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ARPHA Conference Abstracts :
Conference Abstract
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Frederic Rimet‡, Teofana Chonova‡, Gilles Gassiole§, Maria Kahlert|, François Keck¶, Martyn Kelly#, Maxim Kulikovskiy¤, David Mann«, Martin Andreas Pfannkuchen», Ana Baričević˄, Rosa Trobajo˅, Valentin Vasselon¦, Jonas Zimmermannˀ, Carlos Eduardo Wetzelˁ, Agnès Bouchez‡,₵|
Corresponding author: Frederic Rimet (frederic.rimet@inra.fr)
Received: 24 Feb 2021 | Published: 04 Mar 2021
© 2021 Frederic Rimet, Teofana Chonova, Gilles Gassiole, Maria Kahlert, François Keck, Martyn Kelly, Maxim Kulikovskiy, David Mann, Martin Pfannkuchen, Ana Baričević, Rosa Trobajo, Valentin Vasselon, Jonas Zimmermann, Carlos Wetzel, Agnès Bouchez
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Rimet F, Chonova T, Gassiole G, Kahlert M, Keck F, Kelly M, Kulikovskiy M, Mann D, Pfannkuchen MA, Baričević A, Trobajo R, Vasselon V, Zimmermann J, Wetzel CE, Bouchez A (2021) Diat.barcode: a DNA tool to decipher diatom communities for the evaluation environmental pressures. ARPHA Conference Abstracts 4: e64940. https://doi.org/10.3897/aca.4.e64940
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Abstract
Diatoms (Bacillariophyta) are ubiquitous microalgae, which present a huge taxonomic diversity, changing in correlation with differing environmental conditions. This makes them excellent ecological indicators for various ecosystems and ecological problematics (ecotoxicology, biomonitoring, paleo-environmental reconstruction …).
Current standardized methodologies for diatoms are based on microscopic determinations, which is time consuming and prone to identification uncertainties. DNA metabarcoding has been proposed as a way to avoid these flaws, enabling the sequencing of a large quantity of barcodes from natural samples. A taxonomic identity is given to these barcodes by comparing their sequences to a barcoding reference library. However, to identify environmental sequences correctly, the reference database should contain a representative number of reference sequences to ensure a good coverage of diatom diversity. Moreover, the reference database needs to be carefully taxonomically curated by experts, as its content has an obvious impact on species detection.
Diat.barcode is an open-access library for diatoms linking diatom taxonomic identities to rbcL barcode sequences (a chloroplast marker suitable for species-level identification of diatoms), which has been maintained since 2012. Data are accumulated from three sources: (1) the NCBI nucleotide database, (2) unpublished sequencing data of culture collections and more recently (3) environmental sequences. Since 2017, an international network of experts in diatom taxonomy curate this library. The last version of the database (version 9.2), includes 8066 entries that correspond to more than 280 different genera and 1490 different species. In addition to the taxonomic information, morphological features (e.g. biovolumes, chloroplasts, etc.), life-forms (mobility, colony-type) and ecological features (taxa preferences to pollution) are given.
The database can be downloaded from the website (www6.inrae.fr/carrtel-collection/Barcoding-database/) or directly through the R package diatbarcode. Ready-to-use files for commonly used metabarcoding pipelines (Mothur and DADA2) are also available.
Keywords
Diat.barcode, reference database, diatoms, rbcL, DNA metabarcoding, biological indicators, environmental pressures
Presenting author
Frédéric RIMET
Presented at
1st DNAQUA International Conference (March 9-11, 2021)
Author contributions
Frédéric Rimet 1,2*, Teofana Chonova1,2, Gilles Gassiole3, Maria Kahlert4, Francois Keck1, 5,, Martyn G. Kelly6, Maxim Kulikovskiy7, David G. Mann8,9, Martin Pfannkuchen10, Ana Baričević10, Rosa Trobajo9, Valentin Vasselon11, Jonas Zimmermann12, Carlos Wetzel13 & Agnès Bouchez1,2
*corresponding author
underlined: presenting author
>1 INRAE, UMR CARRTEL, 75bis av. de Corzent - CS 50511, FR-74203, Thonon les Bains cedex, France.
2 University of Savoie Mont-Blanc, UMR CARRTEL, FR-73370, Le Bourget du Lac, France.
3 MicPhyc, 88 chemin Manouilh - Ilet à Vidot, 97433 Salazi, France
4 Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE- 750 07, Uppsala, Sweden.
5 Eawag, Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
6 Bowburn Consultancy, 11 Monteigne Drive, Bowburn, Durham, DH6 5QB, UK.
7 Institute of Plant Physiology, Russian Academy of Sciences, 127276, Moscow, Russia.
8 Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, Scotland, UK.
9 Marine and Continental Waters, Institute for Food and Agricultural Research and Technology (IRTA), Crta de Poble Nou Km 5.5, Sant Carles de la Rapita, Catalonia, Spain.
10 Institut Ruđer Bošković, Giordano Paliaga 5, 52210, Rovinj, Croatia.
11 SCIMABIO Interface, 5 rue des Quatre Vents 74200 Thonon-les-Bains, France
12 Botanischer Garten und Botanisches Museum Berlin–Dahlem, Freie Universität Berlin, Königin–Luise–Str. 6–8, 14195, Berlin, Germany.
13 Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, 41 rue du Brill / L-4422 Belvaux, Luxembourg