MicroScope: an Integrated Platform for the Annotation and Exploration of Microbial Gene Functions through Genomic, Pangenomic and Metabolic Comparative Analysis

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Calteau, Alexandra | Dubois, Mathieu | Bazin, Adelme | Beuvin, Mylène | Fouteau, Stéphanie | Lajus, Aurélie | Roche, David | Rouy, Zoé | Stam, Mark | Médigue, Claudine | Vallenet, David

Edité par CCSD -

International audience. Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce avast amount of new information that completely transforms our understanding of thousands of microbialspecies. However, despite the development of powerful bioinformatics approaches, full interpretation of thecontent of these genomes remains a difficult task.To address this challenge, we develop the MicroScope platform, which is an integrated Web platform formanagement, annotation, comparative analysis and visualization of microbial genomes(https://mage.genoscope.cns.fr/microscope). The platform enables collaborative work in a rich comparativegenomic context and improves community-based curation efforts.Launched in 2005, the platform has been under continuous development within the LABGeM team atGenoscope. MicroScope provides analyses for complete and ongoing genome projects together withmetabolic network reconstruction and transcriptomic experiments allowing users to improve theunderstanding of gene functions.Besides automatic functional annotations, we integrated several tools to analyze a wide range of biologicalsystems (antibiotic resistance, virulence, secondary metabolites, integrons, secretions systems, CRISPR-Casclusters…). Particularly, tools from the PPanGGOLiN software suite(https://github.com/labgem/PPanGGOLiN) allows users to analyze pangenomes from several hundreds ofgenomes of the same species and to explore their content in regions of genomic plasticity.The platform also has extensive functionality to explore and compare metabolic pathways.MicroScope platform is widely used by microbiologists from academia and industry all around the world forcollaborative studies and expert annotation. To date, MicroScope contains data for >14,500 microbialgenomes, part of which are manually curated and maintained by microbiologists (>5,400 user accounts inMarch 2021). The platform is also a useful resource for academic training.

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