Prophage border curation reveals horizontal transfer of lysogeny-related elements between filamentous and double jelly-roll phages.
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| Autores principales: | , |
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| Formato: | Artículo científico |
| Lenguaje: | en |
| Publicado: |
Communications biology
2025
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| _version_ | 1868266111360827392 |
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| author | Ma, Ruijie Zhang, Rui |
| author_facet | Ma, Ruijie Zhang, Rui Ma, Ruijie Zhang, Rui |
| collection | PubMed - marine biology |
| contents | Prophage border curation reveals horizontal transfer of lysogeny-related elements between filamentous and double jelly-roll phages. Ma, Ruijie Zhang, Rui Prophages Lysogeny Gene Transfer, Horizontal Vibrio Inovirus Genome, Viral Phylogeny Bacteriophages 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. |
| format | Artículo científico |
| id | pubmed_41413665 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Communications biology |
| record_format | pubmed |
| spellingShingle | Prophage border curation reveals horizontal transfer of lysogeny-related elements between filamentous and double jelly-roll phages. Ma, Ruijie Zhang, Rui Prophages Lysogeny Gene Transfer, Horizontal Vibrio Inovirus Genome, Viral Phylogeny Bacteriophages Prophage border curation reveals horizontal transfer of lysogeny-related elements between filamentous and double jelly-roll phages. Ma, Ruijie Zhang, Rui Prophages Lysogeny Gene Transfer, Horizontal Vibrio Inovirus Genome, Viral Phylogeny Bacteriophages 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. |
| title | Prophage border curation reveals horizontal transfer of lysogeny-related elements between filamentous and double jelly-roll phages. |
| topic | Prophages Lysogeny Gene Transfer, Horizontal Vibrio Inovirus Genome, Viral Phylogeny Bacteriophages |
| url | https://pubmed.ncbi.nlm.nih.gov/41413665/ |