Revision history - detailed

Version 4.12.0

Date : 8 August 2019

https://github.com/pr2database/pr2database/releases/tag/v4.12.0

Major changes

  • Apicomplexa taxonomy completely updated with more than 2600 new sequences
  • Inclusion of more than 6,000 16S plastid and cyanobacteria sequences from the PhytoRef database
  • Stramenopiles taxonomy updated
  • Geolocalisation of sequences more than 90,000 sequences with at least country or ocean coordinates

Version 4.11.1

Date : 13 December 2018

https://github.com/pr2database/pr2database/releases/tag/4.11.1

Mostly small changes and bug fixes

Version 4.11.0

Date : 30 October 2018

https://github.com/pr2database/pr2database/releases/tag/4.11.0

Major changes

  • Chlorophyta
  • Ciliates (from EukRef workshop)
  • Database provided as R datafile

References

  • Boscaro V., Santoferrara L., Zhang Q., Gentekaki E., Syberg-Olsen M., del Campo J., Keeling P., 2018. EukRef–Ciliophora: A manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates. Environmental Microbiology, 20: 2218-2230.

Version 4.10.0

Incorporate data from original PR2 database from L. Guillou

  • 1102 PR2 sequences were longer than the corresponding GenBank sequences (see Issue #6). Some of these sequences were recovered from the original PR2 database (from 2012) while some other were reextracted from the GenBank record.
  • 7 PR2 sequences that were identified as chimeras in the original PR2 database have been removed
  • 21537 PR2 sequences have been labelled as reference sequences from the original PR2 database.

Version 4.9.2

Minor changes. Two entries have been fixed:

  • LC054938.1.1770_U - Taxonomy had a hard return in one the field
  • KJ995958.1.1684_U - Had a space before the PR2 accession id

Version 4.9.1

This is a minor update.

The taxonomy of the following three sequences has been fixed.

  • FJ402948.1.1186_U
  • FJ402949.1.1210_U
  • LC054937.1.1751_U

The wiki has also been updated to explain how to convert files from UNIX to DOS.

Version 4.9.0

Annotators : Solenn Mordret, Roberta Piredda, Diana Sarno, SZN, Naples
Date : 20-02-2018
* R script used to update to 4.9.0

Dinoflagellata

Taxonomy edited following Mordret et al. (2018) .

  • Division : “Dinophyta” changed to “Dinoflagellata”
  • Number of taxa edited : 557
  • Sequences with taxonomy verified and/or updated : 1564
  • Sequences added : 213
  • Sequences with metadata complemented (life_style, host, env_biome, references) : 1658

A set of 1657 sequences have been labelled as references for dinoflagellates.

References

Mordret, S., Piredda, R., Vaulot, D., Montresor, M., Kooistra, W.H.C.F. & Sarno, D. 2018. DINOREF : A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Mol. Ecol. Resour. 18:974–87.

Version 4.8.0

Annotators : “Martina Strittmatter” mstrittmatter@sb-roscoff.fr
Date : 06-02-2018

Cercozoa

  • Taxonomy updated : 12 sequences
  • Added : 16 sequences

Perkinsea

  • Taxonomy updated : 2 sequences

Version 4.7.2

Annotators : Wei-Ting Chen
Date : 22-11-2017

Ciliates

  • Taxonomy updated for 31 sequences

Version 4.7.1

Annotators : Daniel Vaulot (Roscoff)
Date : 07-10-2017

Bug fix

  • Remove space at the end of some taxonomy fields that caused errors in Mothur

Version 4.7.0

Annotators : Charles Bachy and Wei-Ting Chen, Daniel Vaulot (Roscoff)
Date : 27-09-2017

New file type for download

  • pr2_version_4.7_merged_Eukaryota.zip contains the whole PR2 database as flat file (sequence, assignation, metadata)

Updates for constraints for new sequences

  • Number of ambiguities <= 20
  • Length > 600 (to accommodate EukRef)

Ciliates - Class Spirotrichea - Orders Oligotrichia and Choreotrichia (3081 sequences)

Removal of sequences

  • 60 sequences (AB640624 to AB640683) that are questionable in terms of species identification and sequence quality have been removed (Kazama et al., 2012).

Revision in Classification Systems of Choreotrichia and Oligotrichia

  • The order Choreotrichia Oligotrichia is now Subclass Choreotrichia Oligotrichia (note that SubClass is not taken into account in PR2)
  • There are 2 orders in Choreotrichia
    • Choreotrichida
    • Tintinnida.
  • There is 1 order in Oligotrichia.
    • Strombidiida

Tintinnida

  • Change “Choreotrichia” to “Tintinnida”.
  • Updated informal classification of incertae sedis in Tintinnida.
  • Tintinnopsis clades I-IX which are shortened as TIPS I-IX are informal classification for Tintinnopsis (Bachy et al., 2012; Agatha and Strüder-Kypke, 2014; Zhang et al., 2017). Santoferrara et al. ( 2017) added Tintinnopsis and related related genera (Climacocylis, Helicostomella, Leprotintinnus, Rhizodomus and Stylicauda) which are labeled as Tintinnida 1 to 11(TIN_1-11 in PR2).
  • Correction and updated Family names
    • Choreotrichida
      • Change all “Choreotrichia” to “Choreotrichida”
      • Add “Leegaardiellidae”
    • Strombidiida
      • Change all “Oligotrichia” to “Strombidiida”
      • Add “Cyrtostrombidiidae” and “Pelagostrombidiidae”

New sequences

  • 183 sequences were added including 15 sequences submitted to Genbank (accession number MF*)
    • Choreotrichida - 14
    • Strombidiida - 46
    • Tintinnida – 123

References

  • Agatha, S. and Strüder-Kypke, M.C. (2014) What Morphology and Molecules Tell Us about the Evolution of Oligotrichea (Alveolata, Ciliophora). Acta Protozool. 2014: 7790.
  • Bachy, C., Gómez, F., López-García, P., Dolan, J.R., and Moreira, D. (2012) Molecular Phylogeny of Tintinnid Ciliates (Tintinnida, Ciliophora). Protist 163: 873–887.
  • Kazama, T., Ishida, S., Shimano, S., and Urabe, J. (2012) Discrepancy between conventional morphological systematics and nuclear phylogeny of tintinnids (Ciliophora: Choreotrichia). Plankton Benthos Res. Jt. J. Plankton Soc. Jpn. Jpn. Assoc. Benthol. 7: 111–125.
  • Santoferrara, L.F., Alder, V.V., and McManus, G.B. (2017) Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea). Mol. Phylogenet. Evol. 112: 12–22.
  • Zhang, Q., Agatha, S., Zhang, W., Dong, J., Yu, Y., Jiao, N., and Gong, J. (2017) Three rDNA Loci-Based Phylogenies of Tintinnid Ciliates (Ciliophora, Spirotrichea, Choreotrichida). J. Eukaryot. Microbiol. 64: 226–241.

Version 4.6.2

Annotators : Daniel Vaulot (Roscoff)
Date : 11-09-2017

Minor changes

  • Remove 59 sequences which were duplicated
  • All files now are DOS compatible (lines terminated by /r /n)

Version 4.6.1

Annotators : Daniel Vaulot (Roscoff)
Date : 06-09-2017

Minor changes

  • Removed 3091 sequences that had more than 20 ambiguities (“N”)
  • Haptophyta : 32 chimeras detected by B. Edvardsen added (these are not exported but latter we will provide a list of chimeras on the web site)
  • Mothur taxonomy file fixed (taxonomy was separated by tab and not ;)

Version 4.6.0

Annotators : Daniel Vaulot (Roscoff)
Date : 25-08-2017

Bolidophyceae

  • Correct taxonomy based on Kuwata et al. Frontiers in Microbiology in prep.
  • Define a new environmental clade III
  • 5 chimeras removed
  • Add 18 new sequences

    Pelagophyceae

  • Align taxonomy on Algaebase (2 orders)

  • Create a Pelagomonadaceae_clade_A_sp. which corresponds to endosymbiont of Amphisolenia

  • Include 47 new sequences

  • Remove 3 sequences that seem very noisy

Chrysophyceae

  • Add “Chrysophyceae_” to genus and species corresponding to clades, e.g. : “Chrysophyceae_Clade-F_X_sp.” replaces “Clade-F_X_sp.”

Picobiliphyta

  • Name changed to Picozoa

Chlorophyta

  • clade “Indien” moved to “Chlorophyta_X”

Other changes

  • Species containing “strain” have been cleaned by removing the string “strain”
  • Metadata from GenBank added as an additional file available for download

Version 4.5.0

Annotators : Daniel Vaulot (Roscoff)
Date :17-01-2017

Correct inconsistencies in taxonomy

  • If ranks 1 to 6 are inconsistent with ranks 7 and 8 (genus, species), rank 7 and 8 are changed to reflect the real taxonomy (this occurs in particular when sequence of parasites are attributed to the host)
  • When one level (e.g. 7 = genus) corresponds to two different upstream levels, then the taxonomy has been fixed.
  • Following this correction
    • No taxonomic name occurs at two different levels (e.g. the same name occurs at the class and order)
    • Any taxonomic name have only a single parent name (e.g. a given order is always part of the same class)
    • If a parasite has been detected in a host the genus and species are named after the parasite and not the host

Chrysophyceae

  • Break Chrysophyceae-Synurophyceae into Chrysophyceae vs. Synurophyceae according to Algaebase

Haptophyta

  • Correct Haptophyta taxonomy to follow PR2 rules (_X, _XX etc…)

Chlorophyta

  • Change CW-Chlamydomonadales to Chlamydomonadales

Dinophyta

  • Correct minor dinoflagellates taxonomy (Karlodinium)

Version 4.4.0

Annotators : Daniel Vaulot (Roscoff)
Date : 10-11-2016

Bolidophyceae

  • Taxonomy corrected according to Ichinomiya, M., dos Santos, A.L., Gourvil, P., Yoshikawa, S., Kamiya, M., Ohki, K., et al. (2016) Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME J. 10: 2419–2434.

Misc changes

  • Insertion in sequences removed
  • Sequences not in GenBank removed
  • Sequences with a large number of N removed

Version 4.3.0

Annotators : Daniel Vaulot (Roscoff)
Date : 04-09-2016

Chlorophyta

  • “Eukaryota;Archaeplastida;Chlorophyta” replaced by “Eukaryota;Archaeplastida;Chlorophyta” in 199 entries

Version 4.2.0

Annotators : Bente Edvardsen (Oslo)
Date : 13-04-2016

Haptophyta

  • Chimeras checked.

Version 4.1.0

Annotators : Margot Tragin (Roscoff)
Date : 23-10-2015

Chlorophyta

  • 223 Chlorophyta sequences from the RCC (accession number ZZ) were deleted and replaced by 199 RCC Chlorophyta sequences submitted to Genbank (accession number KT)

Version 4.0.0

Annotators : Bente Edvardsen (Oslo)
Date : 21-10-2015

Haptophyta

Version 3.0.0

Annotators : Margot Tragin (Roscoff)
Date : 14-09-2015

Chlorophyta

  • Corrections of Taxonomical Affilation according to Tragin et al. 2016
    • 1225 (on 8777) taxonomical assignations modified
    • Name class Prasino-clade-I corrected in in Prasino-clade-9
    • 3 sequences of Nephroselmidophyceae reassigned to Prasino-clade-VIII:
      • EU143504
      • EU143505
      • EU143506
    • Ulvophyceae, Trebouxiophyceae and Chlorophyceae taxonomical assignation not checked

Reference

Tragin, M., Lopes dos Santos, A., Christen, R. & Vaulot, D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. Perspect. Phycol. 3:141–54.

Chimera

  • 76 sequences tagged as chimera and removed from the mothur files but not from the Access database

New sequences added

  • 223 addition of new sequences from the RCC (accession number ZZ*). These sequences are not submitted to GenBank yet

Version 2.0.0

Annotators : Tristan Biard (Roscoff)
Date : 02-07-2015

Rhizaria : Nasselaria, Collodaria, Phaeodaria

  • Curation Of The Original Pr2 Database:
    • Removal of 6 ambiguous sequences (see Biard et al. 2015 - Protist)
      • AY266297
      • AF057741
      • AF057742
      • AF057743
      • AF057744
      • AF018160
  • Correction Of Taxonomical Classification In The Rhizaria:
    • Collodaria (changes based on Biard et al. 2015 - Protist)
      • Change “Collodaria-Nassellarida” to “Collodaria”
      • Correction of family names (Sphaerozoidae, Collosphaeridae, Collophidiidae)
      • Correct the species name of sequence AF018162 to “Collophidium_serpentinum”
    • Nassellaria (i.e. Nassellarida) (changes based on Suzuki and Not - in press)
      • Change all “Nassellarida” to “Nassellaria”
      • Change “Collodaria-Nassellarida” to “Nassellaria”
      • Correction of family names
    • Phaeodaria (changes based on Nakamura et al. 2015 - Protist)
      • Change “Filosa-Phaeodarea” to “Phaeodarea”
      • Correction of family names

Insertion of new Sequences:

Collodaria

  • 62 new 18S sequences extracted from Biard et al. (2015 - Protist)

Phaeodaria

  • 39 new 18S sequences extracted from Nakamura et al. (2015 - Protist)

Symbiotic Dinoflagellates

  • 2 new sequences from Probert et al. 2014 (J. Phycol)
  • 1 new sequence from Biard et al. (Unpublished)

Version 1.1.0

Annotators : Daniel Vaulot

Data base created

  • from version downloaded from PR2 web site based on Genbank release 203

Changes

  • remove sequences that are only in one of the files
  • remove sequences which were duplicated
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Daniel Vaulot
NTU, Singapore

Focusing on marine (pico)phytoplankton .