Table 3. General features of the Escherichia coli and E. fergusonii genomes sequenced in this work with E. coli K-12 MG1655 as reference (plasmid features).

Plasmid features	E. coli strains					E. fergusonii ATCC
	55989	ED1a	S88	UMN026
Genome Size (bp)	72 482	119 594	133 853	122 301	33 809	55 150
G+C content (%)	46.1	49.2	49.3	50.5	42	48.5
Total Protein-coding genesa	100	150	144	149	49	54
Pseudogenesb (nb)	7	11	9	8	0	5
Protein coding densityc	75.6	86.2	87	79.4	87.5	88.7
Assigned functiond (%)	74	53	65	65.7	35.4	46.6
Orphans (%)	17	31.5	25.8	27.8	12.5	20.7
Hypothetical (%)	9	15.5	9.2	6.5	52.2	32.7
IS-like genes (nb)	18	14	14	15	0	4

^aThe number of protein-coding genes is given without the number of coding sequences annotated as artifactual genes (Supplementary Table 2A).

^bThe number of pseudogenes computed for each genome corresponds to the real number of genes that are pseudogenes: one pseudogene can be made of only one CDS (in this case the gene is partial compared to the wild type form in other E. coli strains) or of several CDSs (generally two or three CDSs corresponding to the different fragments of the wild type form in other E. coli strains). These lists of pseudogenes are available in Supplementary Table 1.

^cThe computed protein coding density takes into account the total length of protein genes excluding overlaps between genes, artifacts, and RNA genes.

^dProtein genes with assigned function include the total number of definitive and putative functional assignments.