Genomic Insights into Vector–Pathogen Adaptation in Haemaphysalis longicornis and Rhipicephalus microplus

As crucial vectors that transmit pathogens to humans and livestock, ticks pose substantial global health threats and economic burdens. We analyzed 328 tick genomes to explore the population's genetic structure and the adaptive evolution of <i>H. longicornis</i> and <i>R. microplus,</i> two tick species with distinct life cycle characteristics. We observed distinct genetic structures in <i>H. longicornis</i> and <i>R. microplus</i>. Gene flow estimation revealed a closer genetic connection in <i>R. microplus</i> than <i>H. longicornis</i>, which was facilitated by geographical proximity. Notably, we identified a set of candidate genes associated with possible adaptations. Specifically, the immune-related gene <i>DUOX</i> and the iron transport gene <i>ACO1</i> showed significant signals of natural selection in <i>R. microplus</i>. Similarly, <i>H. longicornis</i> exhibited selection in pyridoxal-phosphate-dependent enzyme genes associated with heme synthesis. Moreover, we observed significant correlations between the abundance of pathogens, such as <i>Rickettsia</i> and <i>Francisella,</i> and specific tick genotypes, which highlights the role of <i>R. microplus</i> in maintaining these pathogens and its adaptations that influence immune responses and iron metabolism, suggesting potential coevolution between vectors and pathogens. Our study highlights the vital genes involved in tick blood feeding and immunity, and it provides insights into the coevolution of ticks and tick-borne pathogens.