Figure 1.
Compatible reactions to artificial inoculations of P. cannabina pv. alisalensis (Pcal) on monocots and dicots plant species.
Artificial inoculations were performed using the sequenced Pcal strain PSa1_3 on: tomato leaves (A), tomato stem (B), Oat leaves (C) and Bromus diandrus leaves (D). Information for additional artificial inoculations on various plant species can be found in figure S1.
Table 1.
Statistics and features of the sequenced P. cannabina pv. alisalensis strains.
Figure 2.
Phylogenetic tree of P. cannabina pv. alisalensis (Pcal) and the P. syringae species complex based on core genome proteins.
A phylogenetic tree was constructed based on all proteins present exactly one time in each of the Pcal genome sequences and representative P. syringae genome sequences. The Bootstrap values for all branches of the tree are 100. The genomes and their accession numbers are listed in Table S3.
Figure 3.
Pairwise alignment between Pcal ES4326 (previously known as P. s. pv. maculicola ES4326) and the compete genome of P. s. pv. syringae B728a (A) and the draft genomes of Lineage-I Pcal PSa866 and Lineage-II Pcal PSa1_3 (B) using the MAUVE software. Colored blocks outline genome sequence that aligned to part of another genome, and was presumably homologous and internally free from genomic rearrangement (Locally Colinear Blocks or LCBs). White regions are sequence that were not aligned and probably contain sequence elements specific to a particular genome. Blocks below the center line indicate regions that aligned in the reverse complement (inverse) orientation. The height of the profile within each LCB demonstrates the average degree of sequence conservation within an aligned region.
Figure 4.
Presentation of the distribution of various gene categories (COGs) in the respective Pcal strains PSa1_3, PSa866, BS91, T3C and ES4326.
Figure 5.
Schematic representation of the hrp/hrc gene cluster coding for the synthesis of the type III secretion system of Pseudomonas cannabina pv. alisalensis.
The genes were arranged in five operons organized in two main blocks having convergent transcription: the hrpRS, hrpZ and hrpC operons in one orientation, and the hrpU and hrpJ in the opposite direction. The two blocks were separated by a hyper variable region with a very low level of conservation between closely taxonomically related bacteria.
Table 2.
Aminoacid sequence identity percentages between predicted Hrp/Hrc proteins from P. cannabina pv. alisalensis and those from P. syringae pv. syringae B728a, P. syringae pv. tomato DC3000 and P. syringae pv. phaseolicola 1448a.
Figure 6.
Pairwise alignment between the hrp/hrc gene clusters coding for the type III secretion systems of the complete sequenced P. syringae pv. syringae B728a and P. syringae pv. tomato DC3000 and those of P. cannabina pv. alisalensis PSa1_3, PSa866 and T3C. Areas where white is visible, were not aligned and probably contained sequence elements specific to a particular genome. The height of the profile demonstrates the average degree of sequence conservation within an aligned region.
Figure 7.
T3SS core component HrcV phylogenetic analysis.
For the phylogenetic analysis the amino acid (A), as well as the nucleotide sequences (B), were used. Information for additional phylogenetic analysis of various T3SS core components can be found in figures S3. The various MLSA groups [43], [45] are marked in different colors.
Figure 8.
Comparison of the sequenced Pcal strains genomes, as well as of the Pcal ES4326 and P. cannabina pv. cannabina BS0968 genomes, for genes encoding candidate T3SS secreted substrates.
In addition to known hop effector genes, two genes for T3SS helper proteins are also included (hrpZ1 and hrpW1) (A). Occurrence of effector genes in the six strains is indicated: Absence (white), Presence (gray), Truncation (bordeaux), disrupted by a premature stop codon (green). Comparison tree contracted using the information presenting in the presence-absence table (part A of the same Figure) (B).
Figure 9.
T3SS effector proteins (T3EPs) phylogeny.
For the phylogenetic analysis, the amino acid sequences of every effector group were used, as they are presented in the Hop Database website. Additional information for the phylogeny of the rest of Pcal T3EPs can be found in figure S4.
Figure 10.
Schematic representation of the gene cluster coding for the type VI secretion systems (T6SSs) of Pseudomonas cannabina pv. alisalensis.