Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease Honour C. McCann 1,2 , Erik H. A. Rikkerink 3 , Frederic Bertels 1,4 , Mark Fiers 5 , Ashley Lu 5 , Jonathan Rees- George 3 , Mark T. Andersen 3 , Andrew P. Gleave 3 , Bernhard Haubold 6 , Mark W. Wohlers 3 , David S. Guttman 2 , Pauline W. Wang 2 , Christina Straub 1 , Joel Vanneste 7 , Paul B. Rainey 1,6" * Matthew D. Templeton 3,8" * 1 New Zealand Institute for Advanced Study and Allan Wilson Centre, Massey University, Auckland, New Zealand, 2 Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, 3 The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand, 4 Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland, 5 The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand, 6 Max Planck Institute for Evolutionary Biology, Plo ¨ n, Germany, 7 The New Zealand Institute for Plant and Food Research Limited, Ruakura, Hamilton, New Zealand, 8 School of Biological Sciences, University of Auckland, Auckland, New Zealand Abstract The origins of crop diseases are linked to domestication of plants. Most crops were domesticated centuries – even millennia – ago, thus limiting opportunity to understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by P. syringae pv. actinidiae (Psa) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that Psa is comprised of distinct clades exhibiting negligible within-clade diversity, consistent with disease arising by independent samplings from a source population. Three clades correspond to their geographical source of isolation; a fourth, encompassing the Psa-V lineage responsible for the 2008 outbreak, is now globally distributed. Psa has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of Psa-V reveals hundreds of polymorphisms; however, most reside within PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome. Removal of SNPs due to recombination yields an uninformative (star-like) phylogeny consistent with diversification of Psa-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of Psa-V in Actinidia chinensis. Genomic comparisons show a dynamic genome with evidence of positive selection on type III effectors and other candidate virulence genes. Each clade has highly varied complements of accessory genes encoding effectors and toxins with evidence of gain and loss via multiple genetic routes. Genes with orthologs in vascular pathogens were found exclusively within Psa-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild Actinidia species. In addition to candidate genes as targets for resistance breeding programs, our findings highlight the importance of the source population as a reservoir of new disease. Citation: McCann HC, Rikkerink EHA, Bertels F, Fiers M, Lu A, et al. (2013) Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease. PLoS Pathog 9(7): e1003503. doi:10.1371/journal.ppat.1003503 Editor: Jeffery L. Dangl, The University of North Carolina at Chapel Hill, United States of America Received January 20, 2013; Accepted May 28, 2013; Published July 25, 2013 Copyright: ß 2013 McCann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded in part by the New Zealand Ministry for Business, Innovation and Employment (www.mbie.govt.nz) contract C06X0812 (to MDT and EHAR), and Allan Wilson Centre for Molecular Ecology and Evolution (http://www.allanwilsoncentre.ac.nz/) (to PBR). PBR is grateful for support from Zespri International, Mt Maunganui, New Zealand (http://www.Zespri.com). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: rainey@evolbio.mpg.de (PBR); matt.templeton@plantandfood.co.nz (MDT) " PBR and MDT are joint senior authors on this work. Introduction Despite considerable improvements in the management of plant diseases, modern agriculture remains vulnerable to losses caused by microbial pathogens. Plant diseases conservatively account for the loss of at least 10% of annual global food production [1]. The intensive cultivation of clonally propagated plants with low genetic diversity heightens opportunities for the emergence and rapid spread of infectious disease [1–3]. The origins of agricultural plant diseases are unclear [3,4]. The earliest pathogens are likely to have evolved from commensals or pathogens colonizing wild relatives of plants selected for human domestication [5–10]. Given that domestication of staple crop plants took place centuries (and often millennia) ago, the signal of this evolutionary past – the nature of the initial pathogen population, its relationship with commensal types, its diversity and genetic structure, plus factors and processes that might have led to the first outbreaks of disease – is obscured by the passage of PLOS Pathogens | www.plospathogens.org 1 July 2013 | Volume 9 | Issue 7 | e1003503