Changelog for CyanobactChangelog 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 19.0 (April 2024)
Found that the search-data scripts (enabling searching multiple columns) work only in Firefox. Re-added an old version suitable for all browsers; this permits the search of only one (but any) column.
Updated all phylogenetic trees and associated pages.
Release 18.0 (March 2024)
New genera: Ahomia, Almyronema, Azorothrix, Gansulinema, Komarkovaeasiopsis, Maricoleus, Radiculonema, Tumidithrix.
Continued changes to the search data page, added a help document.
This release contains major changes to the phylogenetic trees and to many pages since Release 17.2.
Release 17.2 (February 2024)
New genera: Almyronema, Gansulinema, Karukerafilum, Komarkovaeasiopsis, Radiculonema, Sphaerothrix, Tumidithrix
This release includes many changes to the phylogenetic trees and to many pages since Release 17.0. Continued changes to the search data page.
Release 17.1 (January 2024)
New genera: Karukerafilum
This release includes many changes to the phylogenetic trees and to many pages since Release 17.0, and a total re-write of the search data page.
Release 17.0 (January 2024)
New genera: Almyronema
This release includes the many changes made to the phylogenetic trees and to many pages since Release 16.1, but not uploaded to the server.
Release 16.1 (November 2023)
New genera: Cyanaurora (Candidatus), Limnonema, Pseudocalidococcus, Venetifunis
Release 16.0 (October 2023)
This major release consolidates all changes since release 15.1, none of which were uploaded to the server.
Changed title of the website to permit the use of the Phylum name Cyanobacteriota (Oren et al., 2022).
Finished the changes to the genome metrics page.
New genera: Copelandiella
Release 15.1 (March 2023)
New genera: Candidatus Sivonenia alaskensis, Edaphophycus, Egbenema, Insularia, Katagnymene, Limnofasciculus, Microcrocis, Microlinema, Thermocoleostomius
Release 15.0 (February 2023)
Continued working on the new search function, which was started in the last release. Further changes to many pages, and to all trees.
The genome metrics page requires further attention.
New genera: Khargia, Ocullathermofonsia, Trichothermofontia.
Release 14.1 (September 2022)
Added a new genomic tree (the Picocyanobacterial tree, accessed from the Index page) containing over 250 sequences, many of which are excluded from the other genomic trees. Added a new search function, still under construction, giving strain data for all entries in the 16S rRNA tree.
New genera: Aerofilum, Apatinema, Fulbrightiella, Johanseniella, Ocullathermofontia, Neocylindrospermum, Sherwoodiella, Siamcapillus, Trichothermofontia.
Release 14.0 (July 2022)
Consolidates all changes since release 13.0. Further changes to many pages, and to all trees.
Release 13.3 (July 2022)
Added show/hide capability to the genome metrics page, for the contents table and genome metrics table.
New genera: Hillbrichtia
Release 13.2 (May 2022)
New genera: Argonema, Cyanoplacoma, Sirenicapillaria, Tigrinifilum
Release 13.1 (April 2022)
New genera: Allocoleopsis, Arizonema, Crassifilum, Crustifilum, Funiculus, Leptothermofonsia, Parafilum, Petrachloros
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.
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.
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.
Release 9.1
Minor release.
Release 9.0
Added genera: Amphiheterocytum, Aurora (Candidatus), Dulcicalothrix, Hydrococcus, Leptodesmis, Limnospira, Neolyngbya, Neowestiellopsis, Purpurea, Reptodigitus, Violetonostoc to ARB
Migrated site to new webhost service provider; left a 301 redirect on old site for users who bookmarked the latter.
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
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.
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.)
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.
Data collection for this version of the site stopped on 30:06:2018
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).
Further revised descriptions in the genomic correlations document.
Added new page to show the morphotypes within the Nostocales.
Further revised descriptions in the genomic correlations document.
Added new species to Aliinostoc and Stenomitos.
Revised descriptions in the genomic correlations document.
and new genomes to both genome trees.
Largely re-wrote the correlations document to include Mash-similarity and CGS (our 79 core gene genomic approach) values.
and new genomes to both genome trees.
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
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
Changed the introductory "Notes on web browsers" accordingly