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<p>While tailed bacteriophages dominate contemporary models of phage biology, non-tailed phages—particularly filamentous inoviruses and double jelly-roll (DJR) capsid phages—remain poorly understood, despite their environmental ubiquity and ecological importance. Here, we identify 515 inoviruses and 258 DJR prophages from 688 <i>Vibrio</i> spp. genomes and precisely annotate prophage–bacterium junctions. This curated dataset enables us to systematically classify genomic variations and characterize lysogeny-related elements for each prophage subtype. We discover a conserved lysogeny module shared by specific inoviral and DJR subtypes, which represents an evolutionary strategy where phylogenetically distinct phages use horizontal gene transfer to co-opt host mechanisms for integration. Comparative genomics reveal that phage-encoded hypervariable regions (pHVRs) are hotspots for weaponized genetic innovation, such as anti-phage systems and virulence factors. The significantly higher prevalence of pHVR-encoding prophages compared to their pHVR-deficient counterparts across <i>Vibrio</i> species indicates that acquiring these adaptive genes promotes prophage persistence through mutualistic fitness benefits. Because these non-tailed elements frequently form tandem arrays and existing tools struggle with their accurate characterization, we establish a refined methodology to enhance predictive accuracy.</p>

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Prophage border curation reveals horizontal transfer of lysogeny-related elements between filamentous and double jelly-roll phages

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月18日

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  • Ruijie Ma,
  • Rui Zhang

摘要

While tailed bacteriophages dominate contemporary models of phage biology, non-tailed phages—particularly filamentous inoviruses and double jelly-roll (DJR) capsid phages—remain poorly understood, despite their environmental ubiquity and ecological importance. Here, we identify 515 inoviruses and 258 DJR prophages from 688 Vibrio spp. genomes and precisely annotate prophage–bacterium junctions. This curated dataset enables us to systematically classify genomic variations and characterize lysogeny-related elements for each prophage subtype. We discover a conserved lysogeny module shared by specific inoviral and DJR subtypes, which represents an evolutionary strategy where phylogenetically distinct phages use horizontal gene transfer to co-opt host mechanisms for integration. Comparative genomics reveal that phage-encoded hypervariable regions (pHVRs) are hotspots for weaponized genetic innovation, such as anti-phage systems and virulence factors. The significantly higher prevalence of pHVR-encoding prophages compared to their pHVR-deficient counterparts across Vibrio species indicates that acquiring these adaptive genes promotes prophage persistence through mutualistic fitness benefits. Because these non-tailed elements frequently form tandem arrays and existing tools struggle with their accurate characterization, we establish a refined methodology to enhance predictive accuracy.