dbESG: A Database Curating the Evolution of Salmonella Genomes

dbESG is a specialized database initiated to dynamically illustrate the genome evolution of the Salmonella genus. By tracing ancient orthologous chromosomes across species, subspecies, and major phylogenetic nodes, dbESG delineates evolutionary trajectories to facilitate a deeper understanding of how genome evolution influences molecular and biological phenotypes.

🧬 Biological Context

Salmonella diverged from Escherichia approximately 100 million years ago, subsequently evolving into two distinct species: S. enterica and S. bongori.

• Diversity: S. enterica has further diversified into 7+ subspecies and over 2,000 serovars.
• Host Adaptability: The genus includes generalists with broad host ranges (e.g., S. typhimurium, S. enteritidis) which cause self-limited Non-Typhoidal Salmonellae diseases, and specialists (e.g., S. typhi, S. paratyphi A) which cause invasive infections.
• Phenotypes: Beyond host adaptability, serovars vary extensively in phenotypes such as invasion, persistence, and antibiotic resistance.

🚀 Key Features

dbESG offers three main modules to assist researchers in exploring genomic data:

1. Browser

A visual interface for the evolutionary annotation and comparison of Salmonella genomes.

• Compare ancient and extant representative genomes.
• Visualize evolutionary trajectories.

2. Tools

A collection of software resources for genome analysis.

• Access computational pipelines.
• Utilize custom codes designed for Salmonella genomic research.

3. Datasets

Comprehensive downloadable data resources, including:

• Genomic datasets.
• Comparative genomic data.
• Phylogenomic datasets.

💻 Local Deployment

If you prefer to host the database locally, you can deploy the standalone version using Docker.

Run the following command:

docker run -d --restart=always -p 80:80 ghcr.io/yejunwang/egswebinterface_standalone:v1

Once the container is running, you can access the interface by visiting: http://127.0.0.1:80/

🔗 Related Resources

For a list of external databases, web servers, and other resources relevant to Salmonella research, please visit the Links page.

📚 Citation

If you use dbESG in your research, please cite the following manuscript:

Hu Y, et al. Evolution of Salmonella Chromosomes and Its Influence on Chromosomal Topology, Interaction and Gene Expression. (Submitted).

✉️ Contact & Support

dbESG is maintained by the HCD Lab at Shenzhen University Health Science Center.

• Principal Investigator / Contact: wangyj@szu.edu.cn
• Lab Website: HCD Lab

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© HCD Laboratory, Shenzhen University Health Science Center.