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PR2 version 4.13.0

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@vaulot vaulot released this 17 Mar 01:28
· 74 commits to master since this release
v4.13.0
7f57f11

Summary

List of sequences added or updated

  • Added: 2966
  • Updated: 933
  • Removed: 3817

Contributors

Taxonomy curated

  • Alveolata

    • Dinophyceae - Suessiales curated by J. del Campo following Janouškovec et al. (2017) and LaJeunesse et al. (2018)

  • Stramenopiles

    • Diatoms - Thalassiosirales - L. Arsenieff following Arsenieff et al. (2020)
    • Pelagophyceae - A. M. Cabello - definition of new environmental clades
      • sequences updated: 30
    • Pelagophyceae, Sarcinochrysidales - From Han et al. 2018.
      • sequences added: 14
    • Chrysophyceae - From Andersen et al. 2017

  • Chlorophyta

    • Pyramimonadales replaced by Pyramimonadophyceae following Daugbjerg et al. (2019)
    • New division Prasinodermophyta and new Class Prasinodermophyceae following Li et al. (2020)

Sequences added to PR2

  • 1,129 18S sequences from the Roscoff Culture Collection (script - Cultures)
  • 1,824 18S sequences from Silva version 138 and Genbank annotated based on hash value of sequences

Sequences uploaded but not yet annotated

  • 7,032 18S rRNA sequences added from GenBank - 2018-11 to 2020-05 - script

  • 333,247 18S rRNA sequences from Silva version 138 (2019-12)

Metadata

Sequences removed

  • 3817 sequences have been removed from the database
    • potential chimera
    • bad sequences
    • sequences containing at least 2 consecutive Ns (e.g. ...ATTNNGC..)

References

  • Daugbjerg N., Fassel NMD., Moestrup Ø. 2019. Microscopy and phylogeny of Pyramimonas tatianae sp. nov. (Pyramimonadales, Chlorophyta), a scaly quadriflagellate from Golden Horn Bay (eastern Russia) and formal description of Pyramimonadophyceae classis nova . European Journal of Phycology 0:1–15. DOI: 10.1080/09670262.2019.1638524
  • Janouškovec, Jan, Gregory S. Gavelis, Fabien Burki, Donna Dinh, Tsvetan R. Bachvaroff, Sebastian G. Gornik, Kelley J. Bright, et al. 2017. Major Transitions in Dinoflagellate Evolution Unveiled by Phylotranscriptomics. Proceedings of the National Academy of Sciences 114 (2): E171–80. https://doi.org/10.1073/pnas.1614842114.
  • LaJeunesse, Todd C., John Everett Parkinson, Paul W. Gabrielson, Hae Jin Jeong, James Davis Reimer, Christian R. Voolstra, and Scott R. Santos. 2018. Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts. Current Biology 28 (16): 2570-2580.e6. https://doi.org/10.1016/j.cub.2018.07.008.
  • Arsenieff L., Le Gall F., Rigaut-Jalabert F., Mahé F., Sarno D., Gouhier L., Baudoux A-C., Simon N. 2020. Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. The ISME Journal. DOI: 10.1038/s41396-020-0659-6.
  • Han KY., Graf L., Reyes CP., Melkonian B., Andersen RA., Yoon HS., Melkonian M. 2018. A Re-investigation of Sarcinochrysis marina (Sarcinochrysidales, Pelagophyceae) from its Type Locality and the Descriptions of Arachnochrysis, Pelagospilus, Sargassococcus and Sungminbooa genera nov. Protist 169:79–106. DOI: 10.1016/j.protis.2017.12.004.
  • Andersen RA., Graf L., Malakhov Y., Yoon HS. 2017. Rediscovery of the Ochromonas type species Ochromonas triangulata (Chrysophyceae) from its type locality (Lake Veysove, Donetsk region, Ukraine). Phycologia 56:591–604. DOI: 10.2216/17-15.1.
  • Li L., Wang S., Wang H., Sahu SK., Marin B., Li H., Xu Y., Liang H., Li Z., Cheng S., Reder T., Çebi Z., Wittek S., Petersen M., Melkonian B., Du H., Yang H., Wang J., Wong GK., Xu X., Liu X., Van de Peer Y., Melkonian M., Liu H. 2020. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Nature Ecology & Evolution. DOI: 10.1038/s41559-020-1221-7.

Database structure

  • Table pr2_metadata - add fields

    • pr2_depth: depth of sample in meters
    • gb_id: Genbank ID number (big integer)
    • gb_project_id: Genbank project ID for metagenomes
    • gb_sequence - original gb_sequence (longtext)

  • Table pr2_metadata - remove fields and move to list_countries table

    • pr2_continent
    • pr2_country_geocode
    • pr2_country_lon
    • pr2_country_lat

  • New Tables (for internal use only)

    • list_countries - Table with information on each country
      • pr2_country
      • pr2_continent
      • pr2_country_geocode
      • pr2_country_lon
      • pr2_country_lat
    • pr2_assign_bayes - Contains assignement of uncurated sequences using dada2::AssignTaxonomy against PR2 4.12.0
    • pr2_assign_silva - Contains assignement of uncurated sequences from Silva version 138

Scripts

Scripts (see links above) are just provided to show some of the procedures used to update the PR2 database. Do not try to run them, they will not work as they require access to the MySQL PR2 database.

Files provided

  • For this version we do not provide the SQLite format. It will be provided again for relase 5.0.0
  • A version of the database compatible with the DECIPHER R package is available here
  • Files also available on Zenodo
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