弧菌基因组中抗噬菌体防御系统的构成与分布特征分析

doi:10.16288/j.yczz.24-290

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Hereditas(Beijing) ›› 2025, Vol. 47 ›› Issue (9): 1057-1068.doi: 10.16288/j.yczz.24-290

• Research Article • Previous Articles

Comprehensive analysis of the composition and distribution of anti-phage defense systems in Vibrio genomes

Xuefeng Xu¹^,²(), Xingkun Jin¹^,², Yan Shi¹^,², Zhe Zhao¹^,²()

1. Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210024, China
2. Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210024, China

Received:2024-12-02 Revised:2025-03-07 Online:2025-03-08 Published:2025-03-07
Contact: Zhe Zhao E-mail:jiayueshisan@gmail.com;zhezhao@hhu.edu.cn
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)

Abstract

Abstract:

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.

Key words: Vibrio, phage, anti-phage defense system, microbial interactions, bioinformatics analysis

Xuefeng Xu, Xingkun Jin, Yan Shi, Zhe Zhao. Comprehensive analysis of the composition and distribution of anti-phage defense systems in Vibrio genomes[J]. Hereditas(Beijing), 2025, 47(9): 1057-1068.

Figures/Tables 6

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Supplementary Fig. 1

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