Abstract
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. Usually, diatoms are identified using characteristics of their exoskeleton morphology. 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 analyses under microscope. 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. Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. Since 2017, several experts have collaborated to curate this library for rbcL, a chloroplast marker suitable for species-level identification of diatoms. For the latest version of the database (version 7), 605 of the 3482 taxonomical names originally assigned by the authors of the rbcL sequences were modified after curation. The database is accessible at https://www6.inra.fr/carrtel-collection_eng/Barcoding-database.
Highlights
Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters
Diatoms often represent an important part of the total biomass in aquatic ecosystems and make a major contribution to global productivity, and cannot be ignored in ecological studies (e.g.10)
Diatoms are identified by looking at the gestalt and morphology of their siliceous exoskeleton using a microscope
Summary
Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. By comparing each HTS sequence to the barcode reference library, the composition of the environmental community can be ascertained For diatoms this method was first tested on mock communities made of already-barcoded strains[12] and on natural communities from several temperate or tropical rivers[23,24], lakes[25,26], marine habitats[27,28] and even ancient diatom DNA (e.g.29,30). The general point raised by all these metabarcoding studies is that an Achilles heel of metabarcoding is the barcode reference library It must be as comprehensive as possible in order to be able to assign a high proportion of environmental sequences to known taxa, and it requires regular expert curation in order to maintain its quality (i.e. taxonomic assignments, sequences quality and traceability of data and metadata). E.g. PhytoREF for photosynthetic organisms[34], PFR2 for planktonic foraminifera (Morard et al.35), EukRef-Ciliophora for ciliates[36] and Dinoref for Dinophyceae[37], the last database has been integrated in PR2
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