Genomic characterization of four Escherichia coli strains isolated from oral lichen planus biopsies

Figures & data

Table 1. Sequencing and assembly statistics of the four oral lichen planus (OLP)-isolated Escherichia coli strains

Strain	No. of libraries	No. of reads	Library size (Gbp)	Coverage	No. of contigs	N50 (bp)	SRA accession
5.1	2	4837,727	1.92	195x	126	105,630	SRR12284169
7.1	2	4,366,233	1.57	168x	131	105,630	SRR12284168
7.2	2	4,229,137	1.52	166x	134	95,009	SRR12284167
7.3	2	4,640,289	1.70	172x	123	94,980	SRR12284166

Table 2. Genomic characteristics of four oral lichen planus (OLP)-isolated Escherichia coli strains in comparison with other strains

Species and strain	Source of isolation	Pathotype	Assembly accession	Genome Status	No. of contigs	N50 (bp)	Genome size (bp)	G + C content (%)	No. of CDSs	Mean of CDS lengths (bp)	Mean intergenic lengths (bp)
Escherichia coli 5.1	OLP	Pathobiont?	GCA_013693985.1	Draft	126	105,630	4,688,958	50.7	4,361	940.0	148.0
Escherichia coli 7.1	OLP		GCA_013693995.1	Draft	131	105,630	4,687,682	50.7	4,364	939.7	147.0
Escherichia coli 7.2	OLP		GCA_013694005.1	Draft	134	95,009	4,685,982	50.7	4,360	940.1	147.0
Escherichia coli 7.3	OLP		GCA_013694015.1	Draft	123	94,980	4,685,872	50.7	4,367	939.8	146.0
Escherichia coli K-12 MG1655	Feces	Commensal	GCA_000005845.2	Complete	1	-	4,641,652	50.8	4,319	932.4	131.3
Escherichia coli Nissle 1917	Feces	Commensal	GCA_000714595.1	Complete	1	-	5,441,200	50.6	5,105	923.8	148.2
Shigella flexneri 2457 T	Feces	Enteropathogenic	GCA_000007405.1	Complete	1	-	4,599,354	50.9	4,718	844.9	140.7
Escherichia coli ATCC:BAA-460	Feces	EHEC	GCA_000008865.1	Complete	3	-	5,594,477	50.5	5,386	909.5	142.2
Escherichia coli CFT073	Blood	UPEC	GCA_000007445.1	Complete	1	-	5,231,428	50.5	4,900	934.7	144.7
Escherichia coli JJ2434	Unknown	UPEC	GCA_001513635.1	Complete	3	-	5,317,099	50.8	5,056	924.8	138.9

EHEC: Enterohemorrhagic E. coli; UPEC: Uropathogenic E. coli

Figure 1. Distribution of annotated genes in four oral lichen planus (OLP)-isolated Escherichia coli strains. (a) Distribution based on the Clusters of Orthologous Groups of proteins (COG) functional categories, (b) A Venn diagram showing the distribution of shared and unique pangenome orthologous groups (POGs) among the OLP-isolated strains

Figure 2. Venn diagrams of shared and unique pangenome orthologous groups (POGs)

Figure 3. Kanamycin resistance test. Kanamycin resistance of the four OLP-isolated and two commensal strains was determined by the measurements of growth rates in the presence of various concentrations of kanamycin