Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

Figure 4

Comparative genomic analysis of nine R. equi strains. (a) The nucleotide sequence of R. equi WY was used as a reference (backbone) and compared with those of eight query genomes. Counting from the outside toward the center: gray color (slot 1) indicated unique regions in R. equi WY, which were labeled R1-R7. Slots 2-10 showed that the corresponding query regions had higher sequence identity (>60%) with the reference sequence. Empty regions on the query slots indicated parts without similar hits between the reference sequence and the query sequences. Labels for slots 2-14 are shown in the legend. (b) Phylogenetic analysis (left) and comparison of genome structure (right) of nine R. equi strains. Phylogenetic reconstruction was based on concatenated SNPs of nine R. equi genomes rooted with R. defluvii. The identical sequence regions are connected by light green bars, while nonidentical regions are left empty. The different functional elements are labeled in different colors, with genomic islands in blue, complete prophage regions in red, and incomplete prophage regions in orange.

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