R-Syst::Diatom

A curated barcoding database for diatoms and freshwater metabarcoding

-Microalgae have an exceptional diversity spread other all taxonomic kingdoms. Among the most important freshwater classes, Diatoms (above 100 000 taxa), Cyanobacteria (above 10 000 taxa), Chlorophyceae (above 6000 taxa), Zygophyceae (above 3000 taxa), Dinophyceae (above 500 taxa) show excellent biomonitoring properties for rivers and lakes. They are required by the WFD (Water Framework Directive) for environmental monitoring.

Database content:

Diatoms are the most represented strains in this R-Syst::Diatom. But Cyanobacteria and Chlorophyceae strains of the TCC are also represented: stats

  • Taxonomy:
    • Species name of the strains are given with the highest precision. Photos are available for the TCC strains (Thonon Culture Collection)
    • Taxonomy is following Round et al. 1990, Monnier et al. 2009 and up to date literature
  • Genetic: stats
    • Main barcodes: rbcL, 18S
    • Other barcodes are also available: 28S, cox1
  • Phenotype:
    • Cell sizes, biovolumes, shapes, chloroplasts are given for most diatom species (Rimet & Bouchez 2012)
  • Ecology:
    • biotic indices values, functional groups, life-forms and ecological features are given for most of freshwater and brackish diatom species.

Database management:

  • Data have three origins:
    • barcoded strains from the TCC (Thonon Culture Collection)
    • barcoded strains from the UK (D Mann, M Kelly, S Sato)
    • barcoded strains from NCBI (Nucleotide database)
  • Every 6 months new barcodes and strains from the TCC and NCBI are collected
  • The database is curated every 6 months following a rigorous workflow (Rimet et al. 2015)

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Citations:

Rimet F., Chaumeil P., Keck F., Kermarrec L., Vasselon V., Kahlert M., Franc A., Bouchez A., 2015. R-Syst::diatom: a barcode database for diatoms and freshwater biomonitoring - data sources and curation procedure. INRA Report, 14 pages http://dx.doi.org/10.5281/zenodo.31137

Frederic Rimet; Philippe Chaumeil; Francois Keck; Lenaïg Kermarrec; Valentin Vasselon; Maria Kahlert; Alain Franc; Agnes Bouchez. 2016. R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database, 2016, 1-21. http://database.oxfordjournals.org/content/2016/baw016.full?keytype=ref&ijkey=H324uA95JzzEomz


Database versions:

  • 23-02-2018: R-Syst::diatom v7
  • 20-03-2017: R-Syst::diatom v6
  • 18-02-2016: R-Syst::diatom v5
  • 16-09-2015: R-Syst::diatom v4
  • 13-02-2015: R-Syst::diatom v3
  • 16-09-2014: R-Syst::diatom v2
  • 28-11-2012: R-Syst::diatom v1

References:

Monnier O., Coste M. and Rosebery J. (2009) Une classification des taxons de l'Indice Biologique Diatomées (IBD, norme AFNOR NF T90-354, décembre 2007). Diatomania, 13, 17-47.

Rimet F. & Bouchez A., 2012. Life-forms, cell-sizes and ecological guilds of diatoms in European rivers. Knowledge and management of aquatic ecosystems, 406: 1-14.

Round, F., Crawford, C. G., and Mann, D.G. (1990) The diatoms. Biology and morphology of the genera. Cambridge University Press. 747 p.