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| Natura: | Artículo científico |
| Lingua: | en |
| Pubblicazione: |
Yi chuan = Hereditas
2025
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| Soggetti: | |
| Accesso online: | https://pubmed.ncbi.nlm.nih.gov/40962477/ |
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| _version_ | 1868266152104296449 |
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| author | Xu, Xue-Feng Jin, Xing-Kun Shi, Yan Zhao, Zhe |
| author_facet | Xu, Xue-Feng Jin, Xing-Kun Shi, Yan Zhao, Zhe Xu, Xue-Feng Jin, Xing-Kun Shi, Yan Zhao, Zhe |
| collection | PubMed - marine biology |
| contents | Comprehensive analysis of the composition and distribution of anti-phage defense systems in genomes. Xu, Xue-Feng Jin, Xing-Kun Shi, Yan Zhao, Zhe Vibrio Bacteriophages Genome, Bacterial Computational Biology Phylogeny The long-term co-evolution between bacteria and their viruses (bacteriophages) drives the diversification of anti-phage defense systems. As key members of marine ecosystems, species are known for their large and complex genomes. To investigate the composition and distribution of anti-phage defense systems in genomes, we collect 242 representative genomes from the GTDB and NCBI databases. Using bioinformatics tools (including Defense Finder), we analyze the anti-phage defense systems encoded by these genomes and identify a total of 108 distinct systems, including GAPS, dGTPase, RM systems, etc. We observe significant variation in defense capabilities among different strains: five strains encode more than 20 defense systems, highlighting their high defense potential, while over 30 strains encode five or fewer defense systems. Notably, we find no known defense systems in ''. Furthermore, we note that the diversity of defense systems varies among clades, with the Cholerae clade exhibiting the highest entropy in its defense systems. We conduct a detailed analysis of the composition, structure, and functional mechanisms of these defense systems. Although species exhibit a complex and diverse array of anti-phage defense systems, the specific functions of many remain unknown. Given the complexity of genomes, we suggest that numerous potential defense systems are yet to be discovered. This study provides a comprehensive overview of the genomic characteristics of defense systems, laying a foundation for future research into the interactions and evolutionary dynamics between and bacteriophages. |
| format | Artículo científico |
| id | pubmed_40962477 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Yi chuan = Hereditas |
| record_format | pubmed |
| spellingShingle | Comprehensive analysis of the composition and distribution of anti-phage defense systems in genomes. Xu, Xue-Feng Jin, Xing-Kun Shi, Yan Zhao, Zhe Vibrio Bacteriophages Genome, Bacterial Computational Biology Phylogeny Comprehensive analysis of the composition and distribution of anti-phage defense systems in genomes. Xu, Xue-Feng Jin, Xing-Kun Shi, Yan Zhao, Zhe Vibrio Bacteriophages Genome, Bacterial Computational Biology Phylogeny The long-term co-evolution between bacteria and their viruses (bacteriophages) drives the diversification of anti-phage defense systems. As key members of marine ecosystems, species are known for their large and complex genomes. To investigate the composition and distribution of anti-phage defense systems in genomes, we collect 242 representative genomes from the GTDB and NCBI databases. Using bioinformatics tools (including Defense Finder), we analyze the anti-phage defense systems encoded by these genomes and identify a total of 108 distinct systems, including GAPS, dGTPase, RM systems, etc. We observe significant variation in defense capabilities among different strains: five strains encode more than 20 defense systems, highlighting their high defense potential, while over 30 strains encode five or fewer defense systems. Notably, we find no known defense systems in ''. Furthermore, we note that the diversity of defense systems varies among clades, with the Cholerae clade exhibiting the highest entropy in its defense systems. We conduct a detailed analysis of the composition, structure, and functional mechanisms of these defense systems. Although species exhibit a complex and diverse array of anti-phage defense systems, the specific functions of many remain unknown. Given the complexity of genomes, we suggest that numerous potential defense systems are yet to be discovered. This study provides a comprehensive overview of the genomic characteristics of defense systems, laying a foundation for future research into the interactions and evolutionary dynamics between and bacteriophages. |
| title | Comprehensive analysis of the composition and distribution of anti-phage defense systems in genomes. |
| topic | Vibrio Bacteriophages Genome, Bacterial Computational Biology Phylogeny |
| url | https://pubmed.ncbi.nlm.nih.gov/40962477/ |