Beav: a bacterial genome and mobile element annotation pipeline

Area of Science:

• Genomics
• Bioinformatics
• Microbial Ecology

Background:

• Accurate genome annotation is essential for understanding organismal functions.
• Existing annotation tools often struggle with mobile genetic elements and lack context for larger genomic features.
• Gaps exist in annotating virulence and symbiosis genes in plant-associated bacteria.

Purpose of the Study:

• To develop a comprehensive and user-friendly genome annotation pipeline called Beav.
• To automate the annotation of diverse genomic features, including genes, mobile genetic elements, and gene clusters.
• To improve the annotation accuracy for plant-associated microbes and generate integrated outputs.

Main Methods:

• Developed Beav, a command-line annotation pipeline integrating existing tools with custom models and databases.
• Incorporated custom databases for enhanced annotation of plant-associated microbes.
• Included an optional pipeline for Agrobacterium oncogenic plasmids and features.
• Consolidated all annotations into a single output and generated genome/plasmid maps.

Main Results:

• Beav automates the annotation of bacterial genomes, mobile genetic elements, molecular systems, gene clusters, and regulatory features.
• Custom databases enhance the annotation of virulence and symbiosis genes in agriculturally important plant microbes.
• The pipeline successfully identifies and classifies Agrobacterium oncogenic plasmids and their features.
• Beav produces consolidated annotations and publication-quality genome and plasmid maps.

Conclusions:

• Beav provides a comprehensive, automated solution for bacterial genome annotation.
• The pipeline addresses limitations of existing tools, particularly for mobile elements and plant-associated bacteria.
• Beav facilitates broader access to high-quality genome annotation and visualization tools.