plosone-phylo
Figure 1
Polymorphisms of the adaA genetic region demonstrated using seven C. burnetii reference genomes.Three deletion events resulting in two main deletion types (Q154 and Q212) and three adaA gene variants (adaA, adaASNP and adaArep) resulting from independent mutation processes were identified in silico. The organization of the adaA flanking region of the Dugway genome (displayed in the center) is compared to the other six reference genomes. Just for the purpose of visual compactness, the light orange region was pruned between the ORFs CBUD_1100 and CBUD_1122. Gene annotations are obtained from GenBank. Coding genes are drawn in blue, pseudogenes in white and the adaA gene in red. Arrow direction represents the location of the ORFs at the forward and backward strand. Locus tags are shortened by its common prefix and written above the ORFs. If gene names are known, they are written next to their locus tag and in parentheses. Long collinear blocks (LCBs) are shown as colored rectangles at the backbone of the Dugway genome. The pairwise syntenic regions between the genomes are drawn in lighter color, accordingly. The phylogenetic relationship is shown at the left side. Just for visualization purposes, the Dugway genome was rotated to the middle. The length of the branches encodes the number of mutation events. Three different deletions were identified and its affected LCBs are drawn to the phylogenetic branch where the deletion events may have occurred. Dugway and RSA331 were chosen as representative strains to show the intact adaA gene and adaASNP gene, respectively. A fragment of strain F10 is exposed in the figure to show the inserted repeat variant (adaArep). The figure was drawn using genoPlotR [37]. *Q321 replaces RSA334, which was accidently assigned to the published whole genome data.
Figure 1
Polymorphisms of the adaA genetic region demonstrated using seven C. burnetii reference genomes.Three deletion events resulting in two main deletion types (Q154 and Q212) and three adaA gene variants (adaA, adaASNP and adaArep) resulting from independent mutation processes were identified in silico. The organization of the adaA flanking region of the Dugway genome (displayed in the center) is compared to the other six reference genomes. Just for the purpose of visual compactness, the light orange region was pruned between the ORFs CBUD_1100 and CBUD_1122. Gene annotations are obtained from GenBank. Coding genes are drawn in blue, pseudogenes in white and the adaA gene in red. Arrow direction represents the location of the ORFs at the forward and backward strand. Locus tags are shortened by its common prefix and written above the ORFs. If gene names are known, they are written next to their locus tag and in parentheses. Long collinear blocks (LCBs) are shown as colored rectangles at the backbone of the Dugway genome. The pairwise syntenic regions between the genomes are drawn in lighter color, accordingly. The phylogenetic relationship is shown at the left side. Just for visualization purposes, the Dugway genome was rotated to the middle. The length of the branches encodes the number of mutation events. Three different deletions were identified and its affected LCBs are drawn to the phylogenetic branch where the deletion events may have occurred. Dugway and RSA331 were chosen as representative strains to show the intact adaA gene and adaASNP gene, respectively. A fragment of strain F10 is exposed in the figure to show the inserted repeat variant (adaArep). The figure was drawn using genoPlotR [37]. *Q321 replaces RSA334, which was accidently assigned to the published whole genome data.