Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease

• DOI: 10.1371/journal.ppat.1003503
• Publication Date: 2013-07-25T18:16:55Z
• Authors: Honour C. McCann; Erik H. A. Rikkerink; Frederic Bertels; Mark Fiers; Ashley Lu; Jonathan Rees-George; Mark T. Andersen; Andrew P. Gleave; Bernhard Haubold; Mark W. Wohlers; David S. Guttman; Pauline W. Wang; Christina Straub; Joel Vanneste; Paul B. Rainey; Matthew D. Templeton
• Keywords: Pathovar; Pseudomonas syringae; Actinidia; Genomic island

The origins of crop diseases are linked to domestication plants. Most crops were domesticated centuries – even millennia ago, thus limiting opportunity understand the concomitant emergence disease. Kiwifruit (Actinidia spp.) is an exception: began in 1930s with outbreaks canker disease caused by P. syringae pv. actinidiae (Psa) first recorded 1980s. Based on SNP analyses two circularized and 34 draft genomes, we show that Psa comprised distinct clades exhibiting negligible within-clade diversity, consistent arising independent samplings from a source population. Three correspond their geographical isolation; fourth, encompassing Psa-V lineage responsible for 2008 outbreak, now globally distributed. has overall clonal population structure, however, genomes carry marked signature within-pathovar recombination. analysis reveals hundreds polymorphisms; most reside within PPHGI-1-like conjugative elements whose evolution unlinked core genome. Removal SNPs due recombination yields uninformative (star-like) phylogeny diversification single clone last ten years. Growth assays provide evidence cultivar specificity, rapid systemic movement Actinidia chinensis. Genomic comparisons dynamic genome positive selection type III effectors other candidate virulence genes. Each clade highly varied complements accessory genes encoding toxins gain loss via multiple genetic routes. Genes orthologs vascular pathogens found exclusively Psa-V. Our capture pathogen early stages predicted associated wild species. In addition as targets resistance breeding programs, our findings highlight importance reservoir new