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

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

附加文件2：图S1。基于本研究使用的50个根瘤菌基因组共有的2110个单拷贝核心基因构建的邻接物种树。每个菌株名称前标注有附加文件1表S1中给出的簇编号。本研究鉴定得到的21株根瘤菌以粗体标注。
图S2。选取7株代表性根瘤菌，对红三叶（Trifolium pretense）、含羞草（Mimosa pudica）、菜豆（Phaseolus vulgaris）以及银合欢（Leucaena leucocephala）开展交叉结瘤试验。* 每组处理设置3个培养袋重复。** 菌株名称前的粗斜体字母代表其原始宿主；P代表菜豆（Phaseolus vulgaris），T代表红三叶（Trifolium pretense）。
图S3。29株代表性根瘤菌中与宿主相关的核心基因。选取12个关键共生基因，通过1000次自举重复构建邻接系统发育树（仅展示自举支持值>60%的分支）。标尺代表5%的序列分歧度。共生宿主特征通过不同颜色的实线标注：红色对应菜豆（Phaseolus vulgaris），绿色对应含羞草属（Mimosa spp.），蓝色对应三叶草属（Trifolium spp.）。
图S4。酸根瘤菌（R. acidisoli）FH23完整基因组的环状可视化图谱。最外圈代表基因组序列坐标；从外到内的圆环依次为：蛋白质编码基因、通过BLAST比对至COG（Clusters of Orthologous Groups，同源蛋白簇）、KEGG（京都基因与基因组百科全书）和GO（基因本体论）数据库的基因、非编码RNA、GC含量偏差（绿色/红色）以及GC偏移（浅绿/粉色）；从最外圈至最内圈的圆环分别对应正链和负链的基因。
图S5。基于R18-FH23（酸根瘤菌R. acidisoli）共生质粒中特有基因的COG注释，统计同源基因的分布情况。
图S6。不同豆科植物分离菌株间近期水平基因转移（Horizontal Gene Transfer, HGT）基因的预测结果。a 中华根瘤菌属（Ensifer）菌株；b 慢生根瘤菌属（Bradyrhizobium）菌株。连线宽度与预测得到的近期HGT基因数量呈正比；连线颜色越深，代表该近期HGT事件的预测规模越大。
图S7。展示3个不同属的29株根瘤菌的基因组大小、蛋白质编码序列以及COG注释之间相关性的相关图。正相关通过下三角单元格或上三角中从左下到右上的蓝色圆形/色块表示；负相关则通过从左上到右下的红色色块表示；颜色越深、饱和度越高，代表相关性强度越大；接近零的弱相关性几乎无色。