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

Author

François Keck, Philippe Chaumeil, Alain Franc, Valentin Vasselon, Lenaïg Kermarrec, Frédéric Rimet, Maria Kahlert, Agnès Bouchez, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Asconit Consultants, Swedish University of Agricultural Sciences (SLU), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest

Subjects
0106 biological sciences, code barre adn, taxonomie, Sequencing data, Statistics as Topic, pollution de l'eau, Fresh Water, Biology, Barcode, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, General Biochemistry, Genetics and Molecular Biology, 18S ribosomal RNA, law.invention, Access to Information, diatomées, law, Databases, Genetic, séquençage, DNA Barcoding, Taxonomic, Data Curation, Phylogeny, 2. Zero hunger, Diatoms, Database, Data curation, Base Sequence, 010604 marine biology & hydrobiology, biology.organism_classification, Freshwater algae, Diatom, Phenotype, Identification (biology), Original Article, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], General Agricultural and Biological Sciences, computer, algorithme, Information Systems, Environmental Monitoring
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.[br/] Database URL: http://www.rsyst.inra.fr/

Published
2016

2. A next-generation sequencing approach to river biomonitoring using benthic diatoms

Author

Jean-Marc Frigerio, Philippe Chaumeil, Frédéric Rimet, Lenaïg Kermarrec, Alain Franc, Jean-François Humbert, Agnès Bouchez, Asconit Consultants, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), 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]), Institut d'Ecologie et des Sciences de l'Environnement de Paris, Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Recherche pour le Développement (IRD [France-Ouest])-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Ecology of Forests, Grassland and Freshwaters Division of Institut national de la recherche agronomique (INRA), Plant Health and Environment Division of INRA, French National Agency for Water and Aquatic Environments (ONEMA), and French National Agency for Research and Technology (ANRT)

Subjects
0106 biological sciences, 0303 health sciences, Ecology, [SDV]Life Sciences [q-bio], fungi, 15. Life on land, Aquatic Science, Biology, Ribosomal RNA, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, DNA sequencing, Molecular ecology, 03 medical and health sciences, Taxon, Diatom, Evolutionary biology, Pyrosequencing, Identification (biology), Bioindicator, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

International audience; Diatoms are main bioindicators used to assess the ecological quality of rivers, but their identification is difficult and time-consuming. Next Generation Sequencing (NGS) can be used to study communities of microorganisms, so we carried out a test of the reliability of 454 pyrosequencing for estimating diatom inventories in environmental samples. We used small subunit ribosomal deoxyribonucleic acid (SSU rDNA), ribulose-1, 5-bisphosphate carboxylase (rbcL), and cytochrome oxidase I (COI) markers and examined reference libraries to define thresholds between the intra- and interspecific and intra- and intergeneric genetic distances. Based on tests of 1 mock community, we used a threshold of 99% identity for SSU rDNA and rbcL sequences to study freshwater diatoms at the species level. We applied 454 pyrosequencing to 4 contrasting environmental samples (with one in duplicate), assigned taxon names to environmental sequences, and compared the qualitative and quantitative molecular inventories to those obtained by microscopy. Species richness detected by microscopy was always higher than that detected by pyrosequencing. Some morphologically detected taxa may have been persistent frustules from dead cells. Some taxa detected by molecular analysis were not detected by morphology and vice versa. The main source of divergence appears to be inadequate taxonomic coverage in DNA reference libraries. Only a small percentage of species (but almost all genera) in morphological inventories were included in DNA reference libraries. DNA reference libraries contained a smaller percentage of species from tropical (27.1–38.1%) than from temperate samples (53.7–77.8%). Agreement between morphological and molecular inventories was better for species with relative abundance >1% than for rare species. The rbcL marker appeared to provide more reproducible results (94.9% species similarity between the 2 duplicates) and was very useful for molecular identification, but procedural standardization is needed. The water-quality ranking assigned to a site via the Pollution Sensitivity diatom index was the same whether calculated with molecular or morphological data. Pyrosequencing is a promising approach for detecting all species, even rare ones, once reference libraries have been developed.

Published
2014

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

Author

Lenaïg Kermarrec, Agnès Bouchez, Jean-François Humbert, Frédéric Rimet, Philippe Chaumeil, Alain Franc, 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), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)

Subjects
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
Abstract

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.

Published
2013

4. First Evidence of the Existence of Semi-Cryptic Species and of a Phylogeographic Structure in the Gomphonema parvulum (Kutzing) Kutzing Complex (Bacillariophyta)

Author

Agnès Bouchez, Lenaïg Kermarrec, Frédéric Rimet, Jean-François Humbert, 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, 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), ONEMA (French National Agency for Water and Aquatic Environments), ANRT (French National Agency for Research and Technology), 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), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)

Subjects
0106 biological sciences, Species complex, Biogeography, [SDV]Life Sciences [q-bio], Molecular Sequence Data, DIVERSITY, Zoology, Context (language use), Gomphonema parvulum, Biology, SYSTEMATICS, DNA, Ribosomal, 010603 evolutionary biology, 01 natural sciences, Microbiology, 03 medical and health sciences, Rivers, Species Specificity, Phylogenetics, FRESH-WATER DIATOMS, RBCL, Clade, Phylogeny, biogeography, 030304 developmental biology, Diatoms, 0303 health sciences, Genetic diversity, Sequence Analysis, DNA, genetic diversity, 15. Life on land, NITZSCHIA-PUNGENS BACILLARIOPHYCEAE, ENDEMISM, Europe, Phylogeography, BARCODING DIATOMS, [SDE]Environmental Sciences, PATTERNS, Pyrosequencing, COMMUNITIES, morphological and morphometric variability
Abstract

International audience; The Gomphonema parvulum complex includes species displaying considerable morphological variability and a wide geographical distribution. These characteristics make them difficult to identify by microscopy and raise the question of their taxonomic validity and of the possibility of biogeographical differentiation between them. In this context, we isolated 39 G. parvulum s.l. strains from rivers located in a tropical island (Mayotte) and in mainland Europe. By sequencing three DNA fragments (ITS, rbcL and cox1), four clades (A, B, C and D) were clearly identified, and an additional one (B') was distinguishable only on the rbcL sequence. The main four clades can be separated by their morphological criteria, in particular by the shape of the central area, but some overlaps were found between them. We therefore consider that the G. parvulum complex contains at least four semi-cryptic species corresponding to the four main clades. One of them (A) was found only on Mayotte, while two others (C and D) were found only in Europe. The last clade (B) contained strains from both Europe and Mayotte. Pyrosequencing data confirmed the geographical differences in the distribution of these species, suggesting that the G. parvulum complex displays biogeographic structure. (c) 2013 Elsevier GmbH. All rights reserved.

Published
2013

5. New Biomonitoring Approaches based on Next Generation Sequencing : a Test for Freshwater Diatom Communities

Author

Lenaïg Kermarrec, Frédéric Rimet, Alain Franc, Philippe Chaumeil, Jean Francois Humbert, Agnès Bouchez, 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]), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Biogéochimie et écologie des milieux continentaux (Bioemco), 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), Ghent University [Belgium] (UGENT). National Botanic Garden of Belgium, Ghent, BEL., École normale supérieure - Paris (ENS-PSL), and 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)

Subjects
comparaison de séquences, diatomées, eau douce, évaluation de la qualité, qualité environnementale, [SDV]Life Sciences [q-bio], outil moléculaire, [SDE]Environmental Sciences, marquage génétique, identification moléculaire, ComputingMilieux_MISCELLANEOUS, rivière
Abstract

International audience

Published
2012

6. A pipeline for automatic taxonomic community inventories on data from NGS : an example with freshwater diatoms

Author

Lenaïg Kermarrec, Philippe Chaumeil, Frédéric Rimet, Jean-Marc Frigerio, Valerie Laval, Marc-Henri Lebrun, Agnès Bouchez, Alain Franc, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and University of Adelaide. Adélaide, AUS.

Subjects
comparaison de séquences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, diatomées, eau douce, évaluation de la qualité, qualité environnementale, marquage génétique
Abstract

absent

Published
2011

7. Molecular phylogeny of the family Bacillariaceae based on 18S rDNA sequences: focus on freshwater Nitzschia of the section Lanceolatae

Author

Lenaïg Kermarrec, Luc Ector, Frédéric Rimet, Agnès Bouchez, Linda K. Medlin, Lucien Hoffmann, 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]), Observatoire Océanologique, Université Pierre et Marie Curie - Paris 6 (UPMC), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Observatoire océanologique de Banyuls (OOB), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, biology, Sequence analysis, 010604 marine biology & hydrobiology, phylogenie moleculaire, Aquatic Science, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Monophyly, Taxon, Diatom, Bacillariaceae, Evolutionary biology, Phylogenetics, Molecular phylogenetics, Botany, Clade
Abstract

Sequence analysis of the 18S rDNA gene from 93 taxa belonging to the pennate diatoms plus one centric, Cyclotella meneghiniana Kutzing, were made using two different alignments (Clustal and secondary structure) and two different types of algorithms (neighbour-joining and maximum likelihood). The monophyly of the bacillariacean taxa depends on the type of alignment used for the 18S gene. A secondary structure alignment does not support its monophyly, whereas a Clustal alignment does, but only in the maximum likelihood analysis. The Eunotiales were basal to all other raphid diatoms if a maximum likelihood analysis was used, regardless of the alignment, whereas a neighbour-joining analysis, regardless of the alignment, pulled the Eunotiales inside the raphid diatom sister to one of the bacillariophycean clades in the secondary structure alignment and sister to a monophyletic bacillariophycean clade in the Clustal alignment. The classification of the Bacillariaceae by Krammer & Lange-Bertalot and Round, Crawf...

Published
2011

8. Efficiency of 3 genetic markers to determine the composition of a diatom assemblage using next generation sequencing

Author

Lenaïg Kermarrec, Frédéric Rimet, Alain Franc, Philippe Chaumeil, Jean Francois Humbert, Agnès Bouchez, 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]), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Biogéochimie et écologie des milieux continentaux (Bioemco), 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), University of Adelaide. Adélaide, AUS., École normale supérieure - Paris (ENS-PSL), and 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)

Subjects
comparaison de séquences, protiste, diatomées, eau douce, évaluation de la qualité, qualité environnementale, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, marquage génétique, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2011

9. A preliminary phylogenetic analysis of the Cymbellales based on 18S rDNA gene sequencing

Author

Lenaïg Kermarrec, Agnès Bouchez, Luc Ector, Lucien Hoffmann, Frédéric Rimet, 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, Centre de Recherche Public - Gabriel Lippmann (LUXEMBOURG), Centre de Recherche Public-Gabriel Lippmann (Luxembourg), the CEMAGREF (France), the Conseil General des Alpes Maritimes (France), Universities of Aveiro and Evora (Portugal), University of Barcelona, Leon, Vigo (Spain), University of Camerino, and University of Trento (Italy)

Subjects
0106 biological sciences, Paraphyly, characters, Cymbella, [SDV]Life Sciences [q-bio], diatoms bacillariophyceae, Aquatic Science, phylogeny, 010603 evolutionary biology, 01 natural sciences, Phylogenetics, Genus, Cymbellales, Botany, gomphonema species bacillariophyceae, algae, Bacillariophyceae, algorithm, model, Phylogenetic tree, biology, 18S rDNA, 010604 marine biology & hydrobiology, biology.organism_classification, Taxon, Diatom, fresh-water, Evolutionary biology, GenBank, sp-nov, freshwater diatoms
Abstract

International audience; Although diatom taxa have been observed and described for many years using light and electron microscopy, several taxa have called for some clarifications and taxonomic reassessments. This is the case for the order Cymbellales D.G. Mann, which is widely represented in freshwater. The phylogenetic relationships among taxa belonging to this order are not always clear because their taxonomic status has been repeatedly revised. In this study, diatom cells were isolated from rivers in Italy, Luxembourg, Portugal and Spain. In total, 21 18S rDNA gene sequences, representing six genera of Cymbellales (Cymbella C. Agardh, Didymosphenia M. Schmidt, Encyonema Kutzing, Gomphoneis Cleve, Gomphonema Ehrenberg and Reimeria Kociolek & Stoermer) were determined. These sequences were analyzed along with other known GenBank diatom 18S rDNA gene sequences. The results indicate that the Cymbellaceae Greville and Gomphonemataceae Kutzing, especially the genus Gomphonema, are paraphyletic, and that the significance of some of the morphological characteristics traditionally used for classification purposes requires a reassessment. These results also demonstrate the importance of a polyphasic approach combining both morphological and molecular data in attempting to improve the taxonomy and classification system of diatoms.

Published
2011

10. Etude de la diversité génétique au sein du complexe d’espèce Gomphonema Parvulum

Author

Lenaïg Kermarrec, Bernard Rimet, Jean Francois Humbert, Agnès Bouchez, 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, 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), 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), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, GOMPHONEMA PARVULUM
Abstract

National audience; Pour utiliser les diatomées en tant qu'indicateur écologique de la qualité des eaux courantes, il est nécessaire de mieux connaître les différentes espèces qui peuplent les rivières. De nombreuses espèces appartenant au genre Gomphonema sont abondamment représentées dans les échantillons benthiques d’eau douce sur le continent européen et dans les îles tropicales. Toutefois, plusieurs taxons sont difficiles à identifier en microscopie optique. C'est le cas du complexe d'espèces Gomphonema parvulum. Cette espèce est connue pour sa forte variabilité morphologique et sa large gamme de tolérance écologique. Les taxonomistes ont souvent des difficultés à distinguer morphologiquement les taxons appartenant à ce complexe d'espèces. La distinction de ces formes est pourtant importante, car elles ont souvent des valeurs écologiques différentes dans les indices de diatomées. Les techniques de biologie moléculaire sont des alternatives intéressantes aux observations microscopiques pour l'étude des diatomées. Plusieurs exemples illustrent la façon dont les séquences d'ADN peuvent être utilisées pour stabiliser la taxonomie (Jahn et al. 2008, Evans et Mann 2009). Les séquences d’ADNr 18S, 28S, ITS, et des gènes rbcL et cox1 de plusieurs souches de Gomphonema parvulum des rivières d’îles tropicales françaises (Mayotte, La Réunion), de France métropolitaine, d’Italie, du Luxembourg, du Portugal et d’Espagne ont été déterminées et comparées. Des analyses morphométriques ont également été réalisées afin d’obtenir des critères morphologiques permettant de séparer les taxa. Quatre groupes de G. parvulum peuvent être distingués. La répartition géographique n’est pas le seul facteur expliquant la séparation de ces quatre clades. Les résultats indiquent donc que le complexe d'espèces G. parvulum pourrait être séparé en quatre taxa distincts.

Published
2010

11. Genetic diversity within the Gomphonema Parvulum complex

Author

Lenaïg Kermarrec, Frédéric Rimet, Agnès Bouchez, 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, and Mineapolis, usa.

Subjects
diatomées, eau douce, [SDV]Life Sciences [q-bio], analyse génétique
Published
2010

Catalog

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