Additional file 1 of Comparative genomics in “Candidatus Kuenenia stuttgartiensis” reveal high genomic plasticity in the overall genome structure, CRISPR loci and surface proteins

Additional file 1 Fig. S1. Cumulative GC skew along the genomes of “Ca. Kuenenia stuttgartiensis” strains. Fig. S2. Venn diagram showing the core genome and the genes specific in “Ca. Kuenenia stuttgartiensis” strains. Fig. S3. Unrooted phylogenetic trees of ten S-layer homologous gene constructed based on the Neighbor-Joining method. Fig. S4. Amino acid sequence of the S-layer protein of strain CSTR1 (KsCSTR_09970). Fig. S5. Coverage of SMRT sequencing reads along the genome of “Ca. Kuenenia stuttgartiensis” strain CSTR1. Table S1. Reported genome assemblies of anammox bacteria up to this study (as of 02.02.2020). Table S2. List of the longest 25 contigs obtained by the automatic assembling pipeline in the PacBio SMRT Analysis software package. Table S3. Hypothetical sequential rearrangement events from genome CSTR1 to genome MBR1b as calculated by GRIMM. Table S4. List of the 20 locally collinear blocks (LCBs) of the genome of “Ca. Kuenenia stuttgartiensis” strain CSTR1 after Mauve alignment with MBR1b. Table S5. CRISPR elements in the anammox genomes KUST, MBR1 and CSTR1. Table S6. Comparison of the large CRISPR locus near the type I-B CRISPR-Cas cluster in the three studied anammox genomes. Table S7. Protein-coding genes of “Ca. Kuenenia stuttgartiensis” strain CSTR1 and their abundance in the proteome. Table S8. Transposase genes and their classification in the anammox genomes KUST, MBR1 and CSTR1. Table S9: List of transposase genes and their classification in the anammox genomes KUST, MBR1 and CSTR1. Table S10. Abundances of peptides from two highly similar hydrazine dehydrogenases KsCSTR_46980 and KsCSTR_11820 in the proteome of “Ca. Kuenenia stuttgartiensis” strain CSTR1. Table S11. Detection of three nitrite reductase gene candidates in the proteome of “Ca. Kuenenia stuttgartiensis” strain CSTR1 over time. Table S12. List of peptides detected in the S-layer protein KsCSTR_09970 in a series of “Ca. Kuenenia stuttgartiensis” strain CSTR1 samples. Additional file 1. Genome assembly from the IonTorrent-based resequencing of “Ca. Kuenenia stuttgartiensis” strain KUST in 2012.

附加文件1 补充图S1："Ca. Kuenenia stuttgartiensis"菌株基因组的累积GC偏斜值分布；补充图S2：展示"Ca. Kuenenia stuttgartiensis"菌株核心基因组与特异性基因的维恩图；补充图S3：基于邻接法（Neighbor-Joining）构建的10个S层（Surface Layer, S-layer）同源基因的无根系统发育树；补充图S4：菌株CSTR1（KsCSTR_09970）的S层蛋白氨基酸序列；补充图S5："Ca. Kuenenia stuttgartiensis"菌株CSTR1基因组的单分子实时测序（Single-Molecule Real-Time, SMRT）读段覆盖度分布；补充表S1：截至本研究（2020年2月2日）已报道的厌氧氨氧化菌（anaerobic ammonium oxidation bacteria, anammox bacteria）基因组组装结果；补充表S2：PacBio SMRT Analysis软件包自动组装流程获得的最长25个重叠群（contig）列表；补充表S3：通过GRIMM基因组重排分析软件计算得到的、从基因组CSTR1到MBR1b的假想连续重排事件；补充表S4：经与MBR1b进行Mauve基因组比对软件比对后，"Ca. Kuenenia stuttgartiensis"菌株CSTR1基因组的20个局部共线性区块（locally collinear blocks, LCBs）列表；补充表S5：厌氧氨氧化菌基因组KUST、MBR1和CSTR1中的成簇规律间隔短回文重复序列（Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR）元件；补充表S6：3个研究厌氧氨氧化菌基因组中I-B型CRISPR-Cas簇附近大型CRISPR位点的比较结果；补充表S7："Ca. Kuenenia stuttgartiensis"菌株CSTR1的蛋白质编码基因及其在蛋白质组（proteome）中的丰度；补充表S8：厌氧氨氧化菌基因组KUST、MBR1和CSTR1中的转座酶（transposase）基因及其分类信息；补充表S9：厌氧氨氧化菌基因组KUST、MBR1和CSTR1中的转座酶基因及其分类信息；补充表S10："Ca. Kuenenia stuttgartiensis"菌株CSTR1蛋白质组中两种高度相似的肼脱氢酶（hydrazine dehydrogenase）KsCSTR_46980与KsCSTR_11820的肽段（peptide）丰度；补充表S11：不同时间点下"Ca. Kuenenia stuttgartiensis"菌株CSTR1蛋白质组中3个亚硝酸还原酶（nitrite reductase）基因候选物的检测结果；补充表S12：一系列"Ca. Kuenenia stuttgartiensis"菌株CSTR1样本中检测到的S层蛋白KsCSTR_09970对应的肽段列表；附加文件1：2012年基于IonTorrent测序平台对"Ca. Kuenenia stuttgartiensis"菌株KUST进行重测序获得的基因组组装结果