Extended Data Fig. 4: Genomic characteristics of tick-associated bacteria.

. (a) Number of MAGs in this study. Different colors represent different genera. Each bar represents a species, with an asterisk (*) indicating genomes not present in public databases. (b) Number of rickettsial genomes, categorized by Rickettsia groups. (c) Pathways enriched in genus-specific genes within Anaplasma, Ehrlichia, and Rickettsia, and their significance levels according to Kyoto Encyclopedia of Genes and Genomes (KEGG). (d) Clusters of Orthologous Groups (COG) annotations of genus-specific genes in Anaplasma, Ehrlichia, and Rickettsia, with different colors representing different genera. J: Translation, ribosomal structure and biogenesis; A: RNA processing and modification; K: Transcription; L: Replication, recombination and repair; B: Chromatin structure and dynamics; D: Cell cycle control, cell division, chromosome partitioning; Y: Nuclear structure; V: Defense mechanisms; T: Signal transduction mechanisms; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; Z: Cytoskeleton; W: Extracellular structures; U: Intracellular trafficking, secretion, and vesicular transport; O: Posttranslational modification, protein turnover, chaperones; C: Energy production and conversion; G: Carbohydrate transport and metabolism; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown. (e) Phylogenetic tree of Borrelia genomes. Reference genomes are represented by gray dots. (f) Distribution of pathogens across different tick species in this study. The thickness of the chord represents the number of positive samples. Different colors represent different genera of ticks and the tick species are arranged from left to right as follows: R. microplus, R. turanicus, R. pumilio, R. haemaphysaloides, R. sanguineus, I. persulcatus, I. pomerantzevi, I. ovatus, I. granulatus, I. acutitarsus, Hy. asiaticum, Hy. isaaci, Hae. montgomeryi, Hae. longicornis, Hae. concinna, Hae. japonica, Hae. qinghaiensis, Hae. hystricis, Hae. megaspinosa, Hae. tibetensis, Hae. yeni, Hae. kolonini, Hae. flava, D. silvarum, D. niveus, D. abaensis, D. nuttalli, D. reticulatus, D. everestianus, Ar. persicus, Am. javanense, Am. varanense, Am. geoemydae, Am. helvolum and Al. lahorensis. (g) Phylogenetic tree of Rickettsia primarily annotated as endosymbionts. Species names are abbreviated as follows: Rickettsia endosymbiont of Bemisia tabaci: REBT; Rickettsia endosymbiont of Diachasma alloeum: REDA; Rickettsia endosymbiont of Pyrocoelia pectoralis: REPP; Rickettsia endosymbiont of Culicoides newsteadi: RECN; Rickettsia endosymbiont of Oedothorax gibbosus: REOG; Rickettsia endosymbiont of Cardiosporidium cionae: RECC. (h) Pathogenic features of Rickettsia genomes. The size of the dots indicates coverage, while the shade of the color represents similarity. (I) Evolutionary relationships of Francisella MAGs assembled in this study, showcasing the identity (color) 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: Francisellaceae bacterium (FB), Francisella-like endosymbiont of Amblyomma geoemydae (FLE-Ag), Francisella endosymbiont of Amblyomma maculatum (FEAM), Francisella-like endosymbiont of Amblyomma testudinarium (FLE-At), Francisella endosymbiont of Ornithodoros moubata (FEOM), and Francisella-like endosymbiont of Hyalomma anatolicum (FLE-Ha).