Abstract
<title>Abstract</title> <p>Jingmen tick virus (JMTV) is a segmented positive-sense RNA virus repeatedly detected in ticks, yet the evolutionary organization of its synonymous coding sequence remains poorly understood. We curated 38 natural tick-derived complete genome sets and compared all five canonical coding regions using codon-use metrics, protein divergence and an exact-codon conditional randomization. The randomization retained every amino-acid position and the complete synonymous-codon inventory while changing only codon order. CpG boundary counts were consistently below conditional expectation across the coding repertoire, whereas UpA depletion was also widespread but more gene dependent. Codon usage and boundary ordering differed among proteins, indicating that the four genome segments do not evolve as a compositionally uniform unit. VP3 was the most divergent protein, and its high-variability window showed a possible local change in CpG ordering, although this regional result weakened under stringent identity reduction. Together, the findings support a layered model in which segment history, protein function and RNA-level sequence organization jointly shape JMTV evolution. The shared boundary pattern may represent evolutionary accommodation compatible with circulation through tick- and vertebrate-associated cellular environments and provides testable hypotheses for future vector and functional studies.</p>