Figure 1.
Phylogenetic tree of E. coli/Shigella strains and the number of decayed genes.
The maximum likelihood tree was constructed by using the concatenated nucleotide sequences of 2500 orthologs conserved in all strains. K12 was used as the reference for identifying pseudogenes in the other strains; EFER was used as the outgroup for constructing the phylogenetic tree.
Table 1.
Differential functional assignment between decayed genes and intact genes.
Figure 2.
Correlation between number of decayed genes and percentage of decayed genes in operon.
The dot “combined” represents all decayed genes in the five Shigella strains and the corresponding percentage of decayed genes in operon.
Figure 3.
Comparison of Ka/Ks between different gene groups in SDY.
The Ka/Ks was adjusted following Methods. Group P, Pseudogenes; Group I, the Intact genes in the decayed-operons; Group R, the Rest functional genes in the genome.
Figure 4.
Comparison of CAI between genes in decayed operon and the rest genes in the genome.