弧菌基因组中抗噬菌体防御系统的构成与分布特征分析
收稿日期: 2024-12-02
修回日期: 2025-03-07
网络出版日期: 2025-03-07
基金资助
国家自然科学基金项目(31872597);国家自然科学基金项目(42376119);江苏省农业科技自主创新资金(CX[23]1007)
Comprehensive analysis of the composition and distribution of anti-phage defense systems in Vibrio genomes
Received date: 2024-12-02
Revised date: 2025-03-07
Online published: 2025-03-07
Supported by
National Natural Science Foundation of China(31872597);National Natural Science Foundation of China(42376119);Jiangsu Agricultural Science and Technology Independent Innovation Fund(CX[23]1007)
细菌与其病毒(噬菌体)的长期共同演化推动了抗噬菌体防御系统的多样化发展。弧菌属细菌作为海洋生态系统的重要成员，具有庞大且复杂的基因组。为揭示弧菌属成员基因组中抗噬菌体防御系统的构成及分布特征，本研究从GTDB、NCBI数据库中收集了242个弧菌属代表性基因组，利用Defense Finder等生物信息学工具对其编码的抗噬菌体防御系统进行分析，共鉴定出108种不同的抗噬菌体防御系统，包括GAPS系统、dGTPase系统、RM系统等。不同弧菌菌株的防御能力存在显著差异：5个菌株编码超过20种防御系统，显示出较高的防御潜力；超过30个菌株仅编码5种或更少的防御系统；特别是在‘Vibrio katoptron’中未发现任何已知的防御系统。不同弧菌分支的防御系统多样性也存在差异，其中Cholerae分支的防御系统多样性(防御熵)最高。此外，对这些防御系统的组成、结构及功能机制进行了深入分析。弧菌属细菌拥有复杂多样的抗噬菌体防御系统，但许多系统的具体功能尚未明确。由于弧菌基因组的复杂性，未来仍有许多潜在的防御系统有待发现。本研究系统揭示了弧菌属防御系统的基因组结构特征，为深入探索弧菌与噬菌体的相互作用及其演化动态提供了重要的理论依据。
徐雪峰, 金兴坤, 史燕, 赵哲 . 弧菌基因组中抗噬菌体防御系统的构成与分布特征分析[J]. 遗传, 2025 , 47(9) : 1057 -1068 . DOI: 10.16288/j.yczz.24-290
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, Vibrio species are known for their large and complex genomes. To investigate the composition and distribution of anti-phage defense systems in Vibrio 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 Vibrio 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 ‘Vibrio katoptron’. Furthermore, we note that the diversity of defense systems varies among Vibrio 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 Vibrio species exhibit a complex and diverse array of anti-phage defense systems, the specific functions of many remain unknown. Given the complexity of Vibrio genomes, we suggest that numerous potential defense systems are yet to be discovered. This study provides a comprehensive overview of the genomic characteristics of Vibrio defense systems, laying a foundation for future research into the interactions and evolutionary dynamics between Vibrio and bacteriophages.
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