PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Conjugative plasmids facilitate bacterial adaptation and gene transfer but are difficult to annotate due to complex genetic structures and inconsistent naming.
• Accurate annotation of plasmid-encoded genes is crucial for understanding bacterial evolution and microbial ecology.

Purpose of the Study:

• To develop PlasAnn, a specialized database and annotation pipeline for genes on natural plasmids.
• To provide accurate, standardized gene names and functional annotations for plasmid-encoded genes, enabling comparative analyses.
• To improve the efficiency and accuracy of plasmid annotation compared to general prokaryotic genome annotation tools.

Main Methods:

• Development of the PlasAnn database and annotation pipeline.
• Curating plasmid-type-specific gene names and functional annotations.
• Integrating common plasmid features into the annotation tool.
• Benchmarking PlasAnn against broad prokaryotic genome annotation pipelines.

Main Results:

• PlasAnn provides highly accurate, standardized gene names and functional annotations for plasmid-encoded genes.
• The PlasAnn pipeline outperforms general prokaryotic annotation tools in accuracy and efficiency.
• Analysis revealed conserved gene repertoires across different plasmid groups, suggesting modular gene networks.
• Plasmid-encoded transposable elements were found to carry genes involved in metabolism, virulence, and stress response, beyond antibiotic resistance.

Conclusions:

• PlasAnn significantly enhances plasmid annotation, facilitating comparative studies and advancing the understanding of plasmid biology.
• The tool aids in deciphering the broader roles of plasmid-encoded genes in bacterial adaptation and evolution.
• PlasAnn's findings highlight the dynamic nature of gene sharing on plasmids and their contribution to microbial fitness.