Cyanorak help menu

Cyanorak v2.1 is an information system dedicated to the curation, comparison and visualization of genomes belonging to a major cyanobacterial phylum (Cluster 5 sensu Herdman et al. (2001). The current version encompasses 41 genomes and 2 MAGs of the strictly marine genus Prochlorococcus and 54 marine, brackish or freshwater representatives of the polyphyletic Synechococcus/Cyanobium group. The core of Cyanorak is a database of manually curated ‘Clusters of likely orthologous genes’ (CLOGs) that can be accessed mainly by search tools.

The Top banner on a dark blue background present on all pages gives access to the different menus of the database, including:

• The ‘Home’ page: It shortly describes the origin of the genomes used to build the CLOG database and its history.
• The ‘Organisms’ page: it lists the genomes included in the database, which are split into two tables: ‘Prochlorococcus’ and ‘Synechococcus/Cyanobium’. Each table provides information about taxonomy, pigment type, sequencing center as well as various characteristics (size, GC%, status, clickable accession numbers in Genbank and when available RefSeq, number of CDS, etc.) of each genome included in the database.
• Next to each strain name is a clickable ‘J’ logo that gives access to the JBrowse page of the corresponding genome (see ‘JBrowse viewer’ below).
• Each strain name can be clicked to obtain the full information about the corresponding strain and genome (individual genome pages), including isolation site, depth and date, isolator, Environment Ontology (ENVO) nomenclature, etc. as well as various export options (all genes or all proteins in fasta format, whole genome in Genbank, fasta or GFF format.
• A distribution map of all the strains included in the database is available at the bottom of each table. Tabs above the map allows to select a visualization of strains as ‘clustered’ or ‘individual strains’. In the first case, strains located nearby on the map are gathered under a number that changes when the user zooms in or out using the plus or minus buttons. The map tile button allows to change the map background. The user can also choose to see only Prochlorococcus or only Synechococcus/Cyanobium strains using the barrel button.
• The ‘Genomic search’ menu includes three options:
  • Quick search: the user can enter either a ‘Cyanorak cluster (CLOG) number’ (e.g. CK_00001234), ‘gene names’ (e.g. dnaB) or ‘product’ (e.g. methyltransferase), and the term can be searched either as an exact match or as a pattern. For instance, a search for ‘dna’ in ‘pattern’ configuration will provide a list of CDS clusters whose gene name annotation includes ‘dna’ (e.g. dnaA, dnaB, etc.) as well as a list of products whose description includes DNA (e.g. DNA gyrase, formamidopyrimidine-DNA glycolase, etc.). The ‘advanced search’ option allows the user to look into any field documented in the CLOG, CDS or RNA pages, including functional categories (e.g., EC or K number, InterPro entries, GO terms, etc.) and to select one, all or a specific set of strains.
  • Finally, the ‘phyletic pattern search’ option is used to search for CLOGs, CDS and RNA that are shared by a selection of genomes and that can be either present or absent in other strains depending on the selected option. This search option is for instance most useful to identify genes specific to a particular strain combination, such as all Prochlorococcus, a given clade or a given pigment type.

Genomic Search results are displayed in distinct tabs, as detailed below.

• The ‘Blast search’ scrolldown menu proposes to interrogate the CLOG database using a SequenceServer graphical interface allowing to blast query nucleotide or protein sequence(s) against all genomes, genes, proteins or RNA of either all strains at a time (‘Blast all’) or a selection of strains (‘Blast a selection’). Results of a Blast search returns the Cyanorak ORF_ID, the strain taxonomy (at the subcluster (SC), clades and/or subclade level) and pigment type, the CLOG number as well as the CLOG gene name and product (e.g. CK_Syn_A15-24_00652_III_IIIa_3c CK_00001060!rpoC1!DNA-directed RNA polymerase complex, gamma subunit).
• The ‘JBrowse’ page is most similar to the ‘Organisms’ page except that it shows only the taxonomy and also provide the references for the genomes and transcriptomes that can be visualized in the JBrowse viewer.
• The ‘Previous versions’ page lists the previous version(s) of Cyanorak (currently only v1) and corresponding paper.
• The ‘References’ page lists papers that have used and/or cited Cyanorak v1 or V2.1 clusters.
• The ‘Links’ page provides a number of useful links related to Cyanorak.
• The ‘About us’ page lists all people who have participated in or currently maintain the Cyanorak information system.
• The ‘Cyanorak private’ link is reserved to annotators.

Genomic Search results are organized into three distinct tabs: ‘matching clusters’, ‘matching CDS’ and ‘matching RNAs’. Each list gives the essential information about every match and provides links to access detailed descriptions of these entries and can be exported in various formats (CSV, XLS or pdf).

• By clicking on one of the ‘matching clusters’ (e.g. CK_00000028), the user has access to the corresponding ‘CLOG page’. It offers a highly detailed functional annotation. If the latter has been manually verified, the mention ‘Manually annotated’ with a green background is shown on the upper right part of the page. Most functional categories (e.g., EC or K number, InterPro entries, GO terms, etc.) and domain predictions are connected by hyperlinks to the corresponding public databases. When manually checked, the functional annotation also includes one or several ‘Cyanorak Roles’ term(s), a custom-designed functional classification largely derived from ‘TIGR Roles’ but providing more details on photosynthesis and other key cyanobacterial processes such as ‘Adaptation/acclimation to atypical conditions’. Cyanorak Roles are listed at the end of this help file.

On top left of the CLOG page is a link to the ‘genomic context’, which displays the four genes upstream and downstream of the selected gene in all members of the CLOG. Two possible representations of the context are accessible through a toggle button: genes are shown either all at the same size or in relative size. To ease comparisons, the central gene is always represented in forward direction whatever its original direction in the genome and the context is arranged accordingly. Each CLOG has a (random) color and background (plain or stripped) and the genome context can be regenerated around any gene of the current context by clicking on the ORF_ID of the corresponding gene, while clicking on a CLOG number opens the corresponding CLOG page. All nucleotides and/or amino acid sequences of a given CLOG can be exported in Fasta format using links at the very bottom of the page.

The middle of the CLOG page consists in a phyletic pattern, i.e. the distribution of the genes in the different genomes, classified by taxonomy (genus, clade and, for Synechococcus SC 5.1 only, subclades), and indicating the pigment type of the corresponding strain.

The bottom of the CLOG page lists individual sequences comprised in the CLOG. Of note, for the sake of homogeneity all sequences, even when initially retrieved from  Genbank, have been attributed a standardized Cyanorak ORF_ID consisting in CK_genus name (Pro/Syn or Cya)_strain name_gene number in five digits, the latter digits corresponding to the initial locus tag. For instance, The Prochlorococcus MED4 gene PMM1063 has been given the ORF_ID CK_Pro_MED4_0163 while the Synechococcus sp. CB0205 locus tag SCB02_010100012987 has been given the Cyanorak ORF_ID CK_Syn_CB0205_12987. The annotation provided in this part is the initial gene annotation for genomes coming from Genbank, while the annotation found on the corresponding gene in in genome exports and in the JBrowse viewer will always be the annotation made at the CLOG level (top of page), which is often different.  Many genes, even in genomes initially coming from Genbank, have had their starts corrected when they were either too long or too short. Genomes have also been modified by adding a number of missing ORFs, while many wrong ORF predictions have been suppressed.

• By clicking on one of the ‘matching CDS’ (e.g. CK_Cya_NS01_00001) or on a Cyanorak ORF_ID on the CLOG page, the user has access to the annotation of the corresponding individual gene. This page corresponds to the ‘original’ (e.g. as in Genbank) gene name and product annotations as well as domain predictions for this gene, but the CLOG gene name and product is also recalled. The start may have been manually modified by a curator and comments may specify whether the sequence is frameshifted (see e.g. CK_Syn_WH7803_00748).

JBrowse viewer

The user can explore any ‘manually curated’ genome of the Cyanorak database using a JBrowse viewer. For all genomes of Cyanorak, genes have been attributed the standardized Cyanorak ORF_ID (see above) and have been assigned the detailed functional annotations found in individual CLOG page of the database.

The JBrowse viewer can be accessed by clicking on the ‘J’ logo next to each strain name either on the Organisms or the JBrowse page. The JBrowse environment allows the user to zoom in the genome using the google-plus button to see the local context and detailed annotation of any gene. Genes of interest can be searched for in the genome by entering text (e.g. ‘pheT’ or any Cyanorak ORF_ID) in the box next to chromosome. Arrows allows to navigate in the immediate environment of the gene. Right clicking on a gene gives access to its detailed functional annotation, as derived from the CLOG page, with hyperlinks to Cyanorak or external public databases.

The user can also view other genome information for a number of strains using the ‘select tracks’ menu located top left of JBrowse pages. Tracks of interest must be selected by clicking on boxes then can be visualized below the genome sequence by clicking on “back to browser”.

Available tracks include:

• ‘gained genes’ and ‘genomic islands’, as predicted by Doré et al. (2020) on 81 non-redundant Prochlorococcus and Synechococcus/Cyanobium
• Operon predictions using ProOpDB (Taboada et al. 2012). Note these predictions have only been made for the 81 non-redundant picocyanobacteria genomes studied by Doré et al. (2020).
• Two types of ‘core’ and ‘accessory’ genes:
  • the ‘core genes’ and ‘accessory genes’ tracks correspond to the core and accessory genes, as defined by Doré et al. (2020) on 81 non-redundant Prochlorococcus and Synechococcus/Cyanobium
  • the ‘large core genes’ track displays genes present in at least 90% of these 81 genomes, while the ‘large accessory’ track corresponds to the remaining genes in these genomes.
• Finally, transcriptome data are also available either from our group concerning Synechococcus sp. WH7803 (Blot et al. 2011, Guyet et al. 2020) or from other groups concerning Prochlorococcus MED4, MIT9312, MIT9313 and NATL2a and Synechococcus sp. WH8102 and CC9311. More info can be found in the Jbrowse viewer corresponding to these different strains.

If users have generated transcriptomic data corresponding to one of the genomes included in the Cyanorak database and wish to have Log2(FC) values publicly visualized using the Cyanorak Jbrowse viewer, they should provide us with:

• A bigwig file gathering log2(FC) values after having mapped their expression data on the Cyanorak version of the genomes, accessible through the individual genome pages in gbk format.
• A track_metadata_STRAIN_NAME.csv file describing the experimental set up. Please use the provided example file to generate your track_metadata file (one per strain if several strains). Note that some fields indicated in the headers description part are mandatory).
• The full reference of the paper describing the study.

Exports

Various exports are available from different pages of the Cyanorak v2.1 information system, including strain and genome characteristics from the Organisms page, annotated complete genomes from the individual strain pages, protein and nucleotide sequences in fasta format from individual gene pages and multifasta protein and nucleotide sequences files from individual cluster pages.

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 Database issue, in press.

Cyanorak Roles