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Additional file 2 of Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts

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posted on 28.02.2020 by Wenjun Tong, Xiangchen Li, Entao Wang, Ying Cao, Weimin Chen, Shiheng Tao, Gehong Wei
Additional file 2: Figure S1. Neighbor-joining species tree based on the 2110 single-copy core genes shared by 50 rhizobial genomes used in this study. The name of each strain is preceded by the cluster number indicated in Additional file 1: Table S1. The 21 Rhizobium strains in bold font were determined in this study. Figure S2. Cross-nodulation tests on Trifolium pretense, Mimosa pudica, Phaseolus vulgaris, and Leucaena leucocephala with seven representative Rhizobium strains. * n = 3 cultivation bags per treatment. ** bold italic letters before strain names indicate the original host. P, Phaseolus vulgaris; T, Trifolium pretense. Figure S3. Core genes of 29 representative Rhizobium strains related to hosts. Neighbor-joining trees of 12 critical symbiosis genes were constructed using 1000 bootstrap replicates (only bootstrap support > 60% is shown). Bar = 5% sequence divergence. Symbiotic characteristics are indicated by different colored solid lines (host; red = Phaseolus vulgaris, green = Mimosa spp., blue = Trifolium spp.). Figure S4. Graphical circular map of the complete genome of R. acidisoli FH23. The outermost circle represents the coordinates of the genome sequence. Circles from outside to inside indicate protein-coding genes, genes BLAST searched against COG, KEGG, and GO databases, non-coding RNA, deviations in G + C content (green/red), and G-C skew (light green/pink). Outermost to innermost positions indicate genes in forward and reverse orientations. Figure S5. Distribution of homologous genes based on COG assignment of unique genes within the symbiosis plasmid of R18-FH23 (R. acidisoli). Figure S6. Prediction of recent HGT genes among strains isolated from different legumes. a Ensifer strains. b Bradyrhizobium strains. The width of links is proportional to the number of predicted recent HGT genes. The darker the link color, the larger the predicted magnitude of the recent HGT event. Figure S7. Correlogram showing correlations between genome size, protein-coding sequences, and COG assignments of the 29 rhizobial strains in three distinct genera. Positive correlations are indicated by cells with lower triangles or circles in upper triangles colored blue from lower left to upper right. Negative correlations are represented by red coloring from the upper left to the lower right. The darker and more saturated the color, the greater the magnitude of the correlation. Weak correlations (near zero) are almost colorless

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