1. USDA110 NC6 USDA122 NC4 NK2 USDA124 USDA6 T7 T9 USDA110 NC6 USDA122 NC4 NK2 USDA124 USDA6 T7 T9 110 122 6 B. japonicum strains Genome type TN FN NCL NCS NCR NCN TDW NDW TN FN NCL NCS NCR NCN TDW NDW Plant parameter TN FN NCL NCS NCR NCN TDW NDW Profile DC B A in USDA110 genome ABCD Profile Variable regionsCore regions Supplemental figure 1. Schematic presentation of variable regions of B. japonicum USDA110 genome. Missing region and positive correlation were expressed as red and green colors, respectively. Abbreviations of plant parameters were described in the legend of Figure 5.

2. USDA110 CGH009 ORS278 BTAi1 6.7 5.6 4.7 5.4 6.6 3.5 Supplemental figure 2A. Schematic presentation of distance based on synteny density of the genomes of Bradyrhizobium japonicum USDA110 (Kaneko et al, 2002), Rhodopaeudomonas palustris (Larimer et al, 2004), and Bradyrhizobum sp. BTAi1 and ORS278 (Giraud et al, 2007). Genome synteny analysis between B. japonicum USDA110, Bradyrhizobium sp. BTAi1, ORS278 and R. palustris CGA009 were performed by the G-InforBio software (WFCC-MIRCEN World Data Centre for Microorganisms, Shizuoka, Japan). Parameter sets in this analysis were as follows: minimum percent identity, 80%; minimum alignment length, 100 bp; maximum mismatch, 50%; and maximum gap opening, 20 bp. Distance = 2n AB S A + S B S A :Genome size of bacterium A (kb) S B :Genome size of bacterium B (kb) n AB :Number of alignment between A and B Bradyrhizobium japonicum Rhodopseudomonas palustris Bradyrhizobum sp. 9.1 Mb 8.3 Mb 5.6 Mb 7.5 Mb (kb/alignment)

3. Supplemental figure 2B. Synteny plot among Bradyrhizobium japonicum USDA110 (Kaneko et al, 2002), Rhodopaeudomonas palustris (Larimer et al, 2004), and Bradyrhizobum sp. BTAi1 and ORS278 (Giraud et al, 2007). White arrowheads are GI positions on B. japonicum USDA110 genome.

4. Supplemental figure 2C. Synteny plot among Rhodopaeudomonas palustris (Larimer et al, 2004), and Bradyrhizobum sp. BTAi1 and ORS278 (Giraud et al, 2007).