Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease
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{"title"=>"Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease", "type"=>"journal", "authors"=>[{"first_name"=>"Honour C.", "last_name"=>"McCann", "scopus_author_id"=>"23035689300"}, {"first_name"=>"Erik H.A.", "last_name"=>"Rikkerink", "scopus_author_id"=>"6603042933"}, {"first_name"=>"Frederic", "last_name"=>"Bertels", "scopus_author_id"=>"35180998100"}, {"first_name"=>"Mark", "last_name"=>"Fiers", "scopus_author_id"=>"8866890800"}, {"first_name"=>"Ashley", "last_name"=>"Lu", "scopus_author_id"=>"55867092600"}, {"first_name"=>"Jonathan", "last_name"=>"Rees-George", "scopus_author_id"=>"6506811154"}, {"first_name"=>"Mark T.", "last_name"=>"Andersen", "scopus_author_id"=>"7403198417"}, {"first_name"=>"Andrew P.", "last_name"=>"Gleave", "scopus_author_id"=>"6603080542"}, {"first_name"=>"Bernhard", "last_name"=>"Haubold", "scopus_author_id"=>"56156342400"}, {"first_name"=>"Mark W.", "last_name"=>"Wohlers", "scopus_author_id"=>"12040216100"}, {"first_name"=>"David S.", "last_name"=>"Guttman", "scopus_author_id"=>"7003711151"}, {"first_name"=>"Pauline W.", "last_name"=>"Wang", "scopus_author_id"=>"8868959500"}, {"first_name"=>"Christina", "last_name"=>"Straub", "scopus_author_id"=>"55867087700"}, {"first_name"=>"Joel", "last_name"=>"Vanneste", "scopus_author_id"=>"9435346700"}, {"first_name"=>"Paul B.", "last_name"=>"Rainey", "scopus_author_id"=>"7006507614"}, {"first_name"=>"Matthew D.", "last_name"=>"Templeton", "scopus_author_id"=>"7006832398"}], "year"=>2013, "source"=>"PLoS Pathogens", "identifiers"=>{"pui"=>"369919448", "sgr"=>"84884758493", "issn"=>"15537366", "pmid"=>"23935484", "scopus"=>"2-s2.0-84884758493", "doi"=>"10.1371/journal.ppat.1003503", "isbn"=>"1553-7374 (Electronic)\\r1553-7366 (Linking)"}, "id"=>"eb35e7c6-99eb-30b3-b74d-786c1ceb624b", "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.", "link"=>"http://www.mendeley.com/research/genomic-analysis-kiwifruit-pathogen-pseudomonas-syringae-pv-actinidiae-provides-insight-origins-emer", "reader_count"=>104, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>8, "Researcher"=>29, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>3, "Student > Master"=>16, "Other"=>2, "Student > Bachelor"=>11, "Lecturer"=>2, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>8, "Researcher"=>29, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>3, "Student > Master"=>16, "Other"=>2, "Student > Bachelor"=>11, "Lecturer"=>2, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>78, "Medicine and Dentistry"=>2, "Neuroscience"=>1, "Business, Management and Accounting"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>78}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>6}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"New Zealand"=>1, "United States"=>1, "China"=>1, "United Kingdom"=>1}, "group_count"=>7}

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  • {"files"=>["https://ndownloader.figshare.com/files/1131424"], "description"=>"<p>Neighbor joining tree of <i>Psa</i>-V and C-9 isolates built in PHYLIP using SNPs due to mutation alone. These distances are also displayed in the upper right section of <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003503#ppat-1003503-t003\" target=\"_blank\">Table 3</a>.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "isolates", "divergent", "chinese"], "article_id"=>755390, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.g004", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogeny_of_i_Psa_i_V_isolates_and_the_divergent_Chinese_isolate_C_9_/755390", "title"=>"Phylogeny of <i>Psa</i>-V isolates and the divergent Chinese isolate C-9.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131421"], "description"=>"<p>RAxML Maximum likelihood phylogenetic analysis of 32 draft and complete genome sequences based on 15,329 SNPs and 463,396 invariant sites (A). Each phylogenetic group is assigned its own color. With the exception of a single Italian strain (*) isolated in 1992 grouping with the Japanese clade, the canker-causing Japanese, Korean and low-virulent foliar NZ isolates form monophyletic clades reflecting their geographic origin, while global isolates from the 2008–2010 outbreak form a single clade. Bootstrap scores shown are based on 100 replicates. A Splitstree analysis of recombination predicts recombination between canker-causing clades of <i>Psa</i> (B). All bootstrap scores are 100 (shown and otherwise).</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "recombination", "canker-causing"], "article_id"=>755387, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.g002", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogeny_of_i_Psa_i_and_recombination_between_canker_causing_i_Psa_i_clades_/755387", "title"=>"Phylogeny of <i>Psa</i> and recombination between canker-causing <i>Psa</i> clades.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131420"], "description"=>"<p>MUMmer dotplot displaying stretches of conserved sequence between the genomes of <i>Psa</i> NZ V-13 and J-35 as lines with slope = 1. Inverted and translocated stretches of conserved sequence are displayed as lines with slope = −1.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "nz", "v-13"], "article_id"=>755386, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.g001", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Synteny_plot_of_i_Psa_i_NZ_V_13_and_i_Psa_i_J_35_/755386", "title"=>"Synteny plot of <i>Psa</i> NZ V-13 and <i>Psa</i> J-35.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131433"], "description"=>"<p>The first three rows depict gene conversion events likely to have arisen from recombination events outside of the.</p><p>three compared strains. Rows 4–6 depict gene conversion events likely to have arisen from recombination events.</p><p>between pairs of strains (as listed).12,716 unique recombinant SNPs were identified among all strains, out of a total of 28,403 SNPs.</p>1<p>Strains used for pairwise comparison of recombination using GENECONV.</p>2<p>Total length of genome affected by recombination events.</p>3<p>Individual (discrete) regions involved in a recombination event (P&lt;0.05, GENECONV simulation with 10,000 permutations).</p>4<p>Average length of recombination event.</p>5<p>Proportion of genome affected by recombination.</p>6<p>Total identified SNPs.</p>7<p>Recombination events predicted by GENECONV to have arisen from outside the analyzed set of three genomes are largely the reciprocal of recombination events identified between pairs of strains.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution"], "article_id"=>755399, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.t002", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Recombination_events_between_i_Psa_i_strains_/755399", "title"=>"Recombination events between <i>Psa</i> strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131434"], "description"=>"1<p>A New Zealand <i>Pmp</i> isolate was used solely for the pathogenicity assay.</p>2<p>Italicized contig entries refer to the number of scaffolds in the assembly. Various assembly programs were used by different authors so these data are not directly comparable.</p>3<p>A prior version of NCPPB3739 was deposited in NCBI with the Genbank accession AFTH.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution"], "article_id"=>755400, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.t001", "stats"=>{"downloads"=>1, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Strain_table_and_assembly_statistics_/755400", "title"=>"Strain table and assembly statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131432"], "description"=>"<p>SNPs due to mutation appear above the diagonal; total number of SNPs appear below the diagonal with the number due to recombination included in brackets.</p>1<p><i>Psa</i> C-9 is included here for comparative purposes but is divergent from the global outbreak strains, as shown in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003503#ppat-1003503-g004\" target=\"_blank\">Figure 4</a>.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "distinguishing"], "article_id"=>755398, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.t003", "stats"=>{"downloads"=>3, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/SNPs_distinguishing_i_Psa_i_V_isolates_/755398", "title"=>"SNPs distinguishing <i>Psa</i>-V isolates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131429"], "description"=>"<p>The deletion of the <i>schA</i> chaperone and N-terminus of <i>hopA1</i> in K-28 and deletion of <i>hopA1</i> in J-35 are displayed with grey triangles. The transposon-mediated excision of a region in the <i>hopA1</i> locus and its reintegration 500 kb away in the <i>Psa</i> NZ V-13 genome is shown with a blue triangle. Arrows at the 5′ end of the coding sequence indicate which alleles are functional. Stars above <i>hopA1</i> indicate the presence of non-synonymous (NS) mutations. The white bar in NZ V-13 refers to a deletion and the black bar in <i>Psa</i> K-28 indicates the position of a nonsense mutation in <i>hopA1</i>. The deletion in NZ V-13 includes one of the non-synonymous mutations in K-28.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "insertions", "deletions"], "article_id"=>755395, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.g008", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Rearrangements_insertions_and_deletions_in_the_i_hopA1_i_locus_/755395", "title"=>"Rearrangements, insertions and deletions in the <i>hopA1</i> locus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131428"], "description"=>"<p>The numbers inside each region of the Venn diagram represent T3SEs with orthologs present in the low-virulent (LV), Korean (K), Japanese (J) and recent global outbreak (V) clades (A). The outer boxes in B reflect the clade-specific distribution of T3SEs (italicized) and toxins, while the color of the internal text boxes refers to their occurrence on genomic islands. <sup>1</sup>premature terminations, partial translocations, frame shifts, and out of frame indels in some strains. <sup>2</sup>variation between alleles (&gt;2% variation, in frame fusions/indels). <sup>3</sup>indicates the T3SE may not be in all <i>Psa</i> K strains. <sup>4</sup>indicates the T3SE may not be in all <i>Psa</i> J strains. <sup>5</sup>T3SE that occur within a transposon region. <sup>6</sup>T3SE is present in the conserved effector locus. <sup>7</sup>LV has two effectors in the HopAF1 group, HopAF1-2 is most closely related to HopAF1-1 in the Korean clade while HopAF1-1 is most closely related to HopAF1-1 in the outbreak and Japanese clades.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "secreted", "effector", "toxin"], "article_id"=>755394, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.g007", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Type_3_secreted_effector_and_toxin_distribution_in_i_Psa_i_clades_/755394", "title"=>"Type 3 secreted effector and toxin distribution in <i>Psa</i> clades.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131422"], "description"=>"<p>Sample view from Artemis showing SNPs from <i>Psa</i> J-31 and K-26 aligned against a ∼30 kb region of the NZ V-13 genome. Each line represents a SNP that distinguishes J-31 and/or K-26 from NZ V-13. Over this region, K-26 differs from NZ V-13 by 155 SNPs; J-31 differs by 65 SNPs. In the blue region there are 50 SNPs that distinguish J-31 and K-26 from NZ V-13. Of these, J-31 and K-26 are identical at 42 positions. GENECONV predicts that this region represents a gene conversion event between J-31 and K-26. The purple region denotes a gene conversion event into K-26 from a strain outside the set analyzed here. The set of Artemis input files allowing representation of the full set of SNPs, coverage of SNPs and regions identified by GENECONV as statistically supported regions involved in gene conversion events are available as Supplementary Dataset 1.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "snps", "k-26", "j-31", "compared", "nz"], "article_id"=>755388, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.g003", "stats"=>{"downloads"=>3, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Shared_and_unique_SNPs_in_i_Psa_i_K_26_and_J_31_compared_to_i_Psa_i_NZ_V_13_/755388", "title"=>"Shared and unique SNPs in <i>Psa</i> K-26 and J-31 compared to <i>Psa</i> NZ V-13.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131437", "https://ndownloader.figshare.com/files/1131449", "https://ndownloader.figshare.com/files/1131448", "https://ndownloader.figshare.com/files/1131447", "https://ndownloader.figshare.com/files/1131446", "https://ndownloader.figshare.com/files/1131445", "https://ndownloader.figshare.com/files/1131444", "https://ndownloader.figshare.com/files/1131443", "https://ndownloader.figshare.com/files/1131442", "https://ndownloader.figshare.com/files/1131441", "https://ndownloader.figshare.com/files/1131440", "https://ndownloader.figshare.com/files/1131439", "https://ndownloader.figshare.com/files/1131438", "https://ndownloader.figshare.com/files/1131450"], "description"=>"<div><p>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 (<i>Actinidia</i> spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by <i>P. syringae</i> pv. <i>actinidiae</i> (<i>Psa</i>) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that <i>Psa</i> 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 <i>Psa</i>-V lineage responsible for the 2008 outbreak, is now globally distributed. <i>Psa</i> has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of <i>Psa</i>-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 <i>Psa</i>-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of <i>Psa</i>-V in <i>Actinidia chinensis</i>. 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 <i>Psa</i>-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild <i>Actinidia</i> 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.</p></div>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "genomic", "kiwifruit", "pathogen", "provides", "origins", "emergent"], "article_id"=>755402, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>[nil, nil, nil, nil, nil, nil, nil, nil, nil, nil, nil, nil, nil, nil], "stats"=>{"downloads"=>40, "page_views"=>59, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_Analysis_of_the_Kiwifruit_Pathogen_i_Pseudomonas_syringae_i_pv_i_actinidiae_i_Provides_Insight_into_the_Origins_of_an_Emergent_Plant_Disease/755402", "title"=>"Genomic Analysis of the Kiwifruit Pathogen <i>Pseudomonas syringae</i> pv. <i>actinidiae</i> Provides Insight into the Origins of an Emergent Plant Disease", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131431"], "description"=>"<p>The growth of the canker-causing <i>Psa</i> J-35 (blue), NZ V-13 (red), and K-26 (purple) isolates was assayed on the ‘Hort16A’ (A) and ‘Hayward’ (B) cultivars of kiwifruit, along with the low-virulent NZ LV-5 (green) and a strain of <i>P. syringae</i> pv. <i>morsprunorum</i> (<i>Pmp</i>, yellow),that causes canker disease in <i>Prunus</i> spp. The average bacterial density (cfu ± SE) was assayed in the stem tissue at day 0 immediately following stab inoculation, as well as in the base of the first leaf above the inoculation site (no <i>Psa</i> or <i>Pmp</i> observed, data not shown). The bacterial density was quantified in the base of the first leaf above the inoculation site (dark colored bar), the center of the leaf along the mid-vein (medium colored bar), and at the leaf tip and periphery (light colored bar) 4, 8 and 14 days after inoculation. A mock inoculation with MgSO<sub>4</sub> buffer was also performed, no <i>Psa</i> or <i>Pmp</i> growth was observed (not shown).</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "assay", "strains"], "article_id"=>755397, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.g009", "stats"=>{"downloads"=>5, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Pathogenicity_assay_of_i_Psa_and_Pmp_i_strains_on_kiwifruit_/755397", "title"=>"Pathogenicity assay of <i>Psa and Pmp</i> strains on kiwifruit.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131427"], "description"=>"<p>Grey genes are orthologs with ∼75% nucleotide identity. Blue genes are variable accessory genes. Purple genes are accessory genes with complete conservation across the Pacific, Andean and Mediterranean islands. Red genes have translocated <i>via</i> transposon-mediated insertion events. Each island is bounded by 52 bp <i>att</i> sequences overlapping tRNA-Lys. Primer sites for the confirmation of excision and chromosomal integration are shown in green (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003503#ppat.1003503.s005\" target=\"_blank\">Figure S4</a>).</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "andean", "pphgi-1"], "article_id"=>755393, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.g006", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Structure_of_the_Pacific_Mediterranean_Andean_and_PPHGI_1_islands_/755393", "title"=>"Structure of the Pacific, Mediterranean, Andean and PPHGI-1 islands.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-25 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1131425"], "description"=>"<p>Numbers outside the rainbow plot show the number of ortholog groups with at least one representative ORFs per strain per clade.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Genome evolution", "ortholog", "groups"], "article_id"=>755391, "categories"=>["Biological Sciences"], "users"=>["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"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003503.g005", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Unique_and_shared_ortholog_groups_between_clades_/755391", "title"=>"Unique and shared ortholog groups between clades.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-25 02:47:40"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"14", "full-text"=>"10", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
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  • {"unique-ip"=>"15", "full-text"=>"14", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
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  • {"unique-ip"=>"32", "full-text"=>"31", "pdf"=>"9", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"15", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
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  • {"unique-ip"=>"29", "full-text"=>"38", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"25", "full-text"=>"29", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"33", "full-text"=>"37", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
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  • {"unique-ip"=>"12", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"13", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"14", "full-text"=>"10", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
  • {"unique-ip"=>"9", "full-text"=>"4", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[302, 488, 607, 717, 832, 931, 1024, 1117, 1212, 1302, 1389, 1469, 1535]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Computer and information sciences", "average_usage"=>[297, 488, 616, 724, 828, 939, 1038, 1127, 1223, 1311, 1393, 1479, 1556]}, {"subject_area"=>"/Computer and information sciences/Data management", "average_usage"=>[301, 521, 654, 776, 898, 1028, 1133, 1258, 1373, 1457, 1542, 1648, 1738]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[264, 460, 584, 692, 794, 887, 978, 1067, 1154, 1241, 1328, 1408, 1474]}, {"subject_area"=>"/Medicine and health sciences/Pathology and laboratory medicine", "average_usage"=>[267, 466, 592, 709, 806, 901, 989, 1075, 1162, 1254, 1342, 1424, 1486]}]}
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