Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms

Autor: Lenaïg Kermarrec, Agnès Bouchez, Jean-François Humbert, Frédéric Rimet, Philippe Chaumeil, Alain Franc
Přispěvatelé: Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Asconit Consultants, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Biogéochimie et écologie des milieux continentaux (Bioemco), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)
Jazyk: angličtina
Rok vydání: 2013
Předmět:
0106 biological sciences
benthic diatom diversity
Ribulose-Bisphosphate Carboxylase
species inventories
[SDV]Life Sciences [q-bio]
Molecular Sequence Data
Fresh Water
Biology
01 natural sciences
Genome
DNA
Mitochondrial
DNA
Ribosomal
DNA sequencing
law.invention
Molecular ecology
Electron Transport Complex IV
03 medical and health sciences
law
environmental communities
Genetics
RNA
Ribosomal
18S
molecular ecology
Ecology
Evolution
Behavior and Systematics
Polymerase chain reaction
030304 developmental biology
Diatoms
0303 health sciences
010604 marine biology & hydrobiology
Genetic Variation
High-Throughput Nucleotide Sequencing
high-throughput sequencing
biology.organism_classification
DNA extraction
Diatom
Evolutionary biology
Metagenomics
[SDE]Environmental Sciences
Pyrosequencing
Metagenome
[SDE.BE]Environmental Sciences/Biodiversity and Ecology
Biotechnology
Zdroj: Molecular Ecology Resources
Molecular Ecology Resources, 2013, 13 (4), pp.607-619. ⟨10.1111/1755-0998.12105⟩
Molecular Ecology Resources, Wiley/Blackwell, 2013, 13, pp.607-619
HAL
Molecular Ecology Resources, 2013, 13, pp.607-619
Molecular Ecology Resources, Wiley/Blackwell, 2013, 13 (4), pp.607-619. ⟨10.1111/1755-0998.12105⟩
ISSN: 1755-098X
1755-0998
Popis: International audience; The recent emergence of barcoding approaches coupled to those of next-generation sequencing (NGS) has raised new perspectives for studying environmental communities. In this framework, we tested the possibility to derive accurate inventories of diatom communities from pyrosequencing outputs with an available DNA reference library. We used three molecular markers targeting the nuclear, chloroplast and mitochondrial genomes (SSU rDNA, rbcL and cox1) and three samples of a mock community composed of 30 known diatom strains belonging to 21 species. In the goal to detect methodological biases, one sample was constituted directly from pooled cultures, whereas the others consisted of pooled PCR products. The NGS reads obtained by pyrosequencing (Roche 454) were compared first to a DNA reference library including the sequences of all the species used to constitute the mock community, and second to a complete DNA reference library with a larger taxonomic coverage. A stringent taxonomic assignation gave inventories that were compared to the real one. We detected biases due to DNA extraction and PCR amplification that resulted in false-negative detection. Conversely, pyrosequencing errors appeared to generate false positives, especially in case of closely allied species. The taxonomic coverage of DNA reference libraries appears to be the most crucial factor, together with marker polymorphism which is essential to identify taxa at the species level. RbcL offers a high resolving power together with a large DNA reference library. Although needing further optimization, pyrosequencing is suitable for identifying diatom assemblages and may find applications in the field of freshwater biomonitoring.
Databáze: OpenAIRE
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