Mapping Structural Variations in Haemaphysalis longicornis and  Rhipicephalus microplus Reveals Vector–Pathogen Adaptation

Abstract

As the most common vector only second to mosquitoes, ticks pose an increasing threat to public health and cause economic losses in livestock production. However, the genomic variations of ticks remain largely unknown. Here, we conducted the first whole-genome-sequencing–based analysis of structural variation (SV) to understand the biology and evolution of ticks. We identified 8,370 and 11,537 SVs in 156 Haemaphysalis longicornis and 138 Rhipicephalus microplus, respectively. Different from the close relationship of Hae. longicornis, R. microplus can be clustered into three distinct geographic populations (central, south, and southwest China). Notably, the samples from central and southwest China showed a higher SV burden than those from south China, and there was a positive correlation between the SV burden and latitudes. In particular, a 5.2-kb deletion at the coding region of the cathepsin D gene is highly differentiated between the central/southwest China and south China groups. This gene showed significantly higher gene expression in fully engorged female ticks than in partially engorged ticks, suggesting its contribution to hemoglobin degradation and immune response in R. microplus. In Hae. longicornis, a 4.1-kb duplication in the coding region of the CyPJ gene differentiated between the domestic and overseas groups. Notably, the CyPJ gene was slightly downregulated in pathogen-infected ticks, consistent with its negative regulation of the NF-kB signals and a possible role in vector–pathogen adaptation. We provided a whole-genome SV map of tick species and identified SVs associated with the development and evolution of tick species, which could be candidates for the prevention and control of ticks.

Keywords: Hae. longicornis, R. microplus, Structural variation, Blood digestion, Vector-pathogen adaptation