Abstract
<title>Abstract</title> <p>Feline morbillivirus (FeMV) is a globally distributed morbillivirus of domestic cats, but the evolutionary organization of synonymous sites across its coding genome remains poorly resolved. We analysed 27 exact-deduplicated complete six-gene coding complements (162 principal coding sequences) using gene-resolved codon, 16-dinucleotide, reading-frame, and domestic-cat-relative metrics. FeMV genes occupied distinct synonymous-codon environments, and CpG was depleted in every coding sequence. To separate codon choice from codon order, each coding sequence was randomized 1,999 times while preserving its amino-acid sequence and exact synonymous-codon inventory. After correction, 158 of 162 observed sequences retained fewer CpGs across codon junctions than expected; the signal persisted in GT1-only and two near-identity-reduced datasets. TpA did not show the same corrected sequence-level pattern. Host-reference indices identified P as relatively closest and F as most discordant to domestic-cat coding preferences, but these measures describe correspondence rather than direct translational adaptation. Together, the results support a multiscale evolutionary model in which inherited morbillivirus composition, gene-specific RNA constraints, synonymous-codon neighbourhoods, and possible host-associated pressures jointly shape FeMV coding architecture. Ordered CpG suppression may provide a compositional route to reduce exposure to vertebrate innate RNA recognition, including ZAP-associated restriction, but this immune-evasion hypothesis requires direct testing in feline cells.</p>