Baumannia and <i>Sulcia</i> Coinhabit the Bacteriomes of the Host Insects

<p>Fluorescent in situ hybridizations were performed using oligonucleotide probes designed to hybridize selectively to the ribosomal RNA of <i>Baumannia</i> (green) and of <i>Sulcia</i> (red), respectively. Bacteriomes were obtained from Homalodisca literata (a very close relative of H. coagulata). </p

Predicted Metabolic Pathways in <i>Baumannia</i> and the Predicted Amino Acid Biosynthesis Pathways Encoded by the Partial Genome Sequence of <i>Sulcia</i>

<p>Genes that are present are in red and the corresponding catalytic pathways are illustrated in solid black lines; the genes that are absent in the <i>Baumannia</i> genome and genes that have not been identified in the partial <i>Sulcia</i> genome are in gray, and the corresponding metabolic steps are illustrated in gray lines. </p

The Distribution into Functional Role Categories of the 166 Predicted Genes Encoded in the 146,384-bp Partial Sequence of the <i>Sulcia</i> Genome

<p>Data are shown for all ORFs that encode proteins longer than 45 amino acids that have BLASTP matches with an E-value less than 10⁻³ to proteins in complete genomes. Different fragments of the same gene are counted as one gene in the chart. </p

Circular View of the <i>Baumannia</i> Genome

<p>Circles correspond to the following features, starting with the outermost circle: (1) forward strand genes, (2) reverse strand genes, (3) χ² deviation of local nucleotide composition from the genome average, (4) GC skew, (5) tRNAs (green lines), (6) rRNAs (blue lines); and (7) small RNAs (red lines). Color legend for CDSs and number of genes in each category are at the bottom. </p

Correlation between Genomic G + C Content and the Average pI of the Proteins of Endosymbiotic and Free-Living <i>Gammaproteobacteria</i>

<p>Species shown are Buchnera aphidicola APS (Ba_APS), Buchnera aphidicola BP (Ba_Bp), Buchnera aphidicola SG (Ba_Sg), <i>Baumannia</i> (Bc), Blochmannia floridanus (Bf), Blochmannia pennsylvanicus (Bp), E. coli K12 (Ec), Wigglesworthia glossindia (Wg), and Yersinia pestis KIM (Yp). </p

Genome-Based Phylogenetic Analysis of <i>Baumannia</i>

<div><p>(A) Maximum-likelihood tree of gamma-proteobacterial endosymbionts. The tree was built from concatenated alignments of 45 ribosomal proteins using the PHYML program. The bootstrap value is based upon 1,000 replications.</p> <p>(B) Gene order comparison of <i>Baumannia</i> and Blochmannia floridanus. The plot shows the locations of homologous proteins between the two genomes. </p></div

Maximum-Likelihood Tree of <i>Sulcia</i> with Species in the <i>Bacteroides and Chlorobi</i> Phyla for which Complete Genomes Are Available

<p>The tree was build using the PHYML program from the concatenated alignments of 34 ribosomal proteins. The bootstrap values are based upon 1,000 replications.</p

Maximum Likelihood Bootstrap Majority-Rule Consensus Tree for 16S rRNA Gene Sequences from 19 Strains Phylogenetically Related to A. aurescens TC1

<p>Numbers adjacent to branch points are bootstrap percentages (<i>n</i> = 100 replicates). The bar represents 10% sequence divergence.</p

Comparative Linear Display Representing the Sequence Homologies between the A. aurescens pTC1 Plasmid, the Pseudomonas sp. pADP-1 Plasmid, and the A. nicotinivorans pAO1 Plasmid

<p>Only selected regions for each of the three plasmids are shown. The percent of protein identity is indicated by the color of the connecting lines (legend on the bottom left side of the figure). For clarity, the locus tags (AAur_pTC1 for the pTC1 plasmid, AAK for the pADP-1 plasmid, and CAD for the pAO1 plasmid) were removed from the ORF numbers.</p

Circular Representations of the pTC1 and pTC2 Plasmids of A. aurescens TC1, and Comparative Linear Displays of Some of the Plasmid Regions Shared with the Strain TC1 Chromosome

<div><p>(A and B) Each concentric circle of the circular figures is numbered from the outermost circle to the innermost circle. For each plasmid, the first and second circles represent the predicted coding sequences on the plus and minus strands, respectively, colored by functional role categories (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020214#pgen-0020214-g001" target="_blank">Figure 1</a>). The third circle displays the G + C skew: positive G + C skew in magenta and negative G + C skew in green. The fourth circle displays the repeated sequences of at least 50 bp long (at least 97% identity between two repeats); each color/tick size represents a different repeat. Prophage (blue ticks) and transposon (dark green ticks) genes are displayed on the fifth circle. The sixth circle shows the regions of atypical composition (χ² analysis).</p><p>(C–I) Comparative linear displays of some of the pTC1 and pTC2 sequences matching the TC1 chromosome. The percent of protein identity is indicated by the color of the connecting lines (legend on the right side of the figure). For clarity, the locus tags (AAur_ for the chromosome, and AAur_pTC1 and AAur_pTC2 for the pTC1 and pTC2 plasmids, respectively) were removed from the ORF numbers. For example, the chromosomal ORF number 2549 is AAur_2549, the pTC1 ORF number 0246 is AAur_pTC10246, and the pTC2 ORF number 0054 is AAur_pTC20054.</p></div