Diat.barcode, an open-access barcode library for diatoms

DOI

Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems, and can also be used to reconstruct paleoenvironments. Usually, diatoms are identified using characteristics of their exoskeleton morphology, which can be time consuming and error-prone. DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than if specialist analysts are used. However, to identify environmental sequences correctly, an expertly curated reference library is needed. Several curated libraries for protists exists; none, however, are dedicated to diatoms. Diat.barcode is an open-access library dedicated to diatoms which has been maintained since 2012. It was initiated with the barcoding network of INRA (French National Institute for Agricultural Research) R-Syst, is now an international initiative partly supported by a Cost network (DNAqua-net). Data come from two sources (1) the NCBI nucleotide database (National Center for Biotechnology Information) and (2) unpublished sequencing data of culture collections in France, UK and Russia. Since 2017, several European experts have collaborated to curate this library for rbcL, a chloroplast marker suitable for species-level identification of diatoms. For the latests versions of the database, more than 8100 curated barcodes are available. The database is accessible through https://www6.inra.fr/carrtel-collection_eng/Barcoding-database. A ready-to-use subset of the database for metabarcoding analyses is also accessible.

Identifier
DOI https://doi.org/10.15454/TOMBYZ
Metadata Access https://entrepot.recherche.data.gouv.fr/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.15454/TOMBYZ
Provenance
Creator Rimet, Frederic; Chonova, Teofana; Gassiole, Gilles; Gusev, Evgenuy; Kahlert, Maria; Keck, François; Kelly, Martyn; Kochoska, Hristina; Kulikovskiy, Maxim; Levkov, Zlatko; Maltsev, Yevhen; Mann, David; Nicolosi Gelis, Maria Mercedes; Pfannkuchen, Martin; Trobajo, Rosa; Vasselon, Valentin; Vidakovic, Danijela; Wetzel, Carlos; Zimmermann, Jonas; Bouchez, Agnès
Publisher Recherche Data Gouv
Contributor Rimet, Frederic
Publication Year 2018
Rights etalab 2.0; info:eu-repo/semantics/openAccess; https://spdx.org/licenses/etalab-2.0.html
OpenAccess true
Contact Rimet, Frederic (INRAE - Institut national de recherche pour l'agriculture, l'alimentation et l'environnement)
Representation
Resource Type Dataset
Format application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
Size 1268504; 1509006; 1714558; 1724433; 1857822; 2039691; 4291975; 4300874; 6384192; 6373698; 6709412; 6802232; 6226746; 6250151; 7385769; 7448813; 7445614
Version 17.0
Discipline Geosciences; Life Sciences; Biology; Omics; Microbial Ecology and Applied Microbiology; Ecology; Hydrology and Hydrogeology