MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

Abstract

The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources.

Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation

“…The metagenome of the TRIP culture was sequenced, and genome-resolved analyses (Gkanogiannis et al, 2016) led to the reconstruction of five nearly-complete genomes that were annotated using the MicroScope microbial genome annotation and analysis platform (Médigue et al, 2017;Himmelberg et al, 2018). A general overview of the main genomic features of these organisms is presented in Table 1.…”

“…The genome further contains genes for the subunits of a pyruvate dehydrogenase complex required for transforming pyruvate into acetyl-CoA. All sequence analysis including similarities, synteny and protein domain predictions (Médigue et al, 2017) pointed to the classification of the aforementioned genes as encoding a 2-oxo-acid dehydrogenase and not a 2-oxo-acid:ferredoxin oxidoreductase. This excludes the possibility of producing reduced ferredoxin at this step which is needed for reduction of the ring system in anaerobic naphthalene degradation by Deltaproteobacterium N47 (Weyrauch, unpublished results).…”

“…The expression of these genes was detected by proteomic and/or transcriptomic analyses of the TRIP culture grown on phenanthrene ( Fig. All sequence analysis including similarities, synteny and protein domain predictions (Médigue et al, 2017) pointed to the classification of the aforementioned genes as encoding a 2-oxo-acid dehydrogenase and not a 2-oxo-acid:ferredoxin oxidoreductase. The genome of candidate Desulfatiglans TRIP_1 also encodes the enzymes for the pentose phosphate pathway.…”

“…The preassembly protocol followed the steps described in (Gkanogiannis et al, 2016) and the Spades engine (Bankevich et al, 2012) was used for targeted assemblies. The resulting scaffolds were annotated using the MicroScope microbial genome annotation and analysis platform (Médigue et al, 2017). Complete pathways encoded in the respective genome are indicated in grey.…”

Bacillus subtilis, the model Gram‐positive bacterium: 20 years of annotation refinement

“…Annotation of genome sequences must be imbedded in knowledge generated for as many sources of information as possible. M edigue and co-workers designed an annotation platform, MicroScope/MaGe, meant to make the most of the diverse annotations associated to bacterial genomes by imbedding in the same platform both sequence and annotation data, together with analytical methods designed to explore the data (Medigue et al, 2017;Vallenet et al, 2017). To obtain a cutting-edge annotation of the genome of B. subtilis 168, we used the MicroScope platform to collect information from as many sources as possible, based on literature and extant databases.…”