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.