Assessing genomic diversity and selection signatures of Rhipicephalus microplus in Shaanxi, China based on whole-genome sequences

Abstract Background Ticks play a crucial role in transmitting and carrying various disease-causing microorganisms, which poses a significant risk to public health and the growth of the animal farming industry. Research on the whole genome sequence of ticks is consistently progressing due to the ongoing advancement of high-throughput sequencing technologies. Methods This study performed whole-genome resequencing on Rhipicephalus microplus obtained from free-range cattle in Hanzhong City, Shaanxi Province. The newly obtained data was then combined with existing whole genome resequencing data of R. microplus from the NGDC database (project ID: PRJCA002242) for further analysis. The purpose of this analysis was to assess genomic diversity and selection signatures in the Shaanxi group. Results The study identified single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the Shaanxi group. The R. microplus from China has been classified into three main branches, and there were variations in nucleotide diversity among populations in different places. All populations exhibited a high level of heterozygosity. Additionally, the value of Tajima's D deviated significantly from zero. Upon examining the mitochondrial genetic diversity of the tick, the study observed subtle variations compared to the phylogenetic tree created using the entire autosomal genome. These differences may arise from variances in population structure and migration patterns between the paternal and maternal tick populations. Genes associated with pesticide resistance, metal ion transportation, and antioxidant activity were identified during the selection study of the Shaanxi group. Conclusions The data acquired from our research holds significance in comprehending the biology of ticks, enhancing our understanding of their disease transmission, and formulating efficient strategies for tick management.