Files in this Data Supplement:

• Supplemental file 1 - Fig. S1, gene similarity for A. radiobacter K84 versus 11 other alphaproteobacterial genomes.
  Zipped PDF file, 59K.
• Supplemental file 2 - Fig. S2, phylogenomic tree derived from whole-genome comparisons.
  Zipped PDF file, 51K.
• Supplemental file 3 - Fig. S3, evolution of second chromosomes among the gammaproteobacteria.
  Zipped PDF file, 13K.
• Supplemental file 4 - Fig. S4, evolution of second chromosomes among the betaproteobacteria.
  Zipped PDF file, 19K.
• Supplemental file 5 - Fig. S5, neighbor-joining tree for RepA proteins of fully sequenced Agrobacterium strains.
  Zipped PDF file, 124K.
• Supplemental file 6 - Fig. S6, neighbor-joining tree for RepC proteins of fully sequenced Agrobacterium strains.
  Zipped PDF file, 151K.
• Supplemental file 7 - Fig. S7, comparison of cognate RepA and RepB proteins and RepA and RepC proteins from the same plasmids.
  Zipped PDF file, 143K.
• Supplemental file 8 - Fig. S8, comparison of cognate RepB and RepC proteins and of cognate RepC proteins and oriV from the same plasmids.
  Zipped PDF file, 6K.
• Supplemental file 9 - Table S1, A. tumefaciens C58 genome feature summary.
  Zipped PDF file, 3K.
• Supplemental file 10 - Table S2, A. vitis S4 genome feature summary.
  Zipped PDF file, 3K.
• Supplemental file 11 - Table S3, A. radiobacter K84 genome feature summary.
  Zipped PDF file, 3K.
• Supplemental file 12 - Table S4, genomes used for phylogenetic reconstruction among the Rhizobiaceae with outgroups in the Rhizobiales.
  Zipped PDF file, 66K.
• Supplemental file 13 - Table S5, homology groups used to construct the species phylogeny.
  Zipped PDF file, 162K.
• Supplemental file 14 - Tables S6 to S22, shared gene clusters.
  Zipped PDF file, 218K.