proMGE

proMGE catalogs and classifies six distinct categories of prokaryotic mobile genetic elements (MGEs) across approximately 76,000 genomes to enable analysis of MGE distribution, boundaries, cargo functions, and horizontal transfer.

Key Features:

• Comprehensive coverage: Aggregates over 2.4 million MGEs from ~76,000 prokaryotic genomes covering six distinct MGE categories including transposons, integrons, phages, and plasmids.
• Classification and retrieval: Classifies MGEs from user-provided protein sequences derived from complete genomes and genomic fragments.
• Recombinase-based framework: Uses recombinases as ubiquitous marker genes to capture diverse MGE types and associated cargo functions such as antibiotic resistance.
• Pangenome information integration: Leverages pangenome data to estimate MGE boundaries and improve boundary precision.
• Horizontal transfer analysis: Maps MGE-specific recombinases to operational MGE types across ~84,000 genomes annotated with habitat information to reveal transfer events across phyla and habitats.
• Quantification of hitchhiking events: Disentangles and quantifies hitchhiking where TEs and integrons co‑occur with other MGE types, reporting TEs account for 17% and integrons for 63% of such events.
• Antibiotic resistance carrier identification: Identifies transposable elements as the predominant carriers of antibiotic resistance genes.

Scientific Applications:

• Prokaryotic evolution studies: Enables analyses of MGE distribution and dynamics to inform studies of prokaryotic evolution.
• Antibiotic resistance research: Maps antibiotic resistance genes within MGEs, supporting investigation of resistance dissemination mechanisms.
• Environmental genomics: Uses habitat-annotated genome mappings to study MGE dispersal patterns across different environments.

Methodology:

Integrates recombinase marker identification and pangenome-derived boundary estimation, classifies MGEs from protein sequences of complete genomes and genomic fragments, maps recombinase markers to operational MGE types across ~84,000 habitat-annotated genomes, and quantifies hitchhiking events (TEs 17%, integrons 63%).