Additional file 1 of To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131
Creators: name: Tantoso, Erwin
name: Eisenhaber, Birgit
name: Kirsch, Miles
name: Shitov, Vladimir
name: Zhao, Zhiya
name: Eisenhaber, Frank
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 1: Figures S1-S17. This Additional file 1 provides 17 supplementary figures supporting the conclusions in the main text. Fig. S1. Genome distribution among the most common sequence types and phylogroups. Only common sequence types and phylogroups with at least 10 E. coli genomes are shown. The distribution of sequence types (A) and phylogroups (B) for the selected 674 E. coli genomes is illustrated. Fig. S2. Genome size and proteome size distribution among E. coli genomes. Boxplot illustration of the distribution of genome size (A) and proteome size (B) across different phylogroups of E. coli genomes. The OTH phylogroup represents 4 genomes in clade I (1), E or clade I (2) and unknown (1). Fig. S3. Genome distribution among sequence types and phylogroups. Barplot illustration of the distribution of sequence type (A) and phylogroups (B) among the 1,324 E. coli genomes. The y-axis represents the number of genomes. The horizontal line in (A) represents the threshold at number of genomes equal to 10. Fig. S4. The distribution of virulence categories across the 21 most common sequence types of E. coli. The distribution of virulence categories across the 21 common sequence types of E. coli ordered according to its phylogroups. Based on the total number of virulence factors (VFs) present in the genome, we categorized the genome into four virulence categories, i.e. (1) likely nonpathogenic (#VFs &lt;6); (2) likely virulence (6 &lt;= #VFs &lt;14); (3) high virulence (14 &lt;= #VFs &lt; 22) and (4) very high virulence (#VFs &gt;= 22). The phylogroup B1* represents phylogroup B1 with shiga toxin. Fig. S5. Distribution of COG categories in GFs of the reference genome and in the softcore genome. The distribution of COG categories for the gene families in (A) E. coli reference in the COG database; and (B) the softcore genome. Fig. S6. Distribution of COG categories in GFs in ST 131. The distribution of COG categories for the gene families that are (A) common in E. coli ST131; and (B) rare in E. coli ST131. Fig. S7. The presence of s1-ST131or s2-ST131 in ST131 and other E. coli genomes. The distribution of BLASTN coverage for (A) s1-ST131 and (B) s2-ST131 clusters in ST131 genomes; and non-ST131 genomes. The presence of s1-ST131or s2-ST131 cluster is shown by BLASTN coverage of 95% -100% whereas the absence of these clusters are shown in the BLASTN coverage 0% - 5%. The partial presence of these clusters is shown in between 5% to 95%. Fig. S8. Sequences similar to s1-ST131 among non-E. coli genomes. The top 20 hits of NCBI BLASTN to the nr-database excluding E. coli genomes for the s1-ST131 cluster. Fig. S9. Sequences similar to s2-ST131 among non-E. coli genomes. The top 20 hits of NCBI BLASTN to the nr-database excluding E. coli genomes for the s2-ST131 cluster. Fig. S10. Genome browser results of the s2-ST131 cluster. Genome browser results of the s2-ST131 cluster based upon GCF_000931565.1 as the representative E. coli ST131. The shown region is on chromosome NZ_CP010876.1 (2,042,977 – 2,066,794). The highlighted regions represent the nanomachine (tailocin), the capsid and the lysis-related genes. Fig. S11. The presence of s1-ST11or s2-ST11 in ST11 and other E. coli genomes. The distribution of BLASTN coverage for (A) s1-ST11 and (B) s2-ST11 clusters in the ST11 genomes; and non-ST11 genomes. The presence of s1-ST11 or s2-ST11 cluster is shown by BLASTN coverage of 95% -100% whereas the absence of these clusters are shown in the BLASTN coverage 0% - 5%. The partial presence of these clusters is shown in between 5% to 95%. Fig. S12. Sequences similar to s1-ST11 among non-E. coli genomes. The top 20 hits of NCBI BLASTN to the nr-database excluding E. coli genomes for the s1-ST11 cluster. Fig. S13. Sequences similar to s2-ST11 among non-E. coli genomes. The top 20 hits of NCBI BLASTN to the nr-database excluding E. coli genomes for the s2-ST11 cluster. Fig. S14. Analyzing s1-ST11 with antiSMASH. antiSMASH result from analyzing s1-ST11. It is observed that the aryl polyene biosynthetic gene is observed in the cluster. Also, there are other additional biosynthetic genes as shown in the genes’ cluster. Fig. S15. Analyzing s2-ST11 with antiSMASH. antiSMASH result from analyzing s2-ST11. It is observed that the aryl polyene biosynthetic gene cluster is observed with 94% similarity. BGC0000836 is the biosynthetic cluster in the UPEC strain CFT073. Fig. S16. Histogram of the -log10 P-value generated with CoinFinder. Histogram of the -log10 P-value of the pairwise GF association generated from the CoinFinder output for the all pairwise comparisons. The figure on the right is the enlarged section of the distribution with the y-axis truncated at 106. The P-value 1 x 10-20 is selected as the ad hoc cut-off criterion for significant pairwise comparisons in this study. Fig. S17. Distribution of significantly associated GFs (associated GF cluster sizes). The distribution of number of associated GFs for each significant GF (P-value &lt;= 1 x 10-20). The number of associated GFs for each significant GF ranges from 1 to 607. Though there are overwhelmingly high number of GFs with fewer than 50 associated GFs, there are quite a substantial number of GFs with many associated GFs as well, especially those with more than 300 associated GFs.