1. Figure S1. Neighbour joining tree reconstructed based upon the concatenated sequences of 2822 core genes of the 25 citrus canker causing Xanthomonas strains using MEGA6. A total of 100 bootstrap replicates were made, and bootstrap values were indicated at the branch points MN10 MN12 MN11 JX4 JX5 GD2 GD3 UI6 UI7 A306 NT17 FB19 Miami BL18 MF20 A*270 As9 As8 Aw12879 Aw13 Aw16 Aw14 Aw15 XauB XauC XacA w & XacA* XacA

2. XacA w & XacA* XacA Figure. S2. 3D view of the genome features of the 23 Xac strains. The red triangles denote XacA* strains, the pink circles denote XacA w strains and the yellow diamond denote XacA strains.

3. Core genome Pan-genome Figure S3. Depletion curves of core-genome (left) and accumulation curves of pan-genome (right) of the 23 Xac strains. The fitted curves (red line) were added by using get_homologues based on model proposed by Tettelin in 2005 (Pubmed=16172379)

4. Figure S4. Results of the ClonalFrame analysis on the basis of un-gapped sequences of the longest 9 aligned blocks of 23 Xac genomes generated by progressiveMAUVE. The inferred clonal genealogy was shown on the left and the distribution of the recombination (red) and mutation (green) events estimated by ClonalFrame on the corresponding branches were shown on right. The distribution of the 9 blocks were indicated according to the start and end position on XacA306 chromosome. All possible events revealed by ClonalFrame were shown, and the relationship between event panels and their corresponding nodes were indicated with dash lines. The recombination events (red in the event panels) only occurred in XacA node and A w & A* node (red dash lines). AS8 A*270 AS9 XCAW AW16 NT17 FB19 5208 AW13 AW15 AW14 A306 MF20 BL18 GD3 UI7 JX5 GD2 UI6 JX4 MN12 MN11 MN10 XacA w & A* XacA 1383432- 1908613 687092- 1213596 179310- 687087 4143464- 4454744 3525087- 3803856 3107752- 3355123 3909361- 4143431 2839814- 3068286 4652022- 4864440 start- end