pr2database 4.14.0

Released: 2021-06-25

Detailed changes

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

Major groups for which taxonomy has been updated

  • Apicomplexa
  • Labyrinthulids
  • Radiolaria
  • Foraminifera
  • Radiolaria

pr2database 4.13.0

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)

Other changes

  • Adding sequences from the Roscoff Culture Collection (D. Vaulot)
  • Adding sequences from Silva identical to existing sequences in PR2 based on hash sequence value.
  • Adding Silva taxonomic annotation (D. Vaulot)

pr2database 4.12.0

  • Released: 2019-08-08
  • Geolocalisation of sequences (D. Vaulot)
  • Detailed changes

Major groups for which taxonomy has been updated

  • Apicomplexa - Taxonomy updated - 2619 new sequences, 5889+239 sequences updated, 89 sequences removed (J. del Campo)
  • Chaetoceros - 196 new sequences added and taxonomy updated (C. Gaonkar)
  • Stramenopiles - Taxonomy updated (R. Massana)

Other changes

  • 16S plastid and cyanobacteria sequences added from PhytoRef database (J. Decelle/ D. Vaulot)

pr2database 4.11.1

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 4.3

  • Released: 2016-09-04
  • Chlorophyta (D. Vaulot)
  • Database on Figshare

pr2database 4.2

  • Released: 2016-04-13
  • Haptophyta assignations corrected (B.Edvardsen)
  • Database on Figshare

pr2database 4.1

  • Released: 2015-10-23
  • RCC Chlorophyta (M.Tragin)

pr2database 4.0

  • Released: 2015-10-21
  • Haptophyta (B. Edvardsen)

pr2database 3.0

  • Released: 2015-08-31
  • Chlorophyta (M. Tragin)

pr2database 2.0

  • Released: 2015-02-07
  • Rhizaria (T. Biard)

pr2database 1.1

  • Released: 2015-01-04
  • Transfer from previous PR2 database (D. Vaulot)