We report the first complete genome sequence of cucumber mosaic virus (CMV) and its associated satellite RNA (satRNA) from naturally infected zucchini (Cucurbita pepo) in Iraq. The tripartite CMV-Iq genome (RNA1: 3,358 nt, RNA2: 3,051 nt, RNA3: 2,220 nt) and a 335-nt satRNA were determined by RNA-seq and validated via Sanger sequencing. Genome annotation revealed ORFs encoding replicase (1a), RNA-dependent RNA polymerase (2a), silencing suppressor (2b), movement protein (3a), and coat protein (3b) with conserved domains. Phylogenetic analysis placed CMV-Iq in subgroup I, forming a distinct clade closely related to isolates from East Asia, Europe, the USA and the Middle East, with reassortment detected in RNA2 and RNA3. Viral coding regions showed high haplotype and nucleotide diversity under differential selective pressures, with purifying selection strongest in 1a and weakest in 2b, and episodic positive selection detected at a few sites. Mutations, selection, gene flow, and reassortment shape the genetic structure of CMV populations. The Iraqi satRNA clustered within the necrogenic B subgroup, forming a distinct sublineage with Syrian isolates and retaining the conserved necrogenic motif. Transcriptomic profiling revealed RNA3 as the most abundant segment, followed by RNA2 and RNA1, with satRNA surpassing RNA1 and RNA2 in abundance. At the gene level, 3b and 2a were most expressed, 3a and 1a intermediate, and 2b lowest, consistent with its regulatory function. High 3b expression reflects translation from subgenomic RNA4, enabling coat protein synthesis for virion assembly and systemic movement, while abundant satRNA suggests a modulatory role in viral replication and host interactions.

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