Complete genome analysis of Vibrio mimicus strain SCCF01, a highly virulent isolate from the freshwater catfish
Zehui Yu1,2, Erlong Wang1,3, Yi Geng1
1College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.
Abstract:
Vibrio mimicus is a foodborne pathogen, which is widely distributed in the aquatic environment. Moreover, it is often involved in aquatic animal diseases. In recent years, V. mimicus is an emerging pathogen in some species of Siluriformes. The strain SCCF01 was isolated from yellow catfish (Pelteobagrus fulvidraco). In this study, we aimed to perform genomic analysis of V. mimicus strain SCCF01 to identify genetic features and evolutionary relationships. Information on gene function and classification was obtained by functional annotation, and circular graph of strain SCCF01 genome, which was created by Circos v0.64. Information on virulence genes (adhesion, flagellum system, exotoxin, and secretory system, etc.) was obtained by virulence genes annotation. Genome element prediction showed that most of the mobile elements were distributed in chromosome I. Therefore, chromosome I of SCCF01 genome has more plasticity than chromosome II and might be larger in size. Genomic linear relationship between the strain of V. mimicus and strain SCCF01 was analyzed by linear pairwise comparison but was unable to determine the relationship. Gene family analysis predicted that the evolutionary direction of strain SCCF01 was: clinical strain → environmental strain → SCCF01 strain. Phylogenetic analysis showed that the strain SCCF01 was more closely related to environmental strains. According to gene family analysis and phylogenetic analysis, we speculated that strain SCCF01 has probably diverged from environmental strains.
Insights
Vibrio mimicus strain SCCF01, isolated from yellow catfish, shows genomic plasticity in chromosome I. Phylogenetic analysis suggests this foodborne pathogen diverged from environmental strains.
Area of Science:
- Microbiology
- Genomics
- Aquatic Animal Health
Background:
- Vibrio mimicus is a foodborne pathogen prevalent in aquatic environments.
- It is an emerging pathogen in Siluriformes, including yellow catfish (Pelteobagrus fulvidraco).
Purpose of the Study:
- To conduct a genomic analysis of Vibrio mimicus strain SCCF01.
- To identify genetic features and evolutionary relationships of the strain.
Main Methods:
- Functional annotation and genome circular graph creation (Circos v0.64).
- Virulence gene annotation (adhesion, flagellum, exotoxin, secretory systems).
- Genome element prediction, linear pairwise comparison, gene family analysis, and phylogenetic analysis.
Main Results:
- Chromosome I exhibits greater plasticity and potential size compared to chromosome II, with most mobile elements located here.
- Gene family analysis suggests an evolutionary path from clinical to environmental to SCCF01 strain.
- Phylogenetic analysis indicates SCCF01 is closely related to environmental strains.
Conclusions:
- Vibrio mimicus strain SCCF01 possesses a plastic chromosome I.
- Strain SCCF01 likely diverged from environmental Vibrio mimicus strains.
