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 图S1：‘候选斯图加特库嫩菌（Ca. Kuenenia stuttgartiensis）’各菌株基因组的累积GC偏移（GC skew）。
图S2：展示‘候选斯图加特库嫩菌’各菌株核心基因组与特异性基因的韦恩图。
图S3：基于邻接法（Neighbor-Joining）构建的10个S层（S-layer）同源基因的无根系统发育树。
图S4：菌株CSTR1的S层蛋白（KsCSTR_09970）的氨基酸序列。
图S5：‘候选斯图加特库嫩菌’菌株CSTR1基因组的单分子实时（SMRT）测序读长覆盖度。
表S1：截至本研究提交时（2020年2月2日）已报道的厌氧氨氧化（anammox）菌基因组组装结果。
表S2：PacBio SMRT分析软件包自动组装流程得到的最长25个重叠群（contig）列表。
表S3：通过GRIMM软件计算得到的、从基因组CSTR1到基因组MBR1b的假想连续重排事件。
表S4：‘候选斯图加特库嫩菌’菌株CSTR1基因组与MBR1b经Mauve比对后得到的20个局部共线性区块（LCBs）列表。
表S5：厌氧氨氧化菌基因组KUST、MBR1与CSTR1中的成簇规律间隔短回文重复序列（CRISPR）元件。
表S6：三种研究厌氧氨氧化基因组中I-B型CRISPR-Cas成簇序列附近的大型CRISPR位点比较。
表S7：‘候选斯图加特库嫩菌’菌株CSTR1的蛋白编码基因及其在蛋白质组中的丰度。
表S8：厌氧氨氧化菌基因组KUST、MBR1与CSTR1中的转座酶基因及其分类信息。
表S9：厌氧氨氧化菌基因组KUST、MBR1与CSTR1中的转座酶基因及其分类信息列表。
表S10：‘候选斯图加特库嫩菌’菌株CSTR1蛋白质组中两种高度相似的肼脱氢酶KsCSTR_46980与KsCSTR_11820的肽段丰度。
表S11：随时间变化的‘候选斯图加特库嫩菌’菌株CSTR1蛋白质组中三种亚硝酸盐还原酶候选基因的检测结果。
表S12：一系列‘候选斯图加特库嫩菌’菌株CSTR1样本中S层蛋白KsCSTR_09970检测到的肽段列表。
附加文件1：2012年基于离子激流（IonTorrent）平台对‘候选斯图加特库嫩菌’菌株KUST进行重测序得到的基因组组装结果。