All CitERV sequence

For endogenous reverse-transcribing viruses in plant genomes, their evolutionary dynamics and functional roles have long been characterized as neutral genetic fossils, limiting their potential in host adaptation. In this study, we aimed to decode the diversity, transmission pattern, and immunological significance of CitERVs across major citrus taxa. Here, we integrated comparative genomics and phylogenetic reconciliation across 31 citrus genomes to decode the CitERVs. We identified 15,016 intact CitERVs, dominated by Caulimovirses (2,125), Metaviruses (7,400), and Pseudoviruses (5,491), with a novel lineage Citdovirus discovered. Critically, 9 potentially active CitERVs were identified. Evolutionary event analysis revealed CitERV primarily spreads through host switching with occasional co-speciation, and integration chronologies precisely mirrored host speciation events. Physical embedding in immune genes drove adaptive evolution (5/10 genes under positive selection). Interactome analysis demonstrated functional coupling: an RLK gene overlapping Metaviruses pol interacted with ubiquitin-like proteases and EF-Tu (Xanthomonas effector). An NLR gene embedded in Pseudoviruses gag-pol bound AvrRpt2-like pathogen scissors. More importantly, transcriptome data analysis indicate that the NLR gene is overexpressed in HLB-infected leaves. Collectively, CitERVs emerge as endogenous immune tuners, offering molecular chronometers for citrus evolution and virus-editing strategies for durable resistance.