Position of all identified SNPs in the <i>P. syringae</i> pv. <i>theae</i> NCPPB 2598 genome (and primer sequences to amplify them) that distinguish European strains from each other and European strains from Chinese strains. Primer sequences to distinguish between the European and Asian version of the PPHGI-1 island are also listed. Results obtained by PCR and Sanger sequencing are indicated.

<p>Position of all identified SNPs in the <i>P. syringae</i> pv. <i>theae</i> NCPPB 2598 genome (and primer sequences to amplify them) that distinguish European strains from each other and European strains from Chinese strains. Primer sequences to distinguish between the European and Asian version of the PPHGI-1 island are also listed. Results obtained by PCR and Sanger sequencing are indicated.</p

Neighbor Joining cladogram based on Single Nucleotide Polymorphisms (SNPs) identified between <i>P. syringae</i> pv. <i>actinidiae</i> (PSA) genomes and <i>P. syringae</i> pv. <i>theae</i>.

<p>Sequencing reads of nine PSA genomes were aligned against a draft genome of <i>P. syringae</i> pv. <i>theae</i> pathotype strain NCPPB 2598. A neighbor joining tree was built based on 21,494 SNPs so identified. Country and year of isolation are indicated for each strain. Bootstrap values based on 1000 bootstrap replicates are shown above nodes and number of SNPs compared to <i>P. syringae</i> pv. <i>theae</i> are shown underneath branches. Branches with less than 50% bootstrap support were collapsed. In the Japanese/Korean clade three SNPs group PsaKN.2 with PA459 and thus conflict with the branching pattern obtained in the tree. No SNPs conflict with the branching pattern obtained for the Chinese/European clade. A Bayesian tree was also constructed and had the same topology as the neighbor-joining tree.</p

Number of SNPs distinguishing pairs of strains identified in 3,453,192 bp.

<p>Number of SNPs distinguishing pairs of strains identified in 3,453,192 bp.</p

Genome sequencing and assembly results for the nine sequenced PSA strains and the <i>P. syringae</i> pv. <i>theae</i> pathotype strain NCPPB 2598.

1<p>The versions described in this paper are the first versions xxxx01000000.</p>2<p>pathovar <i>theae</i>.</p

Phylogenetic tree placing <i>P. syringae</i> pv. <i>actinidiae</i> (PSA) within the <i>P. syringae</i> species complex.

<p>1,186 proteins that are present exactly one time in each of the nine PSA strains and the <i>P. syringae</i> pv. <i>theae</i> pathotype strain NCPPB 2598 sequenced here and in each of 35 additional <i>P. syringae</i> strains for which genome sequences are available were aligned and concatenated. A maximum likelihood tree was then built using the two sequenced <i>P. fluorescens</i> strains Pf-0 and Pf5-1 as outgroups. Strains are labeled with pathovar names and strain names (genome accession numbers are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036518#pone.0036518.s001" target="_blank">Table S1</a>). Bootstrap values higher than 95 are shown at nodes. * Strain ES4326 is present twice since two stocks of this strain were sequenced separately. ** Strains 0893-23 and NCPPB 3681 are the same strain sequenced twice in two separate genome sequencing projects.</p