TABLE 1.

Some examples of differences in genome content among closely related strains

Group and species% VGaCommentReference(s)
Completely sequenced genomes
    Chlamydia trachomatis<12 sequenced genomes; orthologs show ∼90% identity46
    Escherichia coli12-262 sequenced genomes; orthologs show 98.4% identity20, 45
    Helicobacter pylori6-72 sequenced genomes; orthologs show 92.6% DNA identity2
    Salmonella enterica10-125 sequenced strains; orthologs show 99.5-97.6% DNA identity11
    Group A Streptococcus6-92 sequenced strains; orthologs show 80-100% DNA identity51
Microarry hybridization
    Campylobacter jejuni0.5-711 strains; total of 21% variable genes in reference genome10
    Escherichia coli1-105 strains41
    Helicobacter pylori6-1815 strains; total of 22% variable genes in reference genome49
    Mycobacterium tuberculosis0-0.716 strains, of which 13 were isolated from patients in San Francisco; total of 1.7% variable genes in reference genome28
    Salmonella enterica8-173 strains37
    Staphylococcus aureus1-1236 strains; total of 22% variable genes in reference genome16
    Streptococcus pneumoniae3-1120 strains; all strains except one differ by 8-11%; total of 24% variable genes in reference genome19
Genomic subtraction
    Escherichia coli8E. coli K-12 strain used as driver against avian pathogenic strain; subtracted DNA hybridized to a cosmid library7
    Listeria monocytogenes5-6Prototype virulent strain genome subtracted from prototype epidemic strain21
    Salmonella enterica2-20Genomic DNA from LT2 was subtracted against 4 different strains and hybridized to a cosmid library32
    Salmonella enterica serovar     Typhimurium3Genomic subtraction using S. enterica serovar Typhi as driver; S. enterica serovar Typhimurium estimated to contain 140 kb not found in S. enterica serovar Typhi13
  • a % VG refers to the percentage of variable genes (i.e., genes missing from one of the sampled genomes).