Last update (v3.0): April 17th, 2024
The Cyanorak Information system is a bioinformatics tool dedicated to the curation, comparison and visualization of genomes of strains belonging to alpha-cyanobacteria, a deeply branching group within the Cyanobacteria phylum, whose members possess a form-1A RuBisCo (Cabello-Yeves et al. 2022). This tool has been designed to perform extensive genomic comparisons in order to better understand the ecology, physiology and evolution of Prochlorococcus and Synechococcus, the two most abundant photosynthetic microorganisms of the ocean.
The first version of this database, Cyanorak v1, was developed in the mid 2000's by Alexis Dufresne to annotate the first 14 available genomes of marine picocyanobacteria (11 Synechococcus and 3 Prochlorococcus, Dufresne et al. 2008, Scanlan et al. 2009). While the v1 version was not scalable, the current Cyanorak v.2.1 information system has been entirely redesigned to allow the import and semi-automatic annotation of new sets of picocyanobacterial genomes. The current public version encompasses 48 Synechococcus, 6 Cyanobium, 41 Prochlorococcus genomes and 2 Prochlorococcus metagenome-assembled genomes. 25 Synechococcus genomes were sequenced by the Genoscope in the framework of the METASYN project at the request of the ECOMAP team and 7 by the Center for Genomic Research (Liverpool, UK) at the request of David J. Scanlan (Warwick University, Coventry, UK). The clustering of picocyanobacterial genes into clusters of likely orthologous genes (CLOGs) and their expert annotation using Cyanorak v.2 has been instrumental in performing extensive comparative genomics analyses of the 81 non-redundant genomes of the database (Doré et al. 2020). The current version of the database is v2.2, which notably includes annotations mentioned in Doré et al. (2023).
How to cite: Garczarek L., Guyet U., Doré H., Farrant G.K., Hoebeke M., Brillet-Guéguen L., Bisch A., Ferrieux M., Siltanen J., Corre E., Le Corguillé G., Ratin M., Pitt F.D., Ostrowski M., Conan M., Siegel A., Labadie K., Aury J.-M., Wincker P., Scanlan D.J. & F. Partensky (2021). Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. Nucleic Acids Research Volume 49, Issue D1: https://doi.org/10.1093/nar/gkaa958
Funding: Cyanorak v.2 was funded by the French ANR Programs PELICAN (Microbial Genomics, ANR-09-GENM-030: 2010-2013), SAMOSA (ANR-13-ADAP-0010: 2014-2019), CINNAMON (ANR-17-CE2-0014-01: 2018-2020) and EMBRC-France as well as the EU-FP7 programs MicroB3 (grant agreement no 287589) and MaCuMBA (grant agreement no 311975).