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Database (Oxford). 2016 Mar 17;2016. pii: baw016. doi: 10.1093/database/baw016. Print 2016.

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.

Author information

1
INRA-UMR Carrtel, 75 Av. De Corzent-BP 511, Thonon Les Bains Cedex FR-74203, France UMR CARRTEL, University of Savoie, Le Bourget Du Lac FR-73370, France frederic.rimet@thonon.inra.fr.
2
INRA, UMR BioGeCo, 69 Route D'arcachon, Cestas Cedex FR-33612, France University of Bordeaux 1, UMR BioGeCo, Talence FR-33400, France.
3
INRA-UMR Carrtel, 75 Av. De Corzent-BP 511, Thonon Les Bains Cedex FR-74203, France UMR CARRTEL, University of Savoie, Le Bourget Du Lac FR-73370, France.
4
ASCONIT Consultants, Naturopôle-Bât. C, 3, Bd De Clairfont, Toulouges FR-66350, France, and.
5
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, PO Box 7050, Uppsala SE-750 07, Sweden.

Abstract

Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/.

PMID:
26989149
PMCID:
PMC4795936
DOI:
10.1093/database/baw016
[Indexed for MEDLINE]
Free PMC Article

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