Alignments of the R. massiliae tra region with the corresponding regions in four Rickettsia species. Genomic coordinates are indicated on both sides of the segments. Blue and red rectangles represent the ORFs inside and outside of the R. massiliae tra cluster, respectively. Green rectangles show predicted ORFs in the compared species. Genomic segments are connected by gray shading when significant nucleotide similarity is detected using BLASTN (E-value < 1 × 10⁻⁵).

Horizontal transfer of the tra cluster region. (A) K_s values estimated between R. massiliae and R. bellii reciprocal best-match genes. (B) Horizontal transfer index (HTI) and horizontal transfer donor index (HTDI) of the R. massiliae genes (red and blue symbols, respectively). (C) HTI and HTDI of the R. bellii genes. Gene pairs are ordered on the X-axis according to the R. massiliae (A and B) or R. bellii (C) gene orders. Solid circles show the data for genes of the tra region. Curves represent moving medians calculated from 20-gene sliding windows. The color of the curve is the same as that of the data points that were used for the calculations (i.e., K_s, HTI, HTDI).

Dot-plot comparison of the R. massiliae and R. conorii genomes. Red and green dots represent forward and reverse BLASTN matches, respectively (E-value value < 1 × 10⁻⁵). Position of the tra cluster is indicated in gray.

Phylogenetic relationships of the tra cluster genes. (A–M) Phylogenetic trees are constructed from protein sequences using the maximum-likelihood method. Models of substitution that best fit the data are as follows: JTT for D and M; JTT + Γ for C, E, and J; JTT + I for K; WAG + Γ for G; WAG + Γ + I for A; CpREV for B, F, and L; CpREV + Γ for I; RtREV for H. The Rickettsia species tree (A) is constructed from the concatenated alignment of 38 ribosomal proteins (6209 sites). Gene names and branch length scales (number of substitution per site) are shown below trees. Bootstrap support values, calculated over 500 alignment replicates, are given beside branches. Consecutive ORFs of pseudogenes (Table 1) were concatenated for the analysis. In addition to the Rickettsia sequences, the O. tsutsugamushi best BLASTP hit was included in the phylogenetic reconstructions when available (E-value < 1 × 10⁻¹⁰).