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MicroScope: an integrated platform for the annotation and axploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
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National audience. Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. To address this challenge, we develop the MicroScope platform, which is an integrated Web platform for management, annotation, comparative analysis and visualization of microbial genomes https://mage.genoscope.cns.fr/microscope) [1]. The platform enablescollaborative work in a rich comparative genomic 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 toanalyze a wide range of biological systems (antibiotic resistance, virulence, secondary metabolites,integrons, secretions systems, CRISPR-Cas clusters…). Particularly, tools from the PPanGGOLiN softwaresuite (https://github.com/labgem/PPanGGOLiN) allows users to analyze pangenomes from several hundredsof genomes of the same species and to explore their content in regions of genomic plasticity [2,3]. Theplatform also has extensive functionality to explore and compare metabolic pathways.MicroScope platform is widely used by microbiologists from academia and industry all around the worldfor collaborative 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.This poster gives an overview of the platform and its evolution and presents new methodologies and toolsalready integrated or currently being developed.AcknowledgementsThis work was supported in part by FRANCE GENOMIQUE [ANR-10-INBS-09–08] and INSTITUT FRANÇAISDE BIOINFORMATIQUE [ANR-11-INBS-0013].References1. David Vallenet, Alexandra Calteau, Mathieu Dubois et al. MicroScope: an integrated platform for the annotationand exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis.Nucleic Acids Research, Jan 8;48(D1):D579-D589, 2020.2. Guillaume Gautreau, Adelme Bazin, Mathieu Gachet et al. PPanGGOLiN: Depicting microbial diversity via apartitioned pangenome graph. PLoS Computational Biology, Mar 19;16(3):e1007732, 2020.3. Adelme Bazin, Guillaume Gautreau, Claudine Médigue et al. panRGP: a pangenome-based method to predictgenomic islands and explore their diversity. Bioinformatics, Dec 30;36(Suppl_2):i651-i658, 2020.
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