cyanobacterial phylogenyChangelog for Cyanobact


Minor releases (e.g. 11.1-11.5) contain updated genomic trees, few new genera and often changes to some of the pages. Major releases (e.g. 11.0) contain additionally revised 16S rRNA-based trees.

Release 13.0 (February 2022)

This release consolidates all changes since release 12.0.
New genera are: Candidatus Paraprochloron terpiosi, Pseudoacaryochloris, Romeriopsis, Thainema, Zarkia

Release 12.3 (January 2022)

Added new genera: Thainema

Reformatted the excluded-genomes, genome metrics, tree-lists, query list, genome metrics, tree summary and type species pages to HTML.

Release 12.2 (December 2021)

Added new genera: Candidatus Paraprochloron terpiosi, Pseudoacaryochloris, Romeriopsis, Zarkia

Release 12.0 (December 2021)

Replaces all intermediate versions from 11.1 onwards.

Added new genera: Chroococcidium, Euryhalinema, Microcoleusiopsis, Tenebriella, Thermospirulina, Waterburya

Included a search function on the main page, to further help in navigation, and a global search function for the entire site.

Excluded a number of strains (from Panou and Gkelis 2021: Mol Phylogenet Evol 166, 107322) from all documents, on the grounds that, although described as new genera (except for 1 strain assigned to Radiocystis), their 16S rRNA sequences contain a high number of mismatches in the paired stems of many helices. This artificially increases their apparent distance from other organisms, creating false "genera". These are: Speleotes anchialus TAU-MAC 1118, Geitleria calcarea TAU-MAC 0118, Radiocystis geminata TAU-MAC 1214, Olisthonema eestii TAU-MAC 3518, Olisthonema eestii TAU-MAC 3318, Speos fyssasii TAU-MAC 5718, Speos fyssasii TAU-MAC 5518, Iphianassa zackieohae TAU-MAC 2318, Haliplanktos anthonyquinnii TAU-MAC 3018. The two 16S rRNA genes extracted from the complete metagenome named as Microcystis aeruginosa NIBR18 (Kim and Park 2021, unpublished; accession CP086723) have also been excluded, for the same reason.

Release 11.5 (September 2021)

Added our chromosome logo to all pages concerned with genomes. This is clickable in the genomic trees, opening the excluded genomes pages.

Release 11.2 (September 2021)

Final corrections to colouring of type species and reference strains in the species tree. Axenic reference strains indicated in the list of type species.

Release 11.1 (August 2021)

Corrections to colouring of type species and reference strains in the species tree. Corrections in the list of type species.

Release 11.0 (August 2021)

Replaces all intermediate versions from 10.2 onwards.

Added new genera: Alborzia, Altericista, Amazonocrinis, Anthocerotibacter, Atlanticothrix, Baaleninema, Constrictifilum, Cryptochroococcus, Dendronalium, Gracilinea, Konicacronema, Mamoreocelis, Pseudochroococcus.

Added further sequences to all trees (16S rRNA and genome-based), updating the genome metrics document to match.

Release 10.2 (May 2021)

Added new genera: Affixifilum, Capilliphycus, Leptochromothrix, Neochroococcus, Ophiophycus, Vermifilum

Added further sequences to all trees, updating the genome metrics document to match.
Removed the outer vertical scrollbar from all pages containing PDF documents, since the latter carry their own.

Renamed all Cylindrospermopsis strains to Raphidiopsis.

Release 10.1

Updated the genome metrics document.

Release 10

Added new genera (since Release 9.6) Parasynechococcus (validation), Perforafilum, Picosynechococcus, Pseudoaliinostoc, Thermostichus, Thermosynechococcus (validation), Trichotorquatus (validation), Vulcanococcus, and many new species to the 16S rRNA trees, and new genomes to both genome trees.
Changed alignment method for genome sequences, from muscle to MAFFT (running within the wrapper programme pagan2).
Since this change, and with the availability of a large number of new genomes, many sequences have been added to the genomic trees. The genomic correlations document has not yet been updated to include these, and still refers to version 9.6 of this site. An updated document will be posted with the next version.
Added tree showing the outgroup taxa (which are presented as collapsed groups in the other 16S rRNA trees).

Release 9.6

Added new genera (since Release 9.1) Aegeococcus, Cymatolege, Gibliniella, Johannesbaptistia, Metis, Monilinema, Parakomarekiella, Parasynechococcus (validation), Picosynechococcus, Pseudoaliinostoc, Rhodoploca, Shackletoniella, Thalassoporum, Thermostichus, Thermosynechococcus (validation), and numerous new species to the 16S rRNA trees, and new genomes to both genome trees.
Further revised descriptions in the genomic correlations document.
Added new page to show the morphotypes within the Nostocales.

Release 9.5

Added new genera Aegeococcus, Cymatolege, Gibliniella, Metis, Parakomarekiella, Rhodoploca, Shackletoniella, Thalassoporum and numerous new species to the 16S rRNA trees, and new genomes to both genome trees.
Further revised descriptions in the genomic correlations document.

Release 9.1

Minor release.
Added new species to Aliinostoc and Stenomitos.
Revised descriptions in the genomic correlations document.

Release 9.0

Added genera: Amphiheterocytum, Aurora (Candidatus), Dulcicalothrix, Hydrococcus, Leptodesmis, Limnospira, Neolyngbya, Neowestiellopsis, Purpurea, Reptodigitus, Violetonostoc to ARB
and new genomes to both genome trees.

Migrated site to new webhost service provider; left a 301 redirect on old site for users who bookmarked the latter.
Largely re-wrote the correlations document to include Mash-similarity and CGS (our 79 core gene genomic approach) values.

Data collection for this release stopped on 01:06:2020

Release 8.5

Added genera: Amphiheterocytum, Dulcicalothrix, Hydrococcus, Leptodesmis, Limnospira, Neolyngbya, Neowestiellopsis, Purpurea, Reptodigitus to ARB
and new genomes to both genome trees.

Changed main.html to replace the "sticky" menu, which was not recognized by IE 11, with CSS-encoded frames (the menu being in the top frame).

Changed magnification factors of strain.html: min-height from 200 to 250vh, width from 100% to 125% and species.html from 150vh, 100% to 250, 125.

Data collection for this release stopped on 27:12:2019

Release 8.0

Added genera: Albertania, Compactonostoc, Cryptococcum, Euryhalinema, Inacoccus, Lagosinema, Leptothoe, Minunostoc, Myxacorys, Rippkaea, Sinocapsa, Zehria.

Redesigned the site. The old menu.html is now the opening page (index.html), with some info transferred from the old main page, the underlined links replaced by buttons, access to a brief description of the three important text documents. The old index.html is now main.html, with an added menu for rapid access to key paragraphs.

Added new genomes to both trees

Added table of type species and reference strains; where aberrant (e.g. one type species falling into several generic clusters) added to new section "Type species" in text.

Extended description of importance of sequence length, making a new section.

Enlarged discussion on sequence identity cutoff values at specific and generic levels.

Changed to ARB style for display of genome trees.

Data collection for this release stopped on 07:11:2019




Release 7.0

Added genera: 'Candidatus curcubocaldaceae cyanobacterium', Capillus, Cartusia, Dapis, Desikacharya, Drouetiella, Geitleria (uncultured), Heteroscytonema, Kaiparowitsia, Klisinema, Komarkovaea, Kyrtuthrix, Laspinema, Marsacia (provis.), Nunduva, Odorella, Pegethrix, Persinema, Potamosiphon, Pycnacronema, Ramsaria, Tildeniella, Trichotorquatus (provis.)

Removed plasmid sequences from the NCBI flatfiles of the complete sequence of Anabaena cylindrica PCC 7122 (CP003659, 5 plasmids) and the draft genomes of Limnothrix rosea IAM M-220 (MRBY00000000, 3 plasmids) and Leptolyngbya sp. JSC-1 (JMKF00000000, 30 contigs)

Added new genomes to both trees

All documents updated and corrected

Data collection for this release stopped on 15:04:2019

Version 6.0

Added genera: Aliinostoc, Amazoninema, Anagnostidinema, Cyanomargarita, Elainella, Foliisarcina, Jacksonvillea, Koinonema, Komarekiella, Kryptousia, Neolyngbya, Onodrimia, Porphyrosiphon, Phyllonema, Rhizonema, Sodaleptolyngbya, Sodalinema, Timaviella

Many new entries in 16S rRNA trees

HTML pages for 16S trees removed, leaving only the PDF trees

Changed method of genome tree inference, permitting trees of over 500 cyanobacterial genomes (draft + complete) and of almost 140 complete genomes

All web browsers tested now read all pages of the site; this applies to Microsoft Internet Explorer and Edge, Google Chrome, Opera and Firefox.
Changed the introductory "Notes on web browsers" accordingly

Data collection for this version of the site stopped on 30:06:2018