ExplorePipolin: reconstruction and annotation of piPolB-encoding bacterial mobile elements from draft genomes

Area of Science:

• Genomics
• Microbiology
• Bioinformatics

Background:

• Mobile genetic elements (MGEs) are crucial in bacterial evolution and the spread of antimicrobial resistance.
• Draft genomes often lack the contiguity needed for accurate MGE analysis.
• Pipolins, a superfamily of MGEs, exhibit diverse genomic structures and are challenging to analyze.

Purpose of the Study:

• To develop a computational tool for the accurate analysis of pipolins in bacterial genomes.
• To facilitate the reconstruction and annotation of pipolin elements from draft genomes.
• To support comparative genomics studies of these mobile genetic elements.

Main Methods:

• Developed ExplorePipolin, a Python-based bioinformatics pipeline.
• The pipeline screens for pipolin elements, reconstructs their structures from contigs, and annotates encoded genes.
• Utilizes a custom database for annotation and outputs standard file formats.

Main Results:

• ExplorePipolin successfully reconstructs and annotates pipolin elements from various bacterial genomes of differing quality.
• The pipeline can assemble pipolins fragmented across multiple contigs.
• Generated data is suitable for comparative genomic analyses.

Conclusions:

• ExplorePipolin provides a robust solution for analyzing pipolins, overcoming limitations of draft genomes.
• This tool aids in understanding the role of MGEs in bacterial adaptation and resistance.
• The pipeline is freely available, promoting further research in mobile element genomics.