the UK. In addition, three DNA regions (ITS, cox II, and nad 5) of additional Phytophthora species were amplified by polymerase chain reaction, sequenced, and analysed to provide better phylogenetic understanding of P. ramorum within the genus Phytophthora. AFLP banding patterns indicate that the 85 isolates form two distinct lineages within a monophyletic group, distinct from the closely related outgroup species P. lateralis. With the exception of two isolates from an Oregon nursery, European and USA isolates clustered separately within individual clades. The AFLP profiles also indicate that a single clonal lineage dominates the North American population, while the European population consists of an array of mainly unique, closely related AFLP types. Sequences from the three DNA regions were identical among all P. ramorum isolates, and phylogenetic analysis indicates that P. ramorum is closely related to P. lateralis and P. hibernalis.

Correlation of isozyme profiles with genomic sequences of Phytophthora ramorum and its P. sojae orthologues

“…Although some variation was detected at the Ldh-2 locus throughout the population the selected isozymes were not suitable to detect the level of variation as revealed by AFLP and microsatellite markers (Ivors et al 2004. With these isozymes it is, however, possible to delineate P. ramorum from the closely related species P. lateralis and P. hibernalis.…”

“…Transatlantic diVerences were also revealed by sequence analysis of the mitochondrial encoded CoxI gene (Kroon et al 2004b) and by AFLP analysis (Ivors et al 2004). It was inferred from AFLP analysis that the North American population was largely dominated by a single clonal lineage, whereas the European population consisted of an array of closely related AFLP lineages (Ivors et al 2004). In contrast, the morphology of the North American isolates showed more variation than the European isolates (Brasier 2003).…”

“…Meanwhile, both mating types have been identiWed on both continents (Hansen et al 2003;Werres and De Merlier 2003;Werres and Kaminski 2005). Transatlantic diVerences were also revealed by sequence analysis of the mitochondrial encoded CoxI gene (Kroon et al 2004b) and by AFLP analysis (Ivors et al 2004). It was inferred from AFLP analysis that the North American population was largely dominated by a single clonal lineage, whereas the European population consisted of an array of closely related AFLP lineages (Ivors et al 2004).…”

AFLP analysis reveals a clonal population of Phytophthora pinifolia in Chile

“…This difference is equivalent to 0.5 % of the scored bands and is a much lower level of diversity than that found in other Phytophthora spp. such as P. infestans (Goodwin et al 1994), Phytophthora cinnamomi (Linde et al 1997;Linde et al 1999) and P. ramorum (Ivors et al 2004;Ivors et al, 2006) that have been defined as clonal. The missing band in isolates CMW 33987 and CMW 34012 could be a consequence of a single mutation in one of the restriction enzyme sites in these two P. pinifolia strains.…”

“…Such host shifts might also result in a clonal population of a pathogen on a new host. However, a review of literature on Phytophthora epidemics (Hansen et al 2000;Ivors et al 2004;Ivors et al 2006;Brasier et al 2005;Denman et al 2006;Prospero et al 2007), as well as emerging plant diseases in general (Anderson et al 2004), indicates that introduction is by far the most common explanation for such patterns. Hence, our data support the hypothesis that P. pinifolia is an introduced pathogen in Chile.…”