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Two search functions are provided. The first reports the pages containing the search term employed, the second gives full details of sequences shown in the 16S rRNA tree, for example references. This is available in two versions: the first, only for Firefox, has full functionality, with over 4000 entries; the second, for all browsers, is limited to descriptions of over 700 genomic sequences.
The Main phylogeny page, opened by clicking the "Main text page" button, covers all aspects of cyanobacterial phylogeny included in this site: sequence length and alignment, methods for building trees based on 16S rRNA and genome sequences, comments on genera and species that are clearly invalid or require attention, polyphyly, the confusion in the placement of type species and gene heterogeneity. An extensive list of references is provided.
IMPORTANT: Please see the main text page for browser configuration required for viewing PDF pages.
In the page opened from the "Genome metrics" button, we correlate 16S rRNA sequence identity with DNA-DNA hybridization (DDH) values, Average Nucleotide Identity (ANI) studies, Mash similarity values (for complete chromosomes only) and those obtained with our 79-gene marker set (CGS). For most genera, the 16S rRNA gene sequence data correlate well with the genome metrics. However, several, including Planktothrix, Sphaerospermopsis, Synechocystis, some extremophiles, Prochlorococcus and the Synechococcus sister group, do not, for reasons which imply different evolutionary strategies in these cyanobacteria.
The clusters in the trees were originally labeled in numerical order; however, addition of new sequences has caused some branch rotation and new genera have been given the next available number in their cluster; this has destroyed to some extent this numerical sequence. We are unable to re-number the taxa because the numbering scheme has been used in publications. A summary of the tree in strict numerical order is therefore accessible from the "Tree summary" button.
The "Type species" button opens a list of genera considered on this site, with the names and authority of their type species, their position in the 16S rRNA tree and, if provided, the living reference strain. Less than 400 genera are represented by type/reference strains, of which fewer than 20 are known to be axenic.
The genomic trees all carry the genome logo in the top left corner; clicking this opens the appropriate excluded genomes pages. For the Picocyanobacteria subtree, it is difficult to categorize organisms from freshwater and saline (coastal, estuarine, intertidal) environments, owing to inprecise habitat information provided by many authors.
Questions or comments: write to mherdman1245(at)gmail.com