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

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.

Seasonal niche differentiation between evolutionary closely related marine bacteria

“…Between the Synechococcus, ASV1 and ASV5, there were only 3-nucleotide divergence (99.26% identity), but the niche was clearly partitioned (Supplementary Figure 11). Since Synechococcus is one of the best known picoplankton groups, we checked the taxonomy at a finer resolution using a picocyanobacterial-specific database (Garczarek et al, 2020). In particular, ASV5 presented a 100% identity match with strain PROS-9-1, belonging to clade Ib, found in cold or temperate waters (Farrant et al, 2016).…”

“…Furthermore, the ASVs assigned to Synechococcus were checked against the Cyanorak database v2.1 (Garczarek et al, 2020) through 100% BLAST matches. ASVs classified as Mitochondria or Chloroplast were removed.…”

Pili allow dominant marine cyanobacteria to avoid sinking and evade predation

“…Single-cell Assembled Genomes (SAGs). Genomic analysis of sequenced marine picocyanobacterial isolates downloaded from the Cyanorak database 23 revealed that 74% of sequenced Synechococcus (n = 46) and 33% of Prochlorococcus (n = 43) encoded pilA1 (Fig. 2 and Supplementary Data 1).…”

“…Cultured marine picocyanobacterial genomes were downloaded from the Cyanorak database v2.1 [http://application.sb-roscoff.fr/ cyanorak] (ref. 23 ). Picocyanobacterial SAGs were downloaded from ref.…”

“…WH7803 using reference proteins from S. elongatus PCC 7942 16 and proposed modelled structure 11 . Genomes from cultured picocyanobacteria (Synechococcus, n = 46, and Prochlorococcus, n = 43) were downloaded from Cyanorak v2.1 23 and re-annotated using PROKKA vs. 1.7 48 . Genomes were then screened for the presence of PilA-like proteins, structural proteins PilQ, PilB and PilC, and competence proteins ComEA and ComEC, via a local BLAST server using the amino acid sequences from Synechococcus sp.…”