Whole-genome resequencing-based assessment of genomic diversity and selection signatures in Rhipicephalus microplus from Shaanxi, China

Ticks are critical vectors of numerous disease-causing microorganisms, posing significant risks to public health and the livestock industry. Research on the whole-genome sequence of ticks should continue to progress consistently, given the ongoing advancement of high-throughput sequencing technologies. In this study, we performed whole-genome resequencing of Rhipicephalus microplus (R. microplus) collected from free-range cattle in Hanzhong City, Shaanxi Province, China. The newly generated data were combined with the existing whole-genome resequencing data of R. microplus from the National Genomics Data Center database (project ID: PRJCA002242) for further analysis. The purpose of this analysis was to assess genomic diversity and selection signatures in the Shaanxi group. The study identified single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the Shaanxi group. R. microplus samples from China were classified into three main branches, with variations in nucleotide diversity observed among populations from different regions. Upon examining the mitochondrial genetic diversity of ticks, subtle variations were observed compared to the phylogenetic tree created using the entire autosomal genome. These differences likely result from variations in the population structure and migration patterns between the paternal and maternal lineages of the tick populations. Additionally, genes associated with pesticide resistance, metal ion transport, and antioxidant activity have been identified in the Shaanxi group. These findings provide valuable insights into tick biology, enhance our understanding of their role in disease transmission, and inform the development of effective tick control strategies.