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Background  Accumulating evidence suggests that genome plasticity allows filamentous plant pathogens to adapt to changing environments. Recently, the generalist plant pathogen  Phytophthora ramorum  has been documented to undergo irreversible phenotypic alterations accompanied by chromosomal aberrations when infecting trunks of mature oak trees (genus  Quercus ) .  In contrast, genomes and phenotypes of the pathogen derived from the foliage of California bay ( Umbellularia californica ) are usually stable. We define this phenomenon as host-induced phenotypic diversification (HIPD).  P. ramorum  also causes a severe foliar blight in some ornamental plants such as  Rhododendron  spp. and  Viburnum  spp., and isolates from these hosts occasionally show phenotypes resembling those from oak trunks that carry chromosomal aberrations. The aim of this study was to investigate variations in phenotypes and genomes of  P. ramorum  isolates from non-oak hosts and substrates to determine whether HIPD changes may be equivalent to those among isolates from oaks.    Results  We analyzed genomes of diverse non-oak isolates including those taken from foliage of  Rhododendron  and other ornamental plants, as well as from natural host species, soil, and water. Isolates recovered from artificially inoculated oak logs were also examined. We identified diverse chromosomal aberrations including copy neutral loss of heterozygosity (cnLOH) and aneuploidy in isolates from non-oak hosts. Most identified aberrations in non-oak hosts were also common among oak isolates; however, trisomy, a frequent type of chromosomal aberration in oak isolates was not observed in isolates from  Rhododendron .    Conclusion  This work cross-examined phenotypic variation and chromosomal aberrations in  P. ramorum  isolates from oak and non-oak hosts and substrates. The results suggest that HIPD comparable to that occurring in oak hosts occurs in non-oak environments such as in  Rhododendron  leaves.  Rhododendron  leaves are more easily available than mature oak stems and thus can potentially serve as a model host for the investigation of HIPD, the newly described plant-pathogen interaction.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4709-7) contains supplementary material, which is available to authorized users.

Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts