SyMAP Synteny Browser
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Enterobacteria

We aligned the sequences of model strains from four species of enterobacteria: Escherichia coli (strain K-12 MG1655) [1], Yersinia pestis (strain KIM) [2], Shigella dysenteriae (strain Sd197) [5], and Salmonella typhimurium (strain LT2) [6].

Enterobacteria are primarily known for their ability to cause intestinal upset and are responsible for a variety of human illnesses, including urinary tract infections, wound infections, gastroenteritis, meningitis, septicemia, and pneumonia. E. coli is one of the best studied prokaryotic model organisms.

Divergence of E. coli and S. typhimurium is estimated at 100 million years ago [3].

Strains of Shigella have arisen through multiple independent origins from within E. coli [4]. Shigella is very closely related to E. coli because the degree of homology in their chomosomal DNA is close to 100%. Consdering Shigella as a member of the genus Escherichia is regarded as justifiable [8].

E. coli and Salmonella diverged 120 to 160 million years ago which coincides with the origin of mammals [7].

E. coli and Y. pestis diverged 375 to 500 million years ago [2].

Synteny Tools

Instructions:
Select one or more species of interest from the left and then click a tool button on the right.
The first three tools, 3D View, Gene Search, and Dot Plot can be used with any number of selected species.
The remaining tools are only be available when one (self-alignment) or two species are selected.

Species

    E. coli
    S. dysenteriae
    S. typhimurium
    Y. pestis

   Select All    Select None

Tools
   
Open a three-dimensional display of synteny block alignments.
   
Search gene annotations by keyword.
   
Open a dot plot display showing individual hits and syteny block alignments.
   
Open a linear display of synteny block alignments.
   
Open a circular display of synteny block alignments.
   
Display summary information.

Important:
SyMAP requires the Java Runtime Environment (JRE) version 5 or later.
Click here to check your Java installation and upgrade if necessary.

References
  1. Blattner, F., et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277(5331):1453-62.
  2. Deng., W., et al. 2002. Genome Sequence of Yersinia pestis KIM. Journal of Bacteriology 184(16): 4601-4611.
  3. Eyre-Walker, A., M. Bulmer. 1995. Synonymous Substitution Rates in Enterobacteria. Genetics Vol 140, 1407-1412.
  4. Francino, M., S. Santos, H. Ochman. 2006. Phylogenetic Relationships of Bacteria with Special Reference to Endosymbionts and Enteric Species. Prokaryotes 6:41-59.
  5. Germani, Y., P. Sansonetti. 2006. The Genus Shigella. Prokaryotes 6:99-122.
  6. McClelland, M., et al. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413(6858):852-6.
  7. Welch, R. 2006. The Genus Escherichia. Prokaryotes 6:60-71.
  8. Yang, F., et al. 2005. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res 33(19):6445-58.
  9. Escherichia coli source: GenBank
  10. Salmonella typhimurium source: GenBank
  11. Shigella dysenteriae source: GenBank
  12. Yersinia pestis source: GenBank