THE CYANOBACTERIAL PHYLOGENY AND TAXONOMY REFERENCE WEBSITE

A curated 16S rRNA phylogeny with over 4000 members. The taxonomy is correlated with trees of 1000 total, 250 complete and 300 picocyanobacterial genomes. Errors in cyanobacterial nomenclature are exposed and type species and problematic genera are discussed.

Click the buttons on the left to navigate among the main pages of this site. New pages open by default in a new tab, the previous tab remaining open at the top of the browser window, allowing a page to be visited again without re-opening from the menu; close any tabs that are no longer needed.

Many pages are formatted as PDF; all pages may be searched, printed or downloaded. All phylogenetic trees, except the orders tree, have multiple, overlapping, pages. Other links are directly available on the main text page. The contents of the site are updated regularly with new or revised genera or species, and new genomic sequences are added when available. All data are available for download.

IMPORTANT NOTE: Please see the main text page for browser configuration required for viewing PDF pages.

This ad-free site was created by Mike Herdman and Rosi Rippka,
January 1 2017

NEW: release 15.0 replaced the previous version (February 2003);
see the changelog for details. Cyanobacterial phylogeny. Some genera added for this release: Khargia, Ocullathermofonsia, Trichothermofonsia.

Questions or comments: write to mherdman1245(at)gmail.com

NAVIGATION MENU

×

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.

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, division of the 16S rRNA tree into higher ranks, genera and species, 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 100 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. Consequently, many strains classed as freshwater may, in fact, be euryhaline.

SEARCH FACILITIES

Search whole site

Search sequence data

TEXT DOCUMENTS

PHYLOGENY

16S rRNA trees:

Tree coloured by
morphotype

Genomic trees:
Complete only

Complete and WGS

Picocyanobacteria
subtree

Site Map