Abstract
Phytophthora cactorum is often described as a generalist pathogen, with isolates causing disease in a range of plant species. It is the causative agent of two diseases in the cultivated strawberry, crown rot (CR; causing whole plant collapse) and leather rot (LR; affecting the fruit). In the cultivated apple, P. cactorum causes girdling bark rots on the scion (collar rot) and rootstock (crown rot), as well as necrosis of the fine root system (root rot) and fruit rots. We investigated evidence for host specialisation within P. cactorum through comparative genomic analysis of 18 isolates. Whole genome phylogenetic analysis provided genomic support for discrete lineages within P. cactorum, with well-supported non-recombining clades for strawberry CR and apple infecting isolates specialised to strawberry crowns and apple tissue. Isolates of strawberry CR are genetically similar globally, while there is more diversity in apple-infecting isolates. We sought to identify the genetic basis of host specialisation, demonstrating gain and loss of effector complements within the P. cactorum phylogeny, representing putative determinants of host boundaries. Transcriptomic analysis highlighted that those effectors found to be specific to a single host or expanded in the strawberry lineage are amongst those most highly expressed during infection of strawberry and give a wider insight into the key effectors active during strawberry infection. Many effectors that had homologues in other Phytophthoras that have been characterised as avirulence genes were present but not expressed in our tested isolate. Our results highlight several RxLR-containing effectors that warrant further investigation to determine whether they are indeed virulence factors and host-specificity determinants for strawberry and apple. Furthermore, additional work is required to determine whether these effectors are suitable targets to focus attention on for future resistance breeding efforts.
Highlights
The Phytophthora genus serves as a model system for studying evolution of pathogenicity and resistance in plant pathosystems
This study provides further evidence that P. cactorum should be regarded as a species complex and not a single species, as it comprises of distinct phylogenetic lineages that resolve groups of isolates with distinct effector profiles and displaying host-preference
Further questions that remain unanswered are to what extent do the expression profiles of effectors in different isolates affect pathogenicity? This highlights the need for further RNAseq from multiple isolates, as well as knockouts to disentangle which effectors are differential for pathogenicity in strawberry and apple? This will help us understand what are the key processes that underpin variation in virulence in P. cactorum
Summary
The Phytophthora genus serves as a model system for studying evolution of pathogenicity and resistance in plant pathosystems. Many Phytophthora spp. are specialised and only able to colonise one or a few host plants, for example Phytophthora fragariae which is thought to only colonise strawberry Some species, such as Phytophthora cactorum (Lebert and Cohn) Schroet, are traditionally considered to be generalists and are able to cause disease on a broad range of plant species, including herbaceous and woody plants (Erwin and Ribeiro, 1996). Two examples of these hosts in the Rosaceae family, are the herbaceous cultivated strawberry (Fragaria × ananassa) and woody cultivated apple (Malus × domestica)
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