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Fig. 4 | BMC Microbiology

Fig. 4

From: Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid

Fig. 4

Heatmap showing conservation of AB2/73 genes across Rhizobium/Agrobacterium genomes. The proteins of 125 Rhizobium and Agrobacterium species including AB2/73 were clustered with OrthoFinder as described in the Methods section. The presence of homologs of the AB2/73 proteins in other genomes is shown for the three largest replicons: the primary chromosome, pAtAB2/73f and pAtAB2/73e. Each row represents an orthogroup (gene) and each column a genome. The columns are ordered by the leaves of the concatenated protein-alignments-based species tree (Fig. S2). The heatmap is vertically split up into five sections based on the structure of the species tree shown at the top and the segments in the color bar indicate a further division of the tree into smaller subclades of related species/strains. The color bar colors are also used in the species tree to show these same clades. The heatmaps consist of small blocks of which the colors represent the relative size-rank of the replicon the gene is located on, as shown in the legend, where 1 represents the largest replicon. Thus, genes present only on the primary chromosome (always the largest replicon), are shown as a small black box, genes present on the semi-largest replicon (in A. tumefaciens and A. fabrum e.g. the linear chromosome) are shown in blue etc. The numbers of replicons per genome and their size is shown in Fig. S6. NB, multiple homologous genes of the same genome may be assigned to the same orthogroup. These genes are either categorized as replicon x + other (s), or “multiple”. For example, in the heatmaps primary chromosome section, genes present both on the primary chromosome and on another replicon are shown in grey, while genes present on multiple replicons but not on the primary chromosome are shown in brown

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