Phylogenetic relationships between Xvv, Xcm and Xoo.
The phylogenetic tree on the left was inferred
using the Maximum Parsimony method based on 39,665 single-nucleotide variants with
respect to the chromosome of Xoo MAFF 311018. Bootstrap values are expressed as
percentages of 500 trials. The tree is drawn to scale with branch lengths calculated using
the average pathway method and are in the units of the number of changes over the whole
sequence.
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Figure S1. Comparison of gene-content based on alignment against the Xcm NCPPB 2005 genome assembly. |
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Figure S2. Comparison of gene-content based on alignment against the Xcm NCPPB 4384 genome assembly. |
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Figure S3. Comparison of gene-content based on alignment against the Xvv NCPPB 895 genome assembly. |
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Figure S4. Comparison of gene-content based on alignment against the Xvv NCPPB 206 genome assembly. |
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Figure S5. Comparison of gene-content based on alignment against the Xvv NCPPB 1326 genome assembly. |
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Figure S6. The genomes of Xvv NCPPB 890, 702, 1326 and 1381 contain extensive sequence similarity to X. axonopodis pv. citri 29-1 plasmid pXAC47. |
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Figure S7. The genomes of Xcm NCPPB 4379, 4380, 4383, 4384, 4392 and 4395 each contain extensive sequence similarity to X. citri pv. malvacearum X20 unnamed plasmid.
Illumina genomic sequence reads are aligned against CM002030.1. |
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Figure S8. The genomes of Xcm NCPPB 895 contains extensive sequence similarity to plasmid sequences from X. citri pv. manihotis.
Illumina genomic DNA sequence reads are aligned against AKEJ01000091.1.
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Figure S9. Xvv NCPPB 206, 890, 702, 1326 and 1381 share a common LPS biosynthesis cluster that is distinct from that of Xvv 895 and Xcm. Illumina genomic sequence reads are aligned against ACHS01000119.1 |
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Figure S10. Xvv NCPPB 206, 890, 702, 1326 and 1381 share a common LPS biosynthesis cluster that is distinct from that of Xvv 895 and Xcm. Illumina genomic sequence reads are aligned against
ACHS01000380.1.
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Figure S11. Xvv NCPPB 895 and Xcm share a common LPS biosynthesis cluster that is distinct from those of Xvv NCPPB 206, 890, 702, 1326 and 1381.
Illumina genomic sequence reads are aligned against AKBE01000022.1.
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Figure S12. The TFP loci of Xvv NCPPB 890, 702, 1326 and 1381 are similar to each other but different to those of Xvv NCPPB 895 and 206.
Illumina genomic DNA sequence reads are aligned against ACHS01000345.1.
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Figure S13. The TFP loci of Xvv NCPPB 895 and 206 are similar to those of Xcm and different from those of Xvv NCPPB 890, 702, 1326 and 1381.
Illumina genomic DNA sequence reads are aligned against AKBM01000028.1.
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Figure S14. Xvv 702, 890 1326 and 1381 contain xopAF-like gene that is absent from Xvv 206 and from Xcm.
Illumina genomic DNA sequence reads are aligned against ACHS01000051.1.
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Figure S15. Xcm genomes contain a xopJ-like gene that is absent from Xvv genomes.
Illumina genomic DNA sequence reads are aligned against AKBE00000192.1.
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Figure S16. Xcm genomes contain a xopJ-like gene that is absent from Xvv genomes.
Illumina genomic DNA sequence reads are aligned against AKBE00000064.1.
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Figure S17. A xopL-like gene is present in Xcm 2005, 2251, 4387, and 4389 but absent from Xcm 4379, 4380, 4381, 4383, 4384, 4394 and 4395.
Illumina genomic DNA sequence reads are aligned against AKBE00000144.1.
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Figure S18. The xopL-like gene contains a C->A substitution resulting in a TCA codon being transformed to a TAA stop codon in Xvv 890, 702, 1326 and 1381.
Illumina genomic DNA sequence reads are aligned against AKBE00000144.1.
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Figure S19. The xopL-like gene contains a C->A substitution resulting in a TCA codon being transformed to a TAA stop codon in Xvv 890, 702, 1326 and 1381.
Illumina genomic DNA sequence reads are aligned against ACHS01000315.1.
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Data file 1. Multiple sequence alignment of SNPs on which phylogentic analysis in the manuscript is based. In FastA format.
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FastA file |
Data file 2. Candidate PIP boxes in the genome sequence of Xvv 702.
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Xvv 702 PIP boxes |
Data file 3. Candidate PIP boxes in the genome sequence of Xcm 4381.
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Xcm 4381 PIP boxes |