Fig. 3

Whole-genome phylogeny highlighting the position of Escherichia coli GM4792 relative to the other E. coli K-12 strains. Up to 10 October 2015, totally 279 genomes of Escherichia coli K-12 strains were released on NCBI. In order to analyze the phylogenetic relationship between GM4792 with other K-12 strains, we downloaded all the genomes of completely assembled and well-annotated K-12 strains. Totally, 44 Escherichia coli K-12 strains together with Escherichia albertii KF1 as outgroup were used to infer the whole-genome phylogeny using collinear genomic segments [53, 54] (Additional file 1: Table S6). The collinear regions were identified by Sibelia v3.0.6 [55], which can efficiently find LCBs among a large number of microbial genomes without alignment, and then collinear regions shared by all strains were concatenated as supermatrix. The Maximum-likelihood (ML) [56] tree was inferred from the data matrices with FastTree v2.1.8 [57]. Local SH-like support was assessed using Shimodaira-Hasegawa (SH) test with 1000 bootstrap replicates, and the support values are given as names for the internal nodes (values below 60 % have been hidden). Escherichia albertii KF1 was used as outgroup to root the tree