Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

• Published in: Nucleic acids research 2021-01, Vol.49 (D1), p.D667-D676
• Main Authors: Garczarek, Laurence, Guyet, Ulysse, Doré, Hugo, Farrant, Gregory K, Hoebeke, Mark, Brillet-Guéguen, Loraine, Bisch, Antoine, Ferrieux, Mathilde, Siltanen, Jukka, Corre, Erwan, Le Corguillé, Gildas, Ratin, Morgane, Pitt, Frances D, Ostrowski, Martin, Conan, Maël, Siegel, Anne, Labadie, Karine, Aury, Jean-Marc, Wincker, Patrick, Scanlan, David J, Partensky, Frédéric
• Format: Article
• Language: English
• Subjects: Aquatic Organisms - genetics; Bacterial Proteins - genetics; Bacteriology; Biodiversity and Ecology; Bioinformatics; Computer Science; Cyanobacteria - genetics; Data Curation; Database Issue; Databases, Genetic; Environmental Sciences; Genome, Bacterial; Geography; Information Systems; Life Sciences; Likelihood Functions; Microbiology and Parasitology; Phylogeny; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkaa958

Abstract Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.