Table 1.
Xanthomonas euvesicatoria pv. perforans strains used in this study.
Fig 1.
Population structure of Xanthomonas euvesicatoria pv. perforans strains collected from tomato production regions.
(A) Maximum likelihood phylogenetic tree of 259 X. euvesicatoria pv. perforans strains constructed with nucleotide sequences from 887 core genes, corrected for recombination by ClonalFrameML. Tips are colored according to clusters identified by hierBAPS. Nucleotide alignment is available as S1 Data. (B) Distribution of 270 strains in each cluster by country or state of collection. Strains designated as cluster 10 (n=11) were genetically distant and excluded from the tree and hierBAPS analysis (see S1 Fig). N indicates total number of strains in each cluster. Geographic abbreviations are as follows: AUS – Australia; BRA – Brazil; CAN – Canada; CHN – China; ETH – Ethiopia; FL – Florida, USA; IN – Indiana, USA; IRN – Iran; ITA – Italy; LOU – Louisiana, USA; MX – Mexico; NC – North Carolina, USA; NI – Nigeria; AL – Alabama, USA; OH – Ohio, USA; SA – South Africa; SC – South Carolina, USA; THA – Thailand; VTM – Vietnam. (C) Map showing distribution of clusters by country of collection. Lines show instances of strains with high core gene sequence identity that were collected in different countries (S3 Table). Base layer of the map is courtesy of Eurostat (https://ec.europa.eu/eurostat/web/gisco). (D) Pairwise comparison of whole genome average nucleotide identity (ANI) confirmed high identity between strains isolated from different continents. For each comparison, genome coverage is shown by grayscale in boxes, scale shown to the right. Values for each comparison are for genomes in rows when compared to genomes in columns. See S3 Table for additional ANI output.
Fig 2.
Dated phylogeny of 259 X. euvesicatoria pv. perforans strains.
BactDating analysis estimated an approximately 130-year history for Xep strains in core gene clusters 1 through 9 (Fig 1). Red dotted line indicates the first documented isolations in 1991. Internal nodes were collapsed for clades containing strains from a single country with branch tips indicating country or strain (for full tree see S4 Fig). Bold vertical lines to the right of tip labels indicate strains from USA; other countries are labeled. Temporal signal was assessed using Phylostems and results are shown for major nodes (for full results see S3 Fig). Empty circles indicate no significant temporal signal. Colored circles indicate nodes with statistically significant temporal signal based on adjusted R2 values: green – 0.13-0.19; yellow – 0.45. The 95% highest posterior density (95% HPD) of date estimates for major nodes with significant temporal signals are shown in brackets.
Fig 3.
Variation in type III effectors (Xop proteins) in Xanthomonas perforans.
Type III effectors are in columns and 270 X. euvesicatoria pv. perforans strain in rows. Effector status is shown by allele type: absence is indicated by allele type 0 (white), while the most frequent allele observed when the effector is present is allele type 1 (purple), second most frequent is allele type 2 (blue), and so on. Putative pseudogenized effectors are shown as allele 13 (gray). The order of columns was determined by hierarchical clustering analysis, placing similarly distributed effectors adjacent to each other. Genomes showing BLAST hits to TAL effector(s) are indicated in S3 Table and not shown in heatmap. X. euvesicatoria pv. perforans strains (rows) are organized by core gene cluster.