USDA110NC6USDA122NC4NK2USDA124USDA6T7T9

USDA110NC6USDA122NC4NK2USDA124USDA6T7T9

110

122

6

B. japonicum strains Genome

type

TNFNNCLNCSNCRNCNTDWNDW

TNFNNCLNCSNCRNCNTDWNDWPlant parameter

TNFNNCLNCSNCRNCNTDWNDW

Profile DC B Ain USDA110 genome

ABCDProfile

Variable regions Core 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.

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 =2nAB

SA + SB

SA :Genome size of bacterium A (kb)

SB :Genome size of bacterium B (kb)

nAB :Number of alignment between A and B

Bradyrhizobium japonicum

Rhodopseudomonas palustris

Bradyrhizobum sp.

9.1 Mb

8.3 Mb5.6 Mb

7.5 Mb

(kb/alignment)

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.

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