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26 results on '"Marie-Mathilde Perrineau"'

1. My seaweed looks weird: a community web portal to accelerate pathogen discovery in seaweeds

Author

Martina Strittmatter, Pedro Murúa, Paola Arce, Marie-Mathilde Perrineau, and Claire Gachon

Subjects
Macroalgae, diseases, diagnostics, portal, cultivation, submission, Aquaculture. Fisheries. Angling, SH1-691, Environmental sciences, GE1-350
Abstract

Worldwide, novel species of pathogens are frequently reported in cultivated and wild macroalgae. Alongside the rapid growth of the seaweed industry, diseases and pests have become an area of significant concern for cultivation and conservation of wild stocks alike: yield and quality of a crop might be greatly affected and sometimes, the losses due to diseases and pests are such that they jeopardize the economic viability of cultivation. Disease management methods and biosecurity are still in their infancy, especially as disease-causing organisms are most often poorly known, with limited options for robust and rapid diagnostics. Here, we describe a community-based, multilingual initiative that aims to foster the description of disease-causing organisms relevant to the seaweed industry worldwide and to underpin the conservation of wild seaweed genetic resources.

Published
2022
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2. Water-Soluble Saccharina latissima Polysaccharides and Relation of Their Structural Characteristics with In Vitro Immunostimulatory and Hypocholesterolemic Activities

Author

Ana S. P. Moreira, Diana Gaspar, Sónia S. Ferreira, Alexandra Correia, Manuel Vilanova, Marie-Mathilde Perrineau, Philip D. Kerrison, Claire M. M. Gachon, Maria Rosário Domingues, Manuel A. Coimbra, Filipe M. Coreta-Gomes, and Cláudia Nunes

Subjects
seaweed, Laminariales, sulphated polysaccharides, fucans, fucoidans, mice, Biology (General), QH301-705.5
Abstract

Brown macroalgae are an important source of polysaccharides, mainly fucose-containing sulphated polysaccharides (FCSPs), associated with several biological activities. However, the structural diversity and structure–function relationships for their bioactivities are still undisclosed. Thus, the aim of this work was to characterize the chemical structure of water-soluble Saccharina latissima polysaccharides and evaluate their immunostimulatory and hypocholesterolemic activities, helping to pinpoint a structure–activity relationship. Alginate, laminarans (F1, neutral glucose-rich polysaccharides), and two fractions (F2 and F3) of FCSPs (negatively charged) were studied. Whereas F2 is rich in uronic acids (45 mol%) and fucose (29 mol%), F3 is rich in fucose (59 mol%) and galactose (21 mol%). These two fractions of FCSPs showed immunostimulatory activity on B lymphocytes, which could be associated with the presence of sulphate groups. Only F2 exhibited a significant effect in reductions in in vitro cholesterol’s bioaccessibility attributed to the sequestration of bile salts. Therefore, S. latissima FCSPs were shown to have potential as immunostimulatory and hypocholesterolemic functional ingredients, where their content in uronic acids and sulphation seem to be relevant for the bioactive and healthy properties.

Published
2023
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3. The Unique Lipidomic Signatures of Saccharina latissima Can Be Used to Pinpoint Their Geographic Origin

Author

João P. Monteiro, Felisa Rey, Tânia Melo, Ana S. P. Moreira, Jean-François Arbona, Jorunn Skjermo, Silje Forbord, Jon Funderud, Diogo Raposo, Philip D. Kerrison, Marie-Mathilde Perrineau, Claire Gachon, Pedro Domingues, Ricardo Calado, and M. Rosário Domingues

Subjects
elemental composition, glycolipids, lipidomics, mass spectrometry, phospholipids, polyunsaturated fatty acids, seaweeds, traceability, Microbiology, QR1-502
Abstract

The aquaculture of macroalgae for human consumption and other high-end applications is experiencing unprecedented development in European countries, with the brown algae Saccharina latissima being the flag species. However, environmental conditions in open sea culture sites are often unique, which may impact the biochemical composition of cultured macroalgae. The present study compared the elemental compositions (CHNS), fatty acid profiles, and lipidomes of S. latissima originating from three distinct locations (France, Norway, and the United Kingdom). Significant differences were found in the elemental composition, with Norwegian samples displaying twice the lipid content of the others, and significantly less protein (2.6%, while French and UK samples contained 6.3% and 9.1%, respectively). The fatty acid profiles also differed considerably, with UK samples displaying a lower content of n-3 fatty acids (21.6%), resulting in a higher n-6/n-3 ratio. Regarding the lipidomic profile, samples from France were enriched in lyso lipids, while those from Norway displayed a particular signature of phosphatidylglycerol, phosphatidylinositol, and phosphatidylcholine. Samples from the UK featured higher levels of phosphatidylethanolamine and, in general, a lower content of galactolipids. These differences highlight the influence of site-specific environmental conditions in the shaping of macroalgae biochemical phenotypes and nutritional value. It is also important to highlight that differences recorded in the lipidome of S. latissima make it possible to pinpoint specific lipid species that are likely to represent origin biomarkers. This finding is relevant for future applications in the field of geographic origin traceability and food control.

Published
2020
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4. Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium

Author

Marie-Mathilde Perrineau, Dana C. Price, Georg Mohr, and Debashish Bhattacharya

Subjects
Group II introns, Twintrons, Red algae, Porphyridium, Mobile genetic elements, Plastids, Medicine, Biology (General), QH301-705.5
Abstract

Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strains of the unicellular red alga Porphyridium purpureum that surprisingly contain 42 group II introns in their plastid genomes. We focused on a subset of these introns that encode mobility-conferring intron-encoded proteins (IEPs) and found them to be distributed among the strains in a lineage-specific manner. The reverse transcriptase and maturase domains were present in all lineages but the DNA endonuclease domain was deleted in vertically inherited introns, demonstrating a key step in the loss of mobility. P. purpureum plastid intron RNAs had a classic group IIB secondary structure despite variability in the DIII and DVI domains. We report for the first time the presence of twintrons (introns-within-introns, derived from the same mobile element) in Rhodophyta. The P. purpureum IEPs and their mobile introns provide a valuable model for the study of mobile retroelements in eukaryotes and offer promise for biotechnological applications.

Published
2015
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5. Using natural selection to explore the adaptive potential of Chlamydomonas reinhardtii.

Author

Marie-Mathilde Perrineau, Jeferson Gross, Ehud Zelzion, Dana C Price, Orly Levitan, Jeffrey Boyd, and Debashish Bhattacharya

Subjects
Medicine, Science
Abstract

Improving feedstock is critical to facilitate the commercial utilization of algae, in particular in open pond systems where, due to the presence of competitors and pests, high algal growth rates and stress tolerance are beneficial. Here we raised laboratory cultures of the model alga Chlamydomonas reinhardtii under serial dilution to explore the potential of crop improvement using natural selection. The alga was evolved for 1,880 generations in liquid medium under continuous light (EL population). At the end of the experiment, EL cells had a growth rate that was 35% greater than the progenitor population (PL). The removal of acetate from the medium demonstrated that EL growth enhancement largely relied on efficient usage of this organic carbon source. Genome re-sequencing uncovered 1,937 polymorphic DNA regions in the EL population with 149 single nucleotide polymorphisms resulting in amino acid substitutions. Transcriptome analysis showed, in the EL population, significant up regulation of genes involved in protein synthesis, the cell cycle and cellular respiration, whereas the DNA repair pathway and photosynthesis were down regulated. Like other algae, EL cells accumulated neutral lipids under nitrogen depletion. Our work demonstrates transcriptome and genome-wide impacts of natural selection on algal cells and points to a useful strategy for strain improvement.

Published
2014
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6. Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution

Author

Marie-Mathilde Perrineau, Isabel C. Azevedo, Claire M. M. Gachon, Philip D. Kerrison, Willem de Visser, Isabel Sousa-Pinto, Kévin Cascella, Philippe Potin, Elisabete da Costa, Ricardo Calado, Johanna E. Beniers, Maria do Rosário Domingues, Ronan Sulpice, Michael D. Guiry, Adrie van der Werf, Antoine Fort, Marcus McHale, Henrice M. Jansen, National University of Ireland [Galway] (NUI Galway), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Scottish Association for Marine Science (SAMS), Laboratorio Associado para a Quimica Verde (LAQV), Requimte, Universidade do Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Centro de Estudos do Ambiante e do Mar (CESAM), Universidade de Aveiro, Interdisciplinary Centre of Marine and Environmental Research [Matosinhos, Portugal] (CIIMAR), Universidade do Porto, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research [Wageningen] (WUR), and Martin Ryan Institute

Subjects
Land Use and Food Security, Aquaculture, phylogeny, Barcode, DNA barcoding, law.invention, Onderz. Form. D, Ulva, Aquaculture and Fisheries, law, DNA BArcoding, Genetics, Sea lettuce, 14. Life underwater, Applied Ecology, Ecology, Evolution, Behavior and Systematics, Phylogeny, Geography, biology, Aquacultuur en Visserij, Ulvophyceae, Toegepaste Ecologie, Species diversity, Landgebruik en Voedselzekerheid, biology.organism_classification, Europe, Ulvales, Herbarium, Taxon, aquaculture, Evolutionary biology, [SDE]Environmental Sciences, Biotechnology
Abstract

Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rarely updated. For instance, species of the Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding unreliable. We DNA barcoded 295 individual distromatic foliose strains of Ulva from the North-East Atlantic for three loci (rbcL, tufA, ITS1). Seven distinct species were found, and we compared our results with all worldwide Ulva spp. sequences present in the NCBI database for the three barcodes rbcL, tufA and the ITS1. Our results demonstrate a large degree of species misidentification, where we estimate that 24%–32% of the entries pertaining to foliose species are misannotated and provide an exhaustive list of NCBI sequences reannotations. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U.lactuca from Northern Europe. We extended our analytical framework to three other genera, Fucus, Porphyra and Pyropia and also identified erroneously labelled accessions and possibly new synonymies, albeit less than for Ulva spp. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations and delivers an improved representation of species diversity and distribution.

Published
2021

7. Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution: a case study of the Sea Lettuce

Author

Adrie van der Werf, Antoine Fort, Johanna E. Beniers, Marcus McHale, Michael D. Guiry, Elisabete da Costa, Kévin Cascella, Isabel C. Azevedo, Philippe Potin, Ricardo Calado, Philip D. Kerrison, Isabel Sousa-Pinto, Henrice M. Jansen, Maria Rosário Domingues, Ronan Sulpice, Willem de Visser, Claire M. M. Gachon, and Marie-Mathilde Perrineau

Subjects
Taxon, Herbarium, biology, Ecology, Ulvophyceae, Species distribution, Species diversity, Lactuca, Ulvaceae, biology.organism_classification, Sea lettuce
Abstract

Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) is an important ecological and economical entity, with a worldwide distribution and is a well-known source of near-shore blooms blighting many coastlines. Species of Ulva are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding hazardous. We investigated the species distribution of 295 individual distromatic foliose strains from the North East Atlantic by traditional barcoding or next generation sequencing. We found seven distinct species, and compared our results with all worldwide Ulva spp sequences present in the NCBI database for the three barcodes rbcL, tufA and the ITS1. Our results demonstrate a large degree of species misidentification in the NCBI database. We estimate that 21% of the entries pertaining to foliose species are misannotated. In the extreme case of U. lactuca, 65% of the entries are erroneously labelled specimens of another Ulva species, typically U. fenestrata. In addition, 30% of U. rigida entries are misannotated, U. rigida being relatively rare and often misannotated U. laetevirens. Furthermore, U. armoricana and U. scandinavica present as being synonymous to U. laetevirens. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U. lactuca from Northern Europe. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations, and delivers an improved representation of Ulva species diversity and distribution. This approach could be easily adapted to other taxa.

Published
2020

8. The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga

Author

Erwan Corre, Didier Jollivet, Xi Liu, Jonas Collén, Noé Pontoizeau, Thierry Tonon, Simon M. Dittami, Gabriel V. Markov, Alexandre Cormier, Dominique Marie, Hwan Su Yoon, Catherine Leblanc, Loraine Brillet-Guéguen, Camille Trottier, Akira F. Peters, André E. Minoche, Sylvie Doubleau, Komlan Avia, Misharl Monsoor, Amandine Siméon, Angélique Gobet, Hetty KleinJan, Catherine Boyen, Christophe Caron, Agnieszka P. Lipinska, Chung Hyun Cho, Clémence Frioux, Agnès Groisillier, Marie-Mathilde Perrineau, Pierre Pericard, Irene González-Navarrete, Heinz Himmelbauer, Cécile Hervé, Méziane Aite, Anne Siegel, Ludovic Delage, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona]-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Tereos, ECOlogy of MArine Plankton (ECOMAP), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189 (CRIStAL), Ecole Centrale de Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2), University of Aberdeen, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), DMAS, ONERA, Université Paris Saclay [Châtillon], ONERA-Université Paris-Saclay, Sung Kyun Kwan University, Max-Planck-Institut für Molekulare Genetik (MPIMG), Max-Planck-Gesellschaft, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Sungkyunkwan University [Suwon] (SKKU), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Key Laboratory of Intelligent Information Processing, Institute of Computing Technology [Beijing], Chinese Academy of Sciences [Changchun Branch] (CAS), Bezhin Rosko, Université de Rennes (UR), Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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, Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Max Planck Institute for Molecular Genetics (MPIMG), University of York [York, UK], This work was funded partially by ANR project IDEALG (ANR-10-BTBR-04) 14'Investissements d’Avenir, Biotechnologies-Bioressources', the European Union’s Horizon 2020 research and innovation Programme under the Marie Sklodowska-Curie grant agreement number 624575 (ALFF), and the CNRS Momentum call. Sequencing was performed at the Genomics Unit of the Centre for Genomic Regulation (CRG), Barcelona, Spain, Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Laboratoire de Biologie Intégrative des Modèles Marins [LBI2M], ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science [ABIMS], Dynamics, Logics and Inference for biological Systems and Sequences [Dyliss], Santé de la vigne et qualité du vin [SVQV], Unité Mathématique Informatique et Génome [MIG], Diversité, adaptation, développement des plantes [UMR DIADE], from patterns to models in computational biodiversity and biotechnology [PLEIADE], Evolution des Protistes et Ecosystèmes Pélagiques [EPEP], Centre for Genomic Regulation [Barcelona] [CRG], ECOlogy of MArine Plankton [ECOMAP], Institut de Génomique Fonctionnelle de Lyon [IGFL], Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL], Laboratoire des symbioses tropicales et méditerranéennes [UMR LSTM], DMAS, ONERA, Université Paris Saclay (COmUE) [Châtillon], and Max-Planck-Institut für Molekulare Genetik [MPIMG]

Subjects
0106 biological sciences, Victoria, Retrotransposon, Aquatic Science, Biology, Phaeophyta, 010603 evolutionary biology, 01 natural sciences, Genome, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Stress, Physiological, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Abiotic stress, Algal Proteins, Ectocarpus, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Brown algae, Multicellular organism, Multigene Family, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Metabolic Networks and Pathways, 010606 plant biology & botany
Abstract

Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.

Published
2020

9. The Unique Lipidomic Signatures of Saccharina latissima Can Be Used to Pinpoint Their Geographic Origin

Author

Felisa Rey, Jon Funderud, Silje Forbord, Ricardo Calado, Jean-François Arbona, João P. Monteiro, Philip D. Kerrison, Diogo Raposo, M. Rosário M. Domingues, Tânia Melo, Pedro Domingues, Claire M. M. Gachon, Ana S. P. Moreira, Marie-Mathilde Perrineau, Jorunn Skjermo, Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Scottish Association for Marine Science, Scottish Marine Institute, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), and University of Algarve [Portugal]

Subjects
0106 biological sciences, glycolipids, lcsh:QR1-502, Aquaculture, Saccharina latissima, 01 natural sciences, Biochemistry, lcsh:Microbiology, Food science, ComputingMilieux_MISCELLANEOUS, Phospholipids, mass spectrometry, chemistry.chemical_classification, 0303 health sciences, biology, Fatty Acids, Galactolipids, Seaweeds, Lipidome, Lipids, Europe, seaweeds, Phylogeography, Elemental composition, Polyunsaturated fatty acid, polyunsaturated fatty acids, Oceans and Seas, Phaeophyta, Article, 03 medical and health sciences, Lipidomics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Molecular Biology, phospholipids, 030304 developmental biology, Mass spectrometry, business.industry, 010604 marine biology & hydrobiology, Fatty acid, Traceability, Seaweed, biology.organism_classification, Brown algae, traceability, chemistry, elemental composition, lipidomics, Polyunsaturated fatty acids, Glycolipids, business
Abstract

The aquaculture of macroalgae for human consumption and other high-end applications is experiencing unprecedented development in European countries, with the brown algae Saccharina latissima being the flag species. However, environmental conditions in open sea culture sites are often unique, which may impact the biochemical composition of cultured macroalgae. The present study compared the elemental compositions (CHNS), fatty acid profiles, and lipidomes of S. latissima originating from three distinct locations (France, Norway, and the United Kingdom). Significant differences were found in the elemental composition, with Norwegian samples displaying twice the lipid content of the others, and significantly less protein (2.6%, while French and UK samples contained 6.3% and 9.1%, respectively). The fatty acid profiles also differed considerably, with UK samples displaying a lower content of n-3 fatty acids (21.6%), resulting in a higher n-6/n-3 ratio. Regarding the lipidomic profile, samples from France were enriched in lyso lipids, while those from Norway displayed a particular signature of phosphatidylglycerol, phosphatidylinositol, and phosphatidylcholine. Samples from the UK featured higher levels of phosphatidylethanolamine and, in general, a lower content of galactolipids. These differences highlight the influence of site-specific environmental conditions in the shaping of macroalgae biochemical phenotypes and nutritional value. It is also important to highlight that differences recorded in the lipidome of S. latissima make it possible to pinpoint specific lipid species that are likely to represent origin biomarkers. This finding is relevant for future applications in the field of geographic origin traceability and food control.

Published
2020

10. Unusual Patterns of Mitochondrial Inheritance in the Brown Alga Ectocarpus

Author

Walid Djema, Florian Pontheaux, Laure Mignerot, J. Mark Cock, Marie-Mathilde Perrineau, Akira F. Peters, Susana M. Coelho, Taizo Motomura, Yacine Badis, Chikako Nagasato, Delphine Scornet, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institute of Algological Research [Muroran], Hokkaido University [Sapporo, Japan], Bezhin Rosko, Scottish Association for Marine Science (SAMS), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Hokkaido University, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Mitochondrial DNA, Lineage (genetic), [SDV]Life Sciences [q-bio], Parthenogenesis, Uniparental inheritance, Mitochondrion, Biology, Phaeophyta, brown algae, 01 natural sciences, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 03 medical and health sciences, Genetics, life cycle, Life History Traits, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Recombination, Genetic, 0303 health sciences, Ectocarpus siliculosus, Inheritance (genetic algorithm), 25 parthenogenesis, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Ectocarpus, biology.organism_classification, mitochondria, Genes, Mitochondrial, Genome, Mitochondrial, recombination 26, uniparental inheritance, 010606 plant biology & botany
Abstract

Most eukaryotes inherit their mitochondria from only one of their parents. When there are different sexes, it is almost always the maternal mitochondria that are transmitted. Indeed, maternal uniparental inheritance has been reported for the brown alga Ectocarpus but we show in this study that different strains of Ectocarpus can exhibit different patterns of inheritance: Ectocarpus siliculosus strains showed maternal uniparental inheritance, as expected, but crosses using different Ectocarpus species 7 strains exhibited either paternal uniparental inheritance or an unusual pattern of transmission where progeny inherited either maternal or paternal mitochondria, but not both. A possible correlation between the pattern of mitochondrial inheritance and male gamete parthenogenesis was investigated. Moreover, in contrast to observations in the green lineage, we did not detect any change in the pattern of mitochondrial inheritance in mutant strains affected in life cycle progression. Finally, an analysis of field-isolated strains provided evidence of mitochondrial genome recombination in both Ectocarpus species.

Published
2019

11. Chytrid infecting the bloom-forming marine diatom Skeletonema sp.: Morphology, phylogeny and distribution of a novel species within the Rhizophydiales

Author

Andrea Garvetto, Yacine Badis, Cecilia Rad-Menéndez, Eileen Bresnan, Claire M. M. Gachon, and Marie-Mathilde Perrineau

Subjects
0106 biological sciences, Rhizophydiales, 01 natural sciences, 03 medical and health sciences, Phylogenetics, Phytoplankton, Genetics, DNA, Fungal, Ecology, Evolution, Behavior and Systematics, Marine fungi, Organism, Phylogeny, 030304 developmental biology, Diatoms, 0303 health sciences, biology, Ecology, Host (biology), fungi, Eutrophication, biology.organism_classification, Molecular Typing, Infectious Diseases, Diatom, Chytridiomycota, Gene pool, 010606 plant biology & botany
Abstract

Chytrids have long been recognised as important parasites of microalgae in freshwater systems, able to shape the dynamics of blooms, the gene pool of their host and phytoplankton succession. In the sea however, where the presence of these organisms is erratic and ephemeral, studies concerning chytrids are sparse and confined to metabarcoding surveys or microscopy observations. Despite the scarcity of data, chytrid epidemics are supposed to play an important role in marine biogeochemical cycles, being one of the drivers of phytoplankton dynamics. Here we combine microscopy observations and in silico mining of a single-cell whole genome to molecularly and morphologically characterise a novel chytrid parasite of the dominant diatom genus Skeletonema. Morphological observations highlight features of the thallus and ascertain the parasitic nature of the interaction whilst the genetic markers obtained allows for a phylogenetic reconstruction, placing the new species in the order Rhizophydiales. Thanks to the molecular data obtained we are also able to provide a first investigation of the global distribution of this organism by screening the Ocean Sampling Day (OSD) dataset, highlighting a northern transatlantic dissemination.

Published
2018

12. The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins that have an unusual distribution across the eukaryotes

Author

Fuli Liu, Delphine Scornet, J. Mark Cock, Agnieszka P. Lipinska, Akira F. Peters, Susana M. Coelho, Marie-Mathilde Perrineau, Nicolas Macaisne, Martina Strittmatter, Antoine Henry, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Bezhin Rosko

Subjects
0106 biological sciences, 0301 basic medicine, Gene Transfer, Horizontal, Cell division, Mutant, Brown algae, virus, Biology, Phaeophyta, 01 natural sciences, initial cell division, Evolution, Molecular, Viral Proteins, 03 medical and health sciences, Phylogenetics, life cycle, Amino Acid Sequence, Cysteine, Cloning, Molecular, Molecular Biology, Gene, Phylogeny, Genetics, Models, Genetic, Sequence Homology, Amino Acid, Gene Expression Profiling, Algal Proteins, Ectocarpus, biology.organism_classification, Multicellular organism, 030104 developmental biology, Multigene Family, Mutation, Horizontal gene transfer, horizontal gene transfer, RNA Interference, Eukaryote, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany, Developmental Biology
Abstract

International audience; The sporophyte generation of the brown alga Ectocarpus sp. exhibits an unusual pattern of development compared to the majority of brown algae. The first cell division is symmetrical and the apical/basal axis is established late in development. In the IMMEDIATE UPRIGHT mutant the initial cell undergoes an asymmetric division to immediately establish the apical/basal axis. We provide evidence which suggests that this phenotype corresponds to the ancestral state of the sporophyte. The IMM gene encodes a protein of unknown function, containing a repeated motif also found in the EsV-1-7 gene of the Ectocarpus virus. Brown algae possess large families of EsV-1-7 domain genes but these genes are rare in other stramenopiles suggesting that the expansion of this family may have been linked with the emergence of multicellular complexity. EsV-1-7 domain genes have a patchy distribution across eukaryotic supergroups and occur in several viral genomes, suggesting possible horizontal transfer during eukaryote evolution.

Published
2017

13. Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus

Author

Erwan Corre, Yves Van de Peer, Valentin Wucher, Misharl Monsoor, Christophe Hitte, Susana M. Coelho, Lieven Sterck, Alexandre Cormier, Agnieszka P. Lipinska, Thomas Derrien, J. Mark Cock, Marie-Mathilde Perrineau, Komlan Avia, Olivier Godfroy, Gwendoline Andres, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique, ANR-10-BLAN-1727, Agence Nationale de la Recherche, Université Pierre et Marie Curie, 638240, European Research Council, ANR-12-JSV7-0008, Sexseaweed, Brittany Region, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Region Bretagne, ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010), European Project: 638240,H2020,ERC-2014-STG,SEXSEA(2015), Universiteit Gent = Ghent University [Belgium] (UGENT), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), Bioinformatics institute Ghent, and University of Pretoria [South Africa]

Subjects
0301 basic medicine, Physiology, [SDV]Life Sciences [q-bio], Brown algae, Library science, Plant Science, Genome, Viral, Biology, Phaeophyta, Genome, Models, Biological, Chromosomes, Plant, Marie curie, 03 medical and health sciences, Annotation, reannotation, Databases, Genetic, long noncoding RNAs, Saccharina japonica, ComputingMilieux_MISCELLANEOUS, Conserved Sequence, Genetics, European research, Algal Proteins, Molecular Sequence Annotation, genome reannotation, Ectocarpus, biology.organism_classification, Stramenopile, 030104 developmental biology, Genetic Loci, Long non-coding RNAs, Genetic markers, DNA, Intergenic, RNA, Long Noncoding, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Alternative splicing
Abstract

International audience; The genome of the filamentous brown alga Ectocarpus was the first to be completely sequenced from within the brown algal group and has served as a key reference genome both for this lineage and for the stramenopiles. We present a complete structural and functional reannotation of the Ectocarpus genome. The large-scale assembly of the Ectocarpus genome was significantly improved and genome-wide gene re-annotation using extensive RNA-seq data improved the structure of 11 108 existing protein-coding genes and added 2030 new loci. A genome-wide analysis of splicing isoforms identified an average of 1.6 transcripts per locus. A large number of previously undescribed noncoding genes were identified and annotated, including 717 loci that produce long noncoding RNAs. Conservation of lncRNAs between Ectocarpus and another brown alga, the kelp Saccharina japonica, suggests that at least a proportion of these loci serve a function. Finally, a large collection of single nucleotide polymorphism-based markers was developed for genetic analyses. These resources are available through an updated and improved genome database.This study significantly improves the utility of the Ectocarpus genome as a high-quality reference for the study of many important aspects of brown algal biology and as a reference for genomic analyses across the stramenopiles.

Published
2017

14. Evolution of salt tolerance in a laboratory reared population ofChlamydomonas reinhardtii

Author

Dana C. Price, Debashish Bhattacharya, Ehud Zelzion, Jeffrey M. Boyd, Jeferson Gross, and Marie-Mathilde Perrineau

Subjects
Genetics, education.field_of_study, Abiotic stress, Population, Chlamydomonas reinhardtii, Biology, biology.organism_classification, Microbiology, Acclimatization, Cell biology, Transcriptome, Downregulation and upregulation, Progenitor cell, education, Gene, Ecology, Evolution, Behavior and Systematics
Abstract

Summary Understanding the genetic underpinnings of adaptive traits in microalgae is important for the study of evolution and for applied uses. We used long-term selection under a regime of serial transfers with haploid populations of the green alga Chlamydomonas reinhardtii raised in liquid TAP medium containing 200 mM NaCl. After 1255 generations, evolved salt (ES) populations could grow as rapidly in high salt medium as progenitor cells (progenitor light [PL]). Transcriptome data were analysed to elucidate the basis of salt tolerance in ES cells when compared with PL cells and to cells incubated for 48 h in high salt medium (progenitor salt [PS], the short-term acclimation response). These data demonstrate that evolved and short-term acclimation responses to salt stress differ fundamentally from each other. Progenitor salt cells exhibit well-known responses to salt stress such as reduction in photosynthesis, upregulation of glycerophospholipid signaling, and upregulation of the transcription and translation machinery. In contrast, ES cells show downregulation of genes involved in the stress response and in transcription/translation. Our results suggest that gene-rich mixotrophic lineages such as C. reinhardtii may be able to adapt rapidly to abiotic stress engendered either by a rapidly changing climate or physical vicariance events that isolate populations in stressful environments.

Published
2014

15. Active dispersal by wild Triatoma infestans in the Bolivian Andes

Author

Mirko Rojas Cortez, François Noireau, Anna Cohuet, Wilfrid Richer, Pierre Kengne, Marie-Mathilde Perrineau, and Didier Fontenille

Subjects
Chagas disease, 0303 health sciences, biology, Ecology, 030231 tropical medicine, Heteroptera, Public Health, Environmental and Occupational Health, 15. Life on land, biology.organism_classification, medicine.disease, Gene flow, 03 medical and health sciences, 0302 clinical medicine, Infectious Diseases, Reduviidae, Vector (epidemiology), Triatoma infestans, medicine, Microsatellite, Biological dispersal, Parasitology, 030304 developmental biology
Abstract

Triatoma infestans is the main vector of Chagas disease and target of control programmes in the Southern Cone countries. So far Bolivia is the only country where true T. infestans wild foci are documented. The dispersal ability for wild T. infestans was studied at microgeographical scale in Bolivian Andes, to assess the possibility for wild populations to actively recolonize insecticide-treated villages. Nine microsatellite loci were used to detect the extent of gene flow between neighbouring collecting sites. The detection of restricted gene flow between close but distinct sylvatic sites supports the hypothesis that wild T. infestans does not disperse by flying at high altitude (2 750 m asl). It gradually disperses over small distances by walking within a 'patch' of continuous land cover. The genetic differentiation detected between sylvatic and domestic populations suggests a limited short-term role of wild insects in the process of recolonization of insecticide-treated houses in the Andes.

Published
2007

16. Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium

Author

Dana C. Price, Marie-Mathilde Perrineau, Debashish Bhattacharya, and Georg Mohr

Subjects
Spliceosome, lcsh:Medicine, Marine Biology, Twintrons, General Biochemistry, Genetics and Molecular Biology, Minor spliceosome, Genetics, Group I catalytic intron, Plastids, Plastid, Red algae, biology, General Neuroscience, lcsh:R, Intron, Genomics, Group II introns, General Medicine, Group II intron, biology.organism_classification, Evolutionary Studies, Mobile genetic elements, Eukaryote, Porphyridium, General Agricultural and Biological Sciences, Biotechnology
Abstract

Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strains of the unicellular red alga Porphyridium purpureum that surprisingly contain 42 group II introns in their plastid genomes. We focused on a subset of these introns that encode mobility-conferring intron-encoded proteins (IEPs) and found them to be distributed among the strains in a lineage-specific manner. The reverse transcriptase and maturase domains were present in all lineages but the DNA endonuclease domain was deleted in vertically inherited introns, demonstrating a key step in the loss of mobility. P. purpureum plastid intron RNAs had a classic group IIB secondary structure despite variability in the DIII and DVI domains. We report for the first time the presence of twintrons (introns-within-introns, derived from the same mobile element) in Rhodophyta. The P. purpureum IEPs and their mobile introns provide a valuable model for the study of mobile retroelements in eukaryotes and offer promise for biotechnological applications.

Published
2014

17. Genome of the red alga Porphyridium purpureum

Author

Steven G. Ball, Andreas P.M. Weber, Simone Zäuner, Hwan Su Yoon, Nicholas Rose, Cheong Xin Chan, Huan Qiu, Bernard Henrissat, Maria Cecilia Arias, Anagha Krishnan, Debashish Bhattacharya, Andrea Egizi, Shannon U. Morath, Marie-Mathilde Perrineau, Pedro M. Coutinho, Frédérique Hilliou, Dana C. Price, Rutgers University [Camden], Rutgers University System (Rutgers), University of Queensland [Brisbane], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Rheinische Friedrich-Wilhelms-Universität Bonn, Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Sung Kyun Kwan University, National Science Foundation (0936884 and 1317114), Department of Defense (DoD) through the National Defense Science and Engineering Graduate (NDSEG) program, Next-Generation BioGreen 21 Program (SSAC, 2013-PJ009525), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, plastendosymbiosis, polypeptide, [SDV]Life Sciences [q-bio], Light-Harvesting Protein Complexes, General Physics and Astronomy, 01 natural sciences, Genome, Cytochrome P-450 Enzyme System, gene transfer, Phylogeny, Genetics, 0303 health sciences, Multidisciplinary, biology, Reproduction, Starch, phycobilisome, Meiosis, Horizontal gene transfer, [SDE]Environmental Sciences, Carbohydrate Metabolism, Gene Transfer, Horizontal, General Biochemistry, Genetics and Molecular Biology, Article, cyanidioschyzon merolae, 03 medical and health sciences, cruentum, Phylogenetics, Botany, evolution, Cyanidiophyceae, Gene, 030304 developmental biology, Whole genome sequencing, Sphingolipids, meiotic genes, Algal Proteins, Intron, Membrane Transport Proteins, General Chemistry, sequence, biology.organism_classification, Sexual reproduction, Molecular Weight, Gene Ontology, Glycolipids, Porphyridium, biosynthesis, 010606 plant biology & botany
Abstract

The limited knowledge we have about red algal genomes comes from the highly specialized extremophiles, Cyanidiophyceae. Here, we describe the first genome sequence from a mesophilic, unicellular red alga, Porphyridium purpureum. The 8,355 predicted genes in P. purpureum, hundreds of which are likely to be implicated in a history of horizontal gene transfer, reside in a genome of 19.7 Mbp with 235 spliceosomal introns. Analysis of light-harvesting complex proteins reveals a nuclear-encoded phycobiliprotein in the alga. We uncover a complex set of carbohydrate-active enzymes, identify the genes required for the methylerythritol phosphate pathway of isoprenoid biosynthesis, and find evidence of sexual reproduction. Analysis of the compact, function-rich genome of P. purpureum suggests that ancestral lineages of red algae acted as mediators of horizontal gene transfer between prokaryotes and photosynthetic eukaryotes, thereby significantly enriching genomes across the tree of photosynthetic life., Red algae form one of the most ancient eukaryotic lineages, and have undergone multiple symbioses. Here, Price et al. report the first genome sequence for a mesophilic red alga, and reveal significant differences between these organisms and hyperthermopilic algae.

Published
2013

18. Monoxenic nodulation process of Acacia mangium (Mimosoideae, Phyllodineae) by Bradyrhizobium sp

Author

Gilles Béna, Antoine Galiana, Marie-Mathilde Perrineau, Paul Reddell, Yves Prin, Robin Duponnois, and Sergio Miana de Faria

Subjects
Fixation de l'azote, Infection threads, F62 - Physiologie végétale - Croissance et développement, nodosité racinaire, Root hair, Bradyrhizobium, Système racinaire, Nitrogen fixation, Acacia mangium, Botany, Axenic, Microscopie, biology, food and beverages, Cytologie, biology.organism_classification, K10 - Production forestière, Symbiosome, Mucilage, Mimosoideae, General Agricultural and Biological Sciences, Indeterminate nodule
Abstract

Acacia mangium Willd., a native tree in Australia and Papua New Guinea, has been introduced to countries in Asia and South America where plantations have been established that cover several hundred thousand ha. The present study investigated the early stages of the nodulation process in A. mangium using an homologous Australian Bradyrhizobium strain. After optimizing the axenic nodulation, histological and cytological studies were conducted using light and electron microscopy. These documented the proliferation of Bradyrhizobium, the lysis of mucilage at the root surface, root hair deformation and initiation, as well as the development and growth of multiple infection threads. A belt of tannin-filled cells was shown to surround the central nodular fixation zone. The nodules were of the indeterminate type and the bacteroids had a rod shape, without size modification and with few polyhydroxybutyrate (PHB) granules. Several bacteroids can share the same symbiosome. A. mangium exhibits both classical and novel features in its nodulation.

Published
2012

19. Genetic diversity of symbiotic Bradyrhizobium elkanii populations recovered from inoculated and non-inoculated Acacia mangium field trials in Brazil

Author

F. de C. Balieiro, S. M. de Faria, Gilles Béna, Antoine Galiana, Y. Prin, C. Le Roux, and Marie-Mathilde Perrineau

Subjects
DNA, Bacterial, Gene Transfer, Horizontal, Context (language use), Controlled inoculation, Plant Root Nodulation, Applied Microbiology and Biotechnology, Microbiology, Bradyrhizobium, Variation génétique, Bacterial Proteins, Nitrogen fixation, Génétique des populations, Acacia mangium, Botany, Symbiosis, Microbial inoculant, Phylogeny, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, Bradyrhizobium elkanii, Molecular systematics, Genetic diversity, biology, Acacia, Genetic Variation, P34 - Biologie du sol, Sequence Analysis, DNA, biology.organism_classification, Recombination, K10 - Production forestière, Genes, Bacterial, Genetic Loci, Root Nodules, Plant, Sequence Alignment, Acyltransferases, Brazil, Symbiotic bacteria, Bradyrhizobium japonicum
Abstract

Acacia mangium is a legume tree native to Australasia. Since the eighties, it has been introduced into many tropical countries, especially in a context of industrial plantations. Many field trials have been set up to test the effects of controlled inoculation with selected symbiotic bacteria versus natural colonization with indigenous strains. In the introduction areas, A. mangium trees spontaneously nodulate with local and often ineffective bacteria. When inoculated, the persistence of inoculants and possible genetic recombination with local strains remain to be explored. The aim of this study was to describe the genetic diversity of bacteria spontaneously nodulating A. mangium in Brazil and to evaluate the persistence of selected strains used as inoculants. Three different sites, several hundred kilometers apart, were studied, with inoculated and non-inoculated plots in two of them. Seventy-nine strains were isolated from nodules and sequenced on three housekeeping genes (glnII, dnaK and recA) and one symbiotic gene (nodA). All but one of the strains belonged to the Bradyrhizobium elkanii species. A single case of housekeeping gene transfer was detected among the 79 strains, suggesting an extremely low rate of recombination within B. elkanii, whereas the nodulation gene nodA was found to be frequently transferred. The fate of the inoculant strains varied depending on the site, with a complete disappearance in one case, and persistence in another. We compared our results with the sister species Bradyrhizobium japonicum, both in terms of population genetics and inoculant strain destiny.

Published
2011

20. Effective arbuscular mycorrhizal fungi in the roots of Tetraclinis articulata and Lavandula multifida in Moroccan Tetraclinis woodlands

Author

Salah Eddine Bakkali Yakhlef, Mohamed Abourouh, Marie-Mathilde Perrineau, Younes Abbas, Y. Prin, and Robin Duponnois

Subjects
Phylogénie, Lavandula, F62 - Physiologie végétale - Croissance et développement, Tetraclinis, Microbiology, Mycorhizé à vésicule et arbuscule, Système racinaire, boats, Glomeraceae, boats.ship_class, Botany, K01 - Foresterie - Considérations générales, Articulata, biology, fungi, biology.organism_classification, Endogonales, Lavandula multifida, Tetraclinis articulata, Infectious Diseases, Restriction fragment length polymorphism, Gigasporaceae
Abstract

The diversity of arbuscular mycorrhizal fungi (AMF) in roots of two plant species (arar, Tetraclinis articulata and lavender, Lavandula multifida) that exist alone or co-occur in Moroccan Tetraclinis woodlands was characterized using molecular techniques. The interaction between the two plant species on their root AMF communities was also studied. We analysed the large subunit (LSU) ribosomal RNA gene amplified by nested PCR from a root DNA extract using AM fungal-specific primers. A total of 200 cloned fragments from five root bulk samples of the two plant species were analysed by restriction fragment length polymorphism (RFLP) and 30 of them were sequenced. Phylogenetic analyses demonstrated that these RFLP types correspond to eight phylotypes: five belonged to the Gigasporaceae and three to the Glomeraceae. The highest diversity was found in the roots of T. articulata alone, followed by the association T. articulata/L. multifida and, finally, L. multifida alone. Many AMF were shared between the two species, although a few of them had a preference for one or the other. In addition, PCA analysis showed clearly that the AMF community colonizing T. articulata differed significantly from that colonizing L. multifida. Our results reveal an impact of plant interactions on the AMF community.

Published
2011

21. Bradyrhizobia nodulating the Acacia mangium x A. auriculiformis interspecific hybrid are specific and differ from those associated with both parental species

Author

Yani Japarudin, Philippe de Lajudie, Doreen Kim Soh Goh, Yves Prin, Antoine Galiana, Odile Domergue, Marie-Mathilde Perrineau, Christine Le Roux, Diana Tentchev, Robin Duponnois, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Yayasan Sabah Group (YSG), Sabah Softwoods Berhad, Partenaires INRAE, Institut de Recherche pour le Développement (IRD), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
F62 - Physiologie végétale - Croissance et développement, Applied Microbiology and Biotechnology, Plant Microbiology, Acacia mangium, Bradyrhizobium, Phylogeny, Soil Microbiology, Acacia auriculiformis, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, biology, Acacia, food and beverages, Biodiversity, RNA, Bacterial, Rhizobium, Root Nodules, Plant, BRADYRHIZOBIUM ELKANII, Biotechnology, DNA, Bacterial, Molecular Sequence Data, BRADYRHIZOBIUM JAPONICUM, 03 medical and health sciences, Species Specificity, Nitrogen Fixation, Botany, Animals, Symbiosis, Bradyrhizobium elkanii, 030304 developmental biology, Hybrid, RELATION HOTE-PARASITE, Chimera, 030306 microbiology, P34 - Biologie du sol, 15. Life on land, biology.organism_classification, K10 - Production forestière, RNA, Ribosomal, RRNA Operon, Food Science, Bradyrhizobium japonicum
Abstract

In the context of an increasing utilization of the interspecific hybrid Acacia mangium × A. auriculiformis as a plantation tree in the tropical humid zone, its symbiotic characterization was carried out in comparison with that of its two parental species. Rhizobium strains of diverse geographical origins were isolated from root nodules of the hybrid and its parents. Almost all Acacia hybrid isolates were fast growing on yeast extract-mannitol medium, in contrast to those isolated from both parental species, which were mostly slow growing. The rhizobium strains were characterized through partial sequencing of the rRNA operon. In the phylogenetic tree, almost all strains isolated from the hybrid were grouped together in a clade close to Bradyrhizobium japonicum , while all strains isolated from both parental species were close to Bradyrhizobium elkanii . Inoculation experiments performed under in vitro or greenhouse conditions showed that all strains were infective with their original hosts but exhibited very variable degrees of effectivity according to the host plant tested. Thus, homologous strain-host associations were more effective than heterologous ones. This shows that there is still a high potential for isolating and testing new strains from hybrids to be used as inoculants in the context of large-scale afforestation programs.

Published
2009

22. Molecular phylogeny of Pisolithus species from Moroccan forest woodlands

Author

Salah Eddine Bakkali Yakhlef, Marc Ducousso, Abdellatif Belkouri, Daniel Mousain, Marie-Mathilde Perrineau, Benaissa Kerdouh, Robin Duponnois, Mohamed Abourouh, Centre de Recherche Forestière, Ecologie Fonctionnelle et Biogéochimie des Sols (Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Ecole Nationale Supérieure Agronomique de Montpellier (ENSA M), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de recherche pour le développement (IRD [Sénégal]), Institut Agronomique Néo-Calédonien (IAC), Ecole Normale Supérieure de Casablanca, and Partenaires INRAE

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Phylogénie, ADN ribosomal, F62 - Physiologie végétale - Croissance et développement, 01 natural sciences, Quercus, taxonomy, growth-stimulation, morphology, ectomycorrhizal fungus, Cistus crispus, 0303 health sciences, ribosomal DNA, tinctorius, Cistus, F70 - Taxonomie végétale et phytogéographie, sequencing, Ectomycorhize, eucalyptus, Provenance, Forêt, Molecular phylogenetics, genetic-variability, RFLP, Taxonomy (biology), General Agricultural and Biological Sciences, Séquence nucléotidique, Distribution géographique, Symbiose, Pisolithus, australia, Biology, diversity, 03 medical and health sciences, pcr, Botany, ITS of, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ectomycorrhizal fungus pisolithus, Internal transcribed spacer, Arbre forestier, Ribosomal DNA, 030304 developmental biology, phylogenetic analysis, P35 - Fertilité du sol, P34 - Biologie du sol, Taxonomie, 15. Life on land, Pinus, biology.organism_classification, K10 - Production forestière, Basidiocarp, 010606 plant biology & botany
Abstract

International audience; The phylogenetic relationships among 200 Pisolithus basidiomata collected from pine, oak, and eucalypt forests and rockrose scrubs in Morocco were investigated. Using PCR-RFLP analysis of the internal transcribed spacer (ITS) of ribosomal DNA, this collection could be divided into 5 groups, by using PCR-RFLP analysis of the internal transcribed spacer (ITS) of ribosomal DNA. The ITS of a representative basidioma of each group was sequenced, and a phylogenetic analysis was performed. The dendrogram suggests that at least five Pisolithus species are present in Morocco. Pisolithus basidiomata collected in the Pinus and Quercus forests correspond to Pisolithus arrhizus and P. species 4 as previously described by Martin and colleagues in 2002. Those collected from the eucalyptus forests, under E. gomphocephala and E. camaldulensis, correspond to P. albus and P. microcarpus. Basidiomata collected from the rockrose scrubs, under Cistus crispus, C. monspeliensis or C. salviifolius, are all identified as Pisolithus species 3. Phylogenetic analyses showed that our different Pisolithus grouped well with Pisolithus specimens from other geographical origins.

Published
2009

23. Effects of Medicago truncatula genetic diversity, rhizobial competition, and strain effectiveness on the diversity of a natural Sinorhizobium species community

Author

Marie-Mathilde Perrineau, Jean-Claude Cleyet-Marel, Brigitte Brunel, Gilles Béna, Cécile Rangin, Institut de Recherche pour le Développement (IRD), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Acteurs, Ressources et Territoires dans le Développement (UMR ART-Dev), and Centre National de la Recherche Scientifique (CNRS)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Université de Perpignan Via Domitia (UPVD)-Université Paul-Valéry - Montpellier 3 (UPVM)

Subjects
DNA, Bacterial, Molecular Sequence Data, Population, NITROGEN FIXATION, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, Rhizobia, 03 medical and health sciences, Plant Microbiology, Species Specificity, RNA, Ribosomal, 16S, Genotype, Botany, Symbiosis, education, Polymorphism, Single-Stranded Conformational, Soil Microbiology, 030304 developmental biology, Genetics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Sinorhizobium meliloti, Genetic diversity, education.field_of_study, Ecology, biology, BIOCHIMIE, 030306 microbiology, Electrophoresis, Capillary, Genetic Variation, food and beverages, Genes, rRNA, Biodiversity, biochemical phenomena, metabolism, and nutrition, SINORHIZOBIUM MEDICAE, biology.organism_classification, Medicago truncatula, Bacterial Typing Techniques, GENOTYPE, Genes, Bacterial, Sinorhizobium, France, Restriction fragment length polymorphism, MEDICAGO TRUNCATULA, Polymorphism, Restriction Fragment Length, Food Science, Biotechnology
Abstract

We investigated the genetic diversity and symbiotic efficiency of 223 Sinorhizobium sp. isolates sampled from a single Mediterranean soil and trapped with four Medicago truncatula lines. DNA molecular polymorphism was estimated by capillary electrophoresis-single-stranded conformation polymorphism and restriction fragment length polymorphism on five loci ( IGS NOD , typA , virB11 , avhB11 , and the 16S rRNA gene). More than 90% of the rhizobia isolated belonged to the Sinorhizobium medicae species (others belonged to Sinorhizobium meliloti ), with different proportions of the two species among the four M. truncatula lines. The S. meliloti population was more diverse than that of S. medicae , and significant genetic differentiation among bacterial populations was detected. Single inoculations performed in tubes with each bacterial genotype and each plant line showed significant bacterium-plant line interactions for nodulation and N 2 fixation levels. Competition experiments within each species highlighted either strong or weak competition among genotypes within S. medicae and S. meliloti , respectively. Interspecies competition experiments showed S. meliloti to be more competitive than S. medicae for nodulation. Although not highly divergent at a nucleotide level, isolates collected from this single soil sample displayed wide polymorphism for both nodulation and N 2 fixation. Each M. truncatula line might influence Sinorhizobium soil population diversity differently via its symbiotic preferences. Our data suggested that the two species did not evolve similarly, with S. meliloti showing polymorphism and variable selective pressures and S. medicae showing traces of a recent demographic expansion. Strain effectiveness might have played a role in the species and genotype proportions, but in conjunction with strain adaptation to environmental factors.

Published
2008

24. Using Natural Selection to Explore the Adaptive Potential of Chlamydomonas reinhardtii

Author

Dana C. Price, Debashish Bhattacharya, Jeferson Gross, Jeffrey M. Boyd, Ehud Zelzion, Marie-Mathilde Perrineau, and Orly Levitan

Subjects
Evolutionary Genetics, Directed Evolution, Evolutionary Processes, Algae, Cellular respiration, Science, Population, Chlamydomonas reinhardtii, Bioengineering, Protein Engineering, Research and Analysis Methods, Photosynthesis, Polymorphism, Single Nucleotide, Cell Growth, Transcriptome, Model Organisms, Plant and Algal Models, Molecular Cell Biology, Botany, Natural Selection, Genetics, Selection, Genetic, education, Gene, Evolutionary Biology, Chlamydomonas Reinhardtii, education.field_of_study, Multidisciplinary, Natural selection, biology, Organisms, Biology and Life Sciences, Computational Biology, Cell Biology, Genomics, Plants, biology.organism_classification, Adaptation, Physiological, Biochemistry, Cell Processes, Genetic Polymorphism, Medicine, Population Genetics, Research Article, Biotechnology
Abstract

Improving feedstock is critical to facilitate the commercial utilization of algae, in particular in open pond systems where, due to the presence of competitors and pests, high algal growth rates and stress tolerance are beneficial. Here we raised laboratory cultures of the model alga Chlamydomonas reinhardtii under serial dilution to explore the potential of crop improvement using natural selection. The alga was evolved for 1,880 generations in liquid medium under continuous light (EL population). At the end of the experiment, EL cells had a growth rate that was 35% greater than the progenitor population (PL). The removal of acetate from the medium demonstrated that EL growth enhancement largely relied on efficient usage of this organic carbon source. Genome re-sequencing uncovered 1,937 polymorphic DNA regions in the EL population with 149 single nucleotide polymorphisms resulting in amino acid substitutions. Transcriptome analysis showed, in the EL population, significant up regulation of genes involved in protein synthesis, the cell cycle and cellular respiration, whereas the DNA repair pathway and photosynthesis were down regulated. Like other algae, EL cells accumulated neutral lipids under nitrogen depletion. Our work demonstrates transcriptome and genome-wide impacts of natural selection on algal cells and points to a useful strategy for strain improvement.

Published
2014

25. 'Ectrogella' Parasitoids of the Diatom Licmophora sp. are Polyphyletic

Author

Eileen Bresnan, Andrea Garvetto, Melina Dressler-Allame, Marie-Mathilde Perrineau, and Claire M. M. Gachon

Subjects
0301 basic medicine, Oomycete, Diatoms, education.field_of_study, biology, Olpidiopsis, Population, Zoology, 030108 mycology & parasitology, biology.organism_classification, Microbiology, single cell, 03 medical and health sciences, Monophyly, Fragilaria, 030104 developmental biology, Diatom, Sensu, Oomycetes, Polyphyly, Peronosporomycota, Taxonomy (biology), Anisolpidium, education, Phylogeny
Abstract

The diatom genera Licmophora and Fragilaria are frequent epiphytes on marine macroalgae and can be infected by intracellular parasitoids traditionally assigned to the oomycete genus Ectrogella. Much debate and uncertainty remains about the taxonomy of these oomycetes, not least due to their morphological and developmental plasticity. Here, we used single-cell techniques to obtain partial sequences of the parasitoids 18S and cox2 genes. The former falls into two recently identified clades of Pseudo-nitzschia parasites temporarily named OOM_1_2 and OOM_2, closely related to the genera of brown and red algal pathogens Anisolpidium and Olpidiopsis. A third group of sequences falls at the base of the red algal parasites assigned to Olpidiopsis. In one instance, two oomycete parasitoids seemed to co-exist in a single diatom cell; this co-occurrence of distinct parasitoid taxa not only within a population of diatom epiphytes, but also within the same host cell, possibly explains the ongoing confusion in the taxonomy of these parasitoids. We demonstrate the polyphyly of Licmophora parasitoids previously assigned to Ectrogella (sensu Sparrow, 1960) and show that parasites of red algae assigned to the genus Olpidiopsis are most likely not monophyletic. We conclude that combining single-cell microscopy and molecular methods is necessary for their full characterisation.

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26. Parallelisable non-invasive biomass, fitness and growth measurement of macroalgae and other protists with nephelometry

Author

Christophe Destombe, Yacine Badis, Claire M. M. Gachon, Marie-Mathilde Perrineau, Benoît Calmes, Myriam Valero, J. Mark Cock, Martina Strittmatter, Céline Rousseau, Bertrand Jacquemin, Scottish Association for Marine Science (SAMS), Evolutionary Biology and Ecology of Algae (EBEA), Pontificia Universidad Católica de Chile (UC)-Sorbonne Université (SU)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Biomass, Biology, 01 natural sciences, 03 medical and health sciences, Aquaculture, Algae, Botany, 14. Life underwater, Chlorophyll fluorescence, business.industry, [SDE.IE]Environmental Sciences/Environmental Engineering, Spectroscopy methods, Non invasive, fungi, Algal cultivation, biology.organism_classification, Spore, 030104 developmental biology, Phenotyping, business, Agronomy and Crop Science, Nephelometry, 010606 plant biology & botany, Biotechnology
Abstract

International audience; With the exponential development of algal aquaculture and blue biotechnology, there is a strong demand for simple, inexpensive, high-throughput, quantitative phenotyping assays to measure the biomass, growth and fertility of algae and other marine protists. Here, we validate nephelometry, a method that relies on measuring the scattering of light by particles in suspension, as a non-invasive tool to measure in real-time the biomass of aquatic micro-organisms, such as microalgae, filamentous algae, as well as non-photosynthetic protists. Nephelometry is equally applicable to optic density and chlorophyll fluorescence measurements for the quantification of some microalgae, but outperforms other spectroscopy methods to quantify the biomass of biofilm-forming and filamentous algae, highly pigmented species and non-photosynthetic eukaryotes. Thanks to its insensitivity to the sample's pigmentation, nephelometry is also the method of choice when chlorophyll content varies between samples or time points, for example due to abiotic stress or pathogen infection. As examples, we illustrate how nephelometry can be combined with fluorometry or image analysis to monitor the quantity and time-course of spore release in fertile kelps or the progression of symptoms in diseased algal cultures.

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