The salivary gland transcriptome of tick Rhipicephalus microplus shaped by the genetic composition of host

The cattle tick Rhipicephalus microplus is a major livestock pest and disease vector in tropical and subtropical regions. Host species exhibit heritable variation in tick susceptibility, resulting in differences in tick burden. Building on our previous finding that R. microplus predominates on both Bos indicus and Bos frontalis across seasons and altitudes, with greater tick diversity in B. frontalis, this study examines host-parasite interactions between these bovine hosts. In Arunachal Pradesh, the semi-domesticated Bos frontalis and domesticated Bos indicus are significant bovine hosts with distinct ecological and management conditions. Bos frontalis is an endangered ruminant indigenous to the eastern Himalayas and plays a crucial role in local traditions. This study employed comparative transcriptomic and metatranscriptomic analyses of R. microplus feeding on these bovine hosts. RNA-Seq of tick salivary glands generated 90,895,164 and 76,273,524 reads from ticks feeding on B. indicus and B. frontalis, respectively, yielding 13,290 annotated coding sequences. Fold-change-based comparison identified 3375 candidate host-associated genes, suggesting host-associated variation in the salivary-gland transcriptome. Selected expression patterns were directionally corroborated using RT-qPCR. Metatranscriptomic screening of host-depleted reads, followed by BioBakery-based reanalysis and reference-mapping validation, supported the presence of selected microbial and viral signals in ticks feeding on these bovine hosts. However, because the study was based on a single pooled RNA-seq library per host group, the transcriptomic and metatranscriptomic findings should be interpreted as exploratory and serve as a basis for future comparative studies. This study provides the first report of the sialotranscriptome of R. microplus feeding on B. frontalis.