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MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis
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National audience. 1 IntroductionLarge-scale genome sequencing and the increasingly massive use of high-throughput approachesproduce a vast amount of new information that completely transforms our understanding of thousandsof microbial species. However, despite the development of powerful bioinformatics approaches, fullinterpretation of the content of these genomes remains a difficult task. To address this challenge, theLABGeM group at Genoscope has developed the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) which provides analysis for complete and ongoing genome projects togetherwith metabolic network reconstruction and post-genomic experiments allowing users to improve theunderstanding of gene functions. MicroScope serves different use cases in bioinformatics:— it supports the integration of newly sequenced or already available prokaryotic genomes throughthe offer of a free-of-charge service to the scientific community— it performs computational inferences including prediction of gene function, metabolic pathways,resistome and virulome— it provides tools for comparative genomics and metabolic analyses— it supports collaborative expert annotation and community-based curation efforts in a richcomparative genomics context through the use of specific curation tools and graphical interfaces.MicroScope contains data for ∼ 10,000 microbial genomes, which are manually curated and analyzedby microbiologists (> 4,000 personal accounts in January 2019).2 ContributionsThe platform has been under continuous development since 2006 [1,2]. We will present an overviewof the MicroScope analysis pipelines and illustrate the use of several new functionalities which concern:— automatic annotation based on the UniRule system— annotation of virulence and antimicrobial resistance genes— comparative genomics with synteny computations and pan-genome analyses— prediction and characterization of regions of genomic plasticity like secretion systems, integronsand secondary metabolite biosynthesis gene clusters— metabolic network reconstructionReferences[1] Claudine M´edigue, Alexandra Calteau, St´ephane Cruveiller, Mathieu Gachet, Guillaume Gautreau, AdrienJosso, Aur´elie Lajus, Jordan Langlois, Hugo Pereira, R´emi Planel, David Roche, Johan Rollin, Zoe Rouy,and David Vallenet. MicroScope—an integrated resource for community expertise of gene functions andcomparative analysis of microbial genomic and metabolic data. Briefings in Bioinformatics, sep 2017.[2] Adrien Josso, Alexandra Calteau, Alexandre Renaux, Aur´elie Lajus, David Roche, Johan Rollin, JonathanMercier, Mathieu Gachet, St´ephane Cruveiller, Zoe Rouy, Claudine M´edigue, David Vallenet, and ClaudeScarpelli. MicroScope in 2017: an expanding and evolving integrated resource for community expertise ofmicrobial genomes. Nucleic Acids Research, 45(D1):D517–D528, nov 2016.
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