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PR2 version 5.1.0

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@vaulot vaulot released this 02 Apr 14:55
· 30 commits to master since this release
v5.1.0.0
3dd700e

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Main changes

Ribosomal Operon database (ROD)

  • Version 1.2 is now integrated in the Web interface.

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

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

Detailed changes

Ribosomal Operon database (ROD)

Taxonomic groups updated

TSAR

  • Apicomplexa
    • Numbers in species names have been removed
    • Numbers are kept in genera names (e.g. Cryptosporidium1, 2 etc...)
  • Dinophyceae - Suessiales
    • Number of chimera : 37
    • Number of sequences annotated : 436
      • Number of sequences reannotated: 189
      • Number of sequences newly annotated: 247
    • Number of taxa added : 6
  • Dinophyceae - Gonyaulax, Alexandrium, Amphidinium, Heterocapsa, Azadinium
    - Number of removed : 25 (Sequences which include ITS and 28S)
    • Number of valid sequences to update : 450
      • Number of sequences in update not annotated: 406
      • Number of sequences in update annotated: 44
    • Number of taxa added : 10
  • Diatoms
    • Minidiscus_comicus renamed Mediolabrus_comicus (Li et al. 2020 J. Phycol)
    • Attheya and Thalassiosira_aestivalis reassigned
  • Foraminifera
    • Number of updated or verified sequences: 158
    • Number of newly annotated sequences: 410
    • Number of taxa updated : 10
    • Number of taxa added : 1

Archaeplastida

  • Rhodophyta - Ceramiales and Batrachospermales
    • Number of quarantined : 3
    • Number of sequences reannotated : 518
    • Number of new sequences added: 150
    • Number of taxa updated : 255
    • Number of taxa added : 70
    • Number of taxa removed : 182
  • Picozoa
    • Tree and alignement available
    • Five clades defined at the subdivision level (1A, AB, 2, 3, 4)
    • Number of updated or verified sequences: 279
    • Number of newly annotated sequences 168
    • Sequences removed: 2 (not Picozoa)
    • Chimera removed: 16
    • Number of taxa added : 6
  • Mamiellophyceae
    * Ostreococcus bengalensis (nomen nudum)
  • Pseudoscourfieldiophyceae - new class
    • Pycnococcus is now a synonym of Pseudoscourfieldia
  • Chloropicophyceae & Picocystophyceae
    * Tree
    * Assignation of 151 sequences
    * 3 chimera detected
    * 1 bad sequence removed
    * 2 ITS sequences removed

Haptista

  • Haptophyta
    • Emiliania_huxleyi renamed Gephyrocapsa_huxleyi (Bendif et al. 2023)

Obazoa

  • Metazoa - Non bilaterian
    • 105 sequences quarantined
  • Fungi
    • New phylum used Sanchytriomycota following Galindo et al. 2021.
    • Chytridiomycota and Aphelidiomycota
      • New taxonomic entries: 25 new species added
      • New sequecnes: 792
      • Sequences quarantined: 19

Excavata

  • Euglenophyceae classification changed to match Botanical code from Algaebase
    • Euglenophyceae is now a class and order and family follow Phycology usage

Taxonomy additions and corrections

  • Taxonomic entries added or corrected: 5874
  • Some species names corrected using -instead of _
  • GBIF database: About 800 taxonomic entries corrected

New, deleted and updated records

  • Detailed changes

  • Annotated entries added: 19,509

    • This includes in particular GenBank records from 2023-02-21 to 2025-03-10

  • Annotated entries with updated taxonomy: 7,375

  • Annotated entries quarantined: 43

  • Annotated entries removed: 2683

  • All entries from version 5.0 (annotated and not) were analyzed with the rRNA detecting program barrnap

    • Entries for which 18S could not be detected were removed: 2450 .
    • Entries for which 18S was coded on reverse strand were removed: 22
    • Entries (27,055) for which the end of the 18S gene was detected more than 50 bp downstream of the present location were shortened, following which some entries were shorter than the minimum requirement of the PR2 sequences (500 bp) and therefore removed.

Traits

The following functional traits are now available

Harmful Algal Bloom species

  • Downloaded from https://www.marinespecies.org/hab/index.php on 2025-02-05
  • Only eukaryotic and accepted species have been included
    Ecological function
  • The traits have been imported from Sommeria-Klein et al. 2021 supplementary material
  • Taxa for which the traits were missing have been added based on the literature.

References

  • Bendif, E.M., Probert, I., Archontikis, O.A., Young, J.R., Beaufort, L., Rickaby, R.E. & Filatov, D. 2023. Rapid diversification underlying the global dominance of a cosmopolitan phytoplankton. ISME J. 1–11.
  • Crépeault, O., Otis, C., Pombert, J.-F., Turmel, M. & Lemieux, C. 2024. Comparative plastome and mitogenome analyses indicate that the marine prasinophyte green algae Pycnococcus provasolii and Pseudoscourfieldia marina (Pseudoscourfieldiophyceae class nov., Chlorophyta) represent morphotypes of the same species. Journal of Phycology. 60:1021–7.
  • Galindo, L.J., López-García, P., Torruella, G. et al. Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota. Nat Commun 12, 4973 (2021). doi/ 10.1038/s41467-021-25308-w
  • Krabberød, A.K., Stokke, E., Thoen, E., Skrede, I. & Kauserud, H. 2025. The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies. Molecular Ecology Resources. 25:e14031.
  • Sommeria-Klein, G., Watteaux, R., Ibarbalz, F.M., Pierella Karlusich, J.J., Iudicone, D., Bowler, C. & Morlon, H. 2021. Global drivers of eukaryotic plankton biogeography in the sunlit ocean. Science. 374:594–9.
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