CyanoType

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What is CyanoType?

CyanoType is a database of information on cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes. Strains are categorized by relevance.

Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies, and important bibliographic references.

A global 16S rDNA-based phylogenetic tree is provided in order to assist users in choosing the appropriate strains for their studies.


Categorization of strains
(see also the Tree caption)

T - Type strain of the Type species (taxon established by modern polyphasic taxonomy); t - not the type strain but known to have the same phylogenetic placement as the Type species, after taxonomic revision; R - Reference strain in Bergey's Manual of Systematic Bacteriology; r - strain known to be included in the same phylogenetic cluster as the reference strain sensu Bergey's Manual; G - strain with its Genome sequenced and publicly available; E - strain studied from Exsiccata (dried herbarium specimens of cyanobacteria).


Citing CyanoType

If using information either directly from the database or from the dataset please cite CyanoType as:

Ramos, V., Morais, J. & Vasconcelos, V. 2017. A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies. Scientific Data 4, Article number: 170054 (link)

Note: for access directly to the CyanoType v.1 dataset (semicolon delimited CSV file; the worksheet can be open in e.g. Excel), take a look at the abovementioned Data Descriptor.


Organisms included

The database list cyanobacterial isolates meeting the criteria for inclusion, as defined in the Data Descriptor (Ramos, Morais & Vasconcelos, in preparation). It includes marine, freshwater and terrestrial organisms.


Data and constraints

Please note that CyanoType is purely meant as an aid to select appropriate strains for taxonomic, phylogenetic and/or phylogenomic studies. Its aim is to allow users to get integrated information as metadata. It is not the ultimate source.

Indeed, data on this manually curated database’ site is not error-free. It is based mainly on published information from different sources and it also faces challenges with respect to keeping data current. Advisably, users should always check the information provided before using it. Whenever available, bibliographic references are provided for each strain, enabling users to get access to the original (and additional) data.


Versions

CyanoType is a work in progress, and is thus incomplete. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. Researchers making use of the database (or dataset) should verify the validity and accuracy of the data. If desired, they can submit feedback directly in the strain’s page, through the ‘Send Feedback’ pane. The information from contributors will be updated after curation by our team.


Data Sources

Whenever appropriate, credit was given to the originator of the data included in CyanoType (see the Data Descriptor, in preparation). For instance, important sources include AlgaeBase or NCBI (e.g. GenBank, Assembly, Genomes), as well as relevant literature such as Komárek et al. (2014), Shih et al. (2013) or the Bergey’s Manual® of Systematic Bacteriology.