Fig. 4: Diversity of tick-associated bacteria.

a, Phylogenetic tree of 582 rickettsial genomes obtained in this study and 149 rickettsial genomes deposited in the Reference Sequence Database. Different colours represent different groups of Rickettsia. TRG, transitional group; TG, typhus group; AG, ancestral group. The genomes assembled in this study are represented by solid dots. b,c, The phylogenetic tree of Anaplasma (b) and Ehrlichia (c), where the size of the dots indicates the number of samples. Red dots indicate a bootstrap value of 100. Reference genomes are represented by grey dots, genomes assembled in this study are marked with turquoise dots, and previously undescribed species identified in this study are annotated in orange. d, Orthologous genes among Ehrlichia, Rickettsia and Anaplasma. Red nodes on the phylogenetic tree indicate genomes assembled in this study. In the heat map, orange denotes the presence of orthologous genes in the genome. The numbers in parentheses indicate the count of orthologous genes. e, Distribution of endosymbionts across different tick species. The thickness of the chord represents the number of positive samples. Different colours represent different genera of ticks. f, Evolutionary relationships of Coxiella MAGs assembled in this study, showcasing the identity (colour) and coverage (size) of virulence and nutritional genes, along with genomic collinearity. The calculation method for coverage is the length of the consistent region divided by the full length of the reference gene. The species names are abbreviated as follows: CEAN, Coxiella endosymbiont of Amblyomma nuttalli; CEOA, Coxiella endosymbiont of Ornithodoros amblus; CERM, Coxiella endosymbiont of R. microplus. CLE-Hy, Coxiella-like endosymbiont of Haemaphysalis hystricis; CLE-Hf, Coxiella-like endosymbiont of Haemaphysalis flava.