Changelog
Source:NEWS.md
pr2database 5.1.0
Released: 2025-04-04
Taxonomic groups updated
- Apicomplexa
- Picozoa (Eukref workshop)
- Choropicophyceae, Picocystophyceae (Eukref workshop)
- Pseudoscourfieldiophyceae: new class for Pseudoscourfieldia and Pycnococcus
- Rhodophyta- Ceramiales and Batrachospermales (Eukref workshop)
- Dinophyceae - Suessiales (Eukref workshop)
- Dinophyceae - Gonyaulax, Alexandrium, Amphidinium, Heterocapsa, Azadinium
- Foraminifera
- Chytrids and Aphelids
- Metazoa - Non bilaterians
Traits
- The following functional traits are now available:
- mixoplankton species (already available in release 5.0)
- HAB (Harmful Algal Bloom) species - from https://www.marinespecies.org/hab/index.php
- ecological function - from Sommeria-Klein et al. 2021
Other databases changes
- Species names corrected using GBIF
- All entries were analyzed with the rRNA detecting program barrnap. Some entries for which the 18S rRNA gene could not be detected were removed
Changes to web interface
- It is now possible to select
- only reference sequences
- 18S, 16S or full operon sequences
- Only sequences from HAB species
- Only sequences from Mixoplankton species
- Species now links to GBIF database instead of WORMS
pr2database 5.0.0
Released: 2023-04-06
Taxonomy updated from 8 to 9 levels
Following Burki et al. 2020. * Burki et al. 2020. The New Tree of Eukaryotes ». Trends in Ecology and Evolution 35: 43‑55. DOI: 10.1016/j.tree.2019.08.008.
Updated groups
- Stramenopiles
- Diatoms
- Chrysophyceae
- Alveolates
- Ciliates
- Dinoflagellates
- Perkinsea
- Fungi
- Chytrids
- New supergroup added: Provora
- Bacteria/Archaea
- Organelles
Linked database
- EukRibo: Berney et al. 2022. EukRibo: A Manually Curated Eukaryotic 18S RDNA Reference Database to Facilitate Identification of New Diversity. Preprint. BiorXiv. DOI: 10.1101/2022.11.03.515105.
- Mixoplankton Database: Mitra et al. 2023. « The Mixoplankton Database – Diversity of Photo-Phago-Trophic Plankton in Form, Function and Distribution across the Global Ocean ». Journal of Eukaryotic Microbiology : e12972. DOI: 10.1111/jeu.12972.
pr2database 4.14.0
Released: 2021-06-25
A single SSU database
From version 4.14.0, a single SSU database is provided which contains sequences for: * 18S rRNA from nuclear and nucleomorph * 16S rRNA from plastid, apicoplast, chromatophore, mitochondrion * 16S rRNA from a small selection of bacteria
The rationale is that the database can now be used to detect bacterial sequences that are amplified with either 18S rRNA or “universal” primers. These sequences can be further assigned with Silva or GTDB.
In order to allow correct assignation with software such as DECIPHER (IDTax) for organelle, the taxonomy is appended with 4 letters corresponding to the organelle
| Organelle | Taxonomy suffix |
|---|---|
| nucleus | |
| nucleomorph | :nucl |
| plastid | :plas |
| apicoplast | :apic |
| chromatophore | :chrom |
| mitochondrion | :mito |
pr2database 4.13.0
- Released: 2021-03-17
- Detailed changes
Major groups for which taxonomy has been updated
- Dinophyceae, Suessiales - Taxonomy updated (J. del Campo)
- Stramenopiles, Diatoms, Thalassiosirales - Taxonomy updated (L. Arsenieff)
- Stramenopiles, Pelagophyceae - Taxonomy updated (Ana Maria Cabello)
- Stramenopiles, Chrysophyceae - Taxonomy updated (D. Vaulot)
pr2database 4.12.0
- Released: 2019-08-08
- Geolocalisation of sequences (D. Vaulot)
- Detailed changes
pr2database 4.11.0
- Released: 2018-10-30
- Various bug fixes. Remove sequences shorter than 500 bp (D. Vaulot)
- Chlorophyta - Three new classes introducted (Chloropicophyceae, Picocystophyceae, Palmophyllophyceae) - 198 sequences updated and 104 sequences added (A. Lopes dos Santos)
- Chlorophyta - Mamiellophyceae (Micromonas, Ostreococcus, Mantoniella) - 872 sequences updated and 8 sequences added (D. Vaulot)
- Ciliophora - Except Spirotrichea - 4550 sequences updated, 2478 sequences added, 652 sequences removed (Eukref - V. Boscaro)
- Detailed changes
pr2database 4.10.0
- Released: 2018-03-08
- Fixing artefactual sequences, removing chimeras and labelling reference sequences (D. Vaulot)
- Detailed changes
pr2database 4.9.0
- Released: 2018-02-20
- Dinophyceae - Incorporation of the DinoRef database (1564 sequences verified and updated, 213 added) (Solenn Mordret, Roberta Piredda, Diana Sarno)
- Detailed changes
pr2database 4.8.0
- Released: 2018-02-06
- Cercozoa, Perkinsea (30 sequences) (Martina Strittmatter)
- Detailed changes
pr2database 4.7.1
- Released: 2017-11-20
- Database transferred to GitHub
- Ciliates (Spirotrichea) (C. Bachy, Wei-Ting Chen)
- Database transferred to GitHub
- Detailed changes
pr2database 4.6
- Released: 2017-08-23
- Bolidophyceae corrected according to Kuwata et al. 2017 (3 env clades) (D. Vaulot)
- Pelagophyceae (D. Vaulot)
- Database on Figshare
pr2database 4.5
- Released: 2016-12-17
- Correct inconsistencies in taxonomy (D. Vaulot)
- Break Chrysophyceae-Synurophyceae into Chrysophyceae vs. Synurophyceae according to Algaebase (D. Vaulot)
- Correct Haptophyta taxonomy to follow PR2 rules (_X, _XX etc…) (D. Vaulot)
- Change CW-Chlamydomonadales to Chlamydomonadales (D. Vaulot)
- Correct minor dinoflagellates taxonomy (Karlodinium) (D. Vaulot)
- Database on Figshare
pr2database 4.4
- Released: 2016-11-10
- Bolidophyceae corrected according to Ichinomya et al. 2016 (D. Vaulot)
- Sequences with N removed (D. Vaulot)
- Sequences not in GenBank removed (D. Vaulot)
- Database on Figshare
pr2database 4.2
- Released: 2016-04-13
- Haptophyta assignations corrected (B.Edvardsen)
- Database on Figshare