File S1 - Comparative Genome Analysis Reveals Metabolic Versatility and Environmental Adaptations of Sulfobacillus thermosulfidooxidans Strain ST

Figures S1, S2, and S3 and Tables S1, S2, S3, S4 and S5. Figure S1. A. Phylogeny of Clostridiales family XVII incertae sedis including S. thermosulfidooxidans. Phylogenetic tree based on the 16S rRNA gene was constructed with the neighbor-joining method. The scale bar represents the number of nucleotide substitutions per site. B. Electron micrograph of S. thermosulfidooxidans shows its morphology. Figure S2. Venn diagrams showing the numbers of COGs shared between the predicted proteomes of S. thermosulfidooxidans, S. acidophilus, and T. marianensis. Proteins that were not grouped into COGs are represented as specific proteins for each organism. Numbers in brackets behind species names indicate total number of predicted proteins. Figure S3. Phylogenetic tree of arsenate reductase. The phylogenetic tree was constructed based on a manually corrected alignment of 159 amino acid positions with the neighbor-joining method. The numbers associated with the branches refer to bootstrap values (confidence limits) resulting from 1,000 replicate resamplings. The scale represents the number of amino acid substitutions per site. The two sequences in S. thermosulfidooxidans are shown in bold. Table S1. Primers used for semi-quantitative RT-PCR. Table S2. Selecting genes encoding informational processing proteins. Table S3. Genes encoding transposase and other enzymes related with gene transposition. Table S4. Genes encoding proteins of diverse metabolic pathways. Table S5. Genes encoding transporter proteins. (ZIP)补充图S1、S2、S3及补充表S1、S2、S3、S4、S5如下： 补充图S1 A. 嗜热硫化物氧化杆菌（S. thermosulfidooxidans）所属的梭菌目XVII科地位未定类群（Clostridiales family XVII incertae sedis）的系统发育关系。基于16S rRNA基因的系统发育树采用邻接法构建，标尺代表每一位点的核苷酸替换数。B. 嗜热硫化物氧化杆菌的电子显微照片，展示其菌体形态。 补充图S2 维恩图展示了嗜热硫化物氧化杆菌、嗜酸链球菌（S. acidophilus）以及马里亚纳海沟菌（T. marianensis）的预测蛋白质组中共享的同源簇（Clusters of Orthologous Groups, COGs）数量。未被归入COGs的蛋白质被视为各物种的特有蛋白；物种名称后的括号内数字为对应物种的预测蛋白总数量。 补充图S3 砷酸还原酶的系统发育树。该系统发育树基于159个氨基酸位点经人工校正后的序列比对结果，采用邻接法构建。分支旁的数值代表1000次重复抽样得到的自举值（置信限）；标尺代表每一位点的氨基酸替换数。嗜热硫化物氧化杆菌的两条序列以粗体标注。 补充表S1 半定量逆转录聚合酶链反应（semi-quantitative RT-PCR）所用引物。 补充表S2 信息处理蛋白编码基因的筛选。 补充表S3 转座酶及其他与基因转座相关酶类的编码基因。 补充表S4 多种代谢通路相关蛋白的编码基因。 补充表S5 转运蛋白的编码基因。（ZIP）