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Roussel Michaël - One of the best experts on this subject based on the ideXlab platform.
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Séquençage du génome du parasite intestinal Blastocystis sp. (ST7) : vers une meilleure compréhension des capacités métaboliques d'organites apparentés aux mitochondries chez ce microorganisme anaérobie
HAL CCSD, 2011Co-Authors: Roussel MichaëlAbstract:Blastocystis sp. is a highly prevalent anaerobic eukaryotic stramenopile parasite found in the intestinal tract of humans and various animals. This microorganism, sometimes associated with acute intestinal disorders, could be responsible for functional intestinal disorders such as the irritable bowel syndrom (IBS). As part of a collaborative sequencing project with the Genoscope (CEA Evry, France), we were able to caracterize the smallest stramenopile genome sequenced to date (18.8 Mbp) with a 6020 genes coding capacity. The gain of many genes through horizontal gene transfer is amajor characteristic of this genome, which shows extensive genomic rearrangements. Despite the anaerobic nature of Blastocytists sp., this eukaryote harbours nevertheless mitochondrion-like organelles (MLOs). We have shown that these organelles have a 29.27 kbp mitochondrial-type circular genome that lacks cytochrome coding genes. In silico analysis allowed us to predict the MLOs proteome (365 proteins), with the subsequent predictive model of the metabolic pathways associated with these organelles, including an electron transport chain (ETC) restricted to complex I and II. We have shown that MLOs shared common characteristics with anaerobic mitochondrion and hydrogenosomes (presence of a PFOR and an iron-hydrogenase), which could mean that Blastocystis sp. harbours modified anaerobic mitochondrion that resulted from the parasite adaptation to its anaerobic environment. In addition, Blastocytis sp. secretome prediction reveals the presence of potential virulence factors, which could be involved in the degradation of the intestinal epithelium as well as the host immune system bypass.Blastocystis sp., est un straménopile parasite anaérobie fréquemment rencontré dans le tractus gastro-intestinal de l’homme et de divers animaux. Ce microorganisme, parfois responsable de désordres digestifs aigus, pourrait conduire à des troubles fonctionnels intestinaux tels que le syndrome de l’intestin irritable (IBS). Le génome de Blastocystis sp., qui a fait l'objet d'un projet de séquençage en collaboration avec le Génoscope d’Evry, nous a permis de caractériser le plus petit génome de straménopile séquencé à ce jour (18,8 Mpb), avec une capacité codante de 6020 gènes. L’acquisition de nombreux gènes par transferts horizontaux est une caractéristique majeure de ce génome, qui montre d’abondants réarrangements génomiques. Bien qu’évoluant en anaérobiose, Blastocystis sp. possède des organites morphologiquement proches des mitochondries, appelés mitochondrion-like organelles (MLOs). Nous avons montré que ces organites comportaient un génome circulaire de type mitochondrial de 29,27 kpb, mais dépourvu des gènes codant pour les cytochromes. Des analyses in silico nous ont permis de caractériser le protéome des MLOs (365 protéines), conduisant à l’établissement d’un modèle prédictif des voies métaboliques associées à ces organites, avec notamment une chaine respiratoire limitée aux complexes I et II. Nous avons ainsi montré que les MLOs présentent des caractères communs aux mitochondries anaérobies et aux hydrogénosomes (présence d’une PFOR et d’une hydrogénase à fer), suggérant que Blastocystis sp. comporte des mitochondries anaérobies modifiées, qui résulteraient d’une adaptation du parasite à son environnement. Par ailleurs, la prédiction du sécrétome de Blastocystis sp. révèle la présence de facteurs de virulence potentiels, pouvant être impliqués dans l’altération de l’épithélium intestinal et le contournement du système immunitaire de l’hôte
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Genome sequencing of the intestinal parasite Blastocystis sp. (ST7) : towards a better understanding of the metabolic capacities of mitochondria-related organelles in this anaerobic microorganism
2011Co-Authors: Roussel MichaëlAbstract:Blastocystis sp., est un straménopile parasite anaérobie fréquemment rencontré dans le tractus gastro-intestinal de l’homme et de divers animaux. Ce microorganisme, parfois responsable de désordres digestifs aigus, pourrait conduire à des troubles fonctionnels intestinaux tels que le syndrome de l’intestin irritable (IBS). Le génome de Blastocystis sp., qui a fait l'objet d'un projet de séquençage en collaboration avec le Génoscope d’Evry, nous a permis de caractériser le plus petit génome de straménopile séquencé à ce jour (18,8 Mpb), avec une capacité codante de 6020 gènes. L’acquisition de nombreux gènes par transferts horizontaux est une caractéristique majeure de ce génome, qui montre d’abondants réarrangements génomiques. Bien qu’évoluant en anaérobiose, Blastocystis sp. possède des organites morphologiquement proches des mitochondries, appelés mitochondrion-like organelles (MLOs). Nous avons montré que ces organites comportaient un génome circulaire de type mitochondrial de 29,27 kpb, mais dépourvu des gènes codant pour les cytochromes. Des analyses in silico nous ont permis de caractériser le protéome des MLOs (365 protéines), conduisant à l’établissement d’un modèle prédictif des voies métaboliques associées à ces organites, avec notamment une chaine respiratoire limitée aux complexes I et II. Nous avons ainsi montré que les MLOs présentent des caractères communs aux mitochondries anaérobies et aux hydrogénosomes (présence d’une PFOR et d’une hydrogénase à fer), suggérant que Blastocystis sp. comporte des mitochondries anaérobies modifiées, qui résulteraient d’une adaptation du parasite à son environnement. Par ailleurs, la prédiction du sécrétome de Blastocystis sp. révèle la présence de facteurs de virulence potentiels, pouvant être impliqués dans l’altération de l’épithélium intestinal et le contournement du système immunitaire de l’hôte.Blastocystis sp. is a highly prevalent anaerobic eukaryotic stramenopile parasite found in the intestinal tract of humans and various animals. This microorganism, sometimes associated with acute intestinal disorders, could be responsible for functional intestinal disorders such as the irritable bowel syndrom (IBS). As part of a collaborative sequencing project with the Genoscope (CEA Evry, France), we were able to caracterize the smallest stramenopile genome sequenced to date (18.8 Mbp) with a 6020 genes coding capacity. The gain of many genes through horizontal gene transfer is amajor characteristic of this genome, which shows extensive genomic rearrangements. Despite the anaerobic nature of Blastocytists sp., this eukaryote harbours nevertheless mitochondrion-like organelles (MLOs). We have shown that these organelles have a 29.27 kbp mitochondrial-type circular genome that lacks cytochrome coding genes. In silico analysis allowed us to predict the MLOs proteome (365 proteins), with the subsequent predictive model of the metabolic pathways associated with these organelles, including an electron transport chain (ETC) restricted to complex I and II. We have shown that MLOs shared common characteristics with anaerobic mitochondrion and hydrogenosomes (presence of a PFOR and an iron-hydrogenase), which could mean that Blastocystis sp. harbours modified anaerobic mitochondrion that resulted from the parasite adaptation to its anaerobic environment. In addition, Blastocytis sp. secretome prediction reveals the presence of potential virulence factors, which could be involved in the degradation of the intestinal epithelium as well as the host immune system bypass
Mark J Cock - One of the best experts on this subject based on the ideXlab platform.
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development and physiology of the brown alga ectocarpus siliculosus two centuries of research
New Phytologist, 2007Co-Authors: Benedicte Charrier, Gurvan Michel, Thierry Tonon, Akira F Peters, Bernard Kloareg, Aude Le Bail, Catherine Boyen, Susana M Coelho, Philippe Potin, Mark J CockAbstract:Contents Summary 319 I. Introduction 320 II. Diversity and taxonomy, distribution and ecology 321 III. Development 321 IV. Metabolism 326 V. Interactions with the environment 327 VI. Conclusion 328 Acknowledgements 329 References 329 Summary Brown algae share several important features with land plants, such as their photoautotrophic nature and their cellulose-containing wall, but the two groups are distantly related from an evolutionary point of view. The heterokont phylum, to which the brown algae belong, is a eukaryotic crown group that is phylogenetically distinct not only from the green lineage, but also from the red algae and the opisthokont phylum (fungi and animals). As a result of this independent evolutionary history, the brown algae exhibit many novel features and, moreover, have evolved complex multicellular development independently of the other major groups already mentioned. In 2004, a consortium of laboratories, including the Station Biologique in Roscoff and Genoscope, initiated a project to sequence the genome of Ectocarpus siliculosus, a small filamentous brown alga that is found in temperate, coastal environments throughout the globe. The E. siliculosus genome, which is currently being annotated, is expected to be the first completely characterized genome of a multicellular alga. In this review we look back over two centuries of work on this brown alga and highlight the advances that have led to the choice of E. siliculosus as a genomic and genetic model organism for the brown algae.
Benedicte Charrier - One of the best experts on this subject based on the ideXlab platform.
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development and physiology of the brown alga ectocarpus siliculosus two centuries of research
New Phytologist, 2007Co-Authors: Benedicte Charrier, Gurvan Michel, Thierry Tonon, Akira F Peters, Bernard Kloareg, Aude Le Bail, Catherine Boyen, Susana M Coelho, Philippe Potin, Mark J CockAbstract:Contents Summary 319 I. Introduction 320 II. Diversity and taxonomy, distribution and ecology 321 III. Development 321 IV. Metabolism 326 V. Interactions with the environment 327 VI. Conclusion 328 Acknowledgements 329 References 329 Summary Brown algae share several important features with land plants, such as their photoautotrophic nature and their cellulose-containing wall, but the two groups are distantly related from an evolutionary point of view. The heterokont phylum, to which the brown algae belong, is a eukaryotic crown group that is phylogenetically distinct not only from the green lineage, but also from the red algae and the opisthokont phylum (fungi and animals). As a result of this independent evolutionary history, the brown algae exhibit many novel features and, moreover, have evolved complex multicellular development independently of the other major groups already mentioned. In 2004, a consortium of laboratories, including the Station Biologique in Roscoff and Genoscope, initiated a project to sequence the genome of Ectocarpus siliculosus, a small filamentous brown alga that is found in temperate, coastal environments throughout the globe. The E. siliculosus genome, which is currently being annotated, is expected to be the first completely characterized genome of a multicellular alga. In this review we look back over two centuries of work on this brown alga and highlight the advances that have led to the choice of E. siliculosus as a genomic and genetic model organism for the brown algae.
Delbac Frédéric - One of the best experts on this subject based on the ideXlab platform.
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Séquençage du génome du parasite intestinal Blastocystis sp. (ST7) (vers une meilleure compréhension des capacités métaboliques d'organites apparentés aux mitochondries chez ce microorganisme anaérobie)
2011Co-Authors: Roussel, Michaël Frédéric Pierre, Delbac FrédéricAbstract:Blastocystis sp., est un straménopile parasite anaérobie fréquemment rencontré dans le tractus gastro-intestinal de l homme et de divers animaux. Ce microorganisme, parfois responsable de désordres digestifs aigus, pourrait conduire à des troubles fonctionnels intestinaux tels que le syndrome de l intestin irritable (IBS). Le génome de Blastocystis sp., qui a fait l'objet d'un projet de séquençage en collaboration avec le Génoscope d Evry, nous a permis de caractériser le plus petit génome de straménopile séquencé à ce jour (18,8 Mpb), avec une capacité codante de 6020 gènes. L acquisition de nombreux gènes par transferts horizontaux est une caractéristique majeure de ce génome, qui montre d abondants réarrangements génomiques. Bien qu évoluant en anaérobiose, Blastocystis sp. possède des organites morphologiquement proches des mitochondries, appelés mitochondrion-like organelles (MLOs). Nous avons montré que ces organites comportaient un génome circulaire de type mitochondrial de 29,27 kpb, mais dépourvu des gènes codant pour les cytochromes. Des analyses in silico nous ont permis de caractériser le protéome des MLOs (365 protéines), conduisant à l établissement d un modèle prédictif des voies métaboliques associées à ces organites, avec notamment une chaine respiratoire limitée aux complexes I et II. Nous avons ainsi montré que les MLOs présentent des caractères communs aux mitochondries anaérobies et aux hydrogénosomes (présence d une PFOR et d une hydrogénase à fer), suggérant que Blastocystis sp. comporte des mitochondries anaérobies modifiées, qui résulteraient d une adaptation du parasite à son environnement. Par ailleurs, la prédiction du sécrétome de Blastocystis sp. révèle la présence de facteurs de virulence potentiels, pouvant être impliqués dans l altération de l épithélium intestinal et le contournement du système immunitaire de l hôte.Blastocystis sp. is a highly prevalent anaerobic eukaryotic stramenopile parasite found in the intestinal tract of humans and various animals. This microorganism, sometimes associated with acute intestinal disorders, could be responsible for functional intestinal disorders such as the irritable bowel syndrom (IBS). As part of a collaborative sequencing project with the Genoscope (CEA Evry, France), we were able to caracterize the smallest stramenopile genome sequenced to date (18.8 Mbp) with a 6020 genes coding capacity. The gain of many genes through horizontal gene transfer is amajor characteristic of this genome, which shows extensive genomic rearrangements. Despite the anaerobic nature of Blastocytists sp., this eukaryote harbours nevertheless mitochondrion-like organelles (MLOs). We have shown that these organelles have a 29.27 kbp mitochondrial-type circular genome that lacks cytochrome coding genes. In silico analysis allowed us to predict the MLOs proteome (365 proteins), with the subsequent predictive model of the metabolic pathways associated with these organelles, including an electron transport chain (ETC) restricted to complex I and II. We have shown that MLOs shared common characteristics with anaerobic mitochondrion and hydrogenosomes (presence of a PFOR and an iron-hydrogenase), which could mean that Blastocystis sp. harbours modified anaerobic mitochondrion that resulted from the parasite adaptation to its anaerobic environment. In addition, Blastocytis sp. secretome prediction reveals the presence of potential virulence factors, which could be involved in the degradation of the intestinal epithelium as well as the host immune system bypass.CLERMONT FD-Bib.électronique (631139902) / SudocSudocFranceF
Wincker Patrick - One of the best experts on this subject based on the ideXlab platform.
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Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
'Springer Science and Business Media LLC', 2019Co-Authors: Sieracki, Michael E., Wincker Patrick, Logares Ramiro, Poulton N.j., Jaillon Olivier, Colomban De ,vargas, Rubinat-ripoll Laura, Stepanauskas R., Massana RamonAbstract:This article is Tara Oceans contribution number 87.-- 11 pages, 6 figures, 1 table, supplemental material https://dx.doi.org/10.1038/s41598-019-42487-1Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filteredFunding was provided by the following sponsors: U.S. NSF grant DEB-1031049; CNRS (in particular Groupement de Recherche GDR3280); European Molecular Biology Laboratory (EMBL), Genoscope/CEA; the French Government ‘Investissements d’Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08; Agence Nationale de la Recherche; European Union FP7 (MicroB3/No.287589); and EU project SINGEK (H2020-MSCA-ITN-2015-675752). RL was supported by a RyC fellowship (RYC-2013-12554, MINECO, Spain). We also thank the support and commitment of agnès b. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the Eléctricité de France (EDF) Foundation, Fondation pour la recherche sur la biodiversité (FRB), the Foundation Prince Albert II de Monaco, the Tara Foundation, its schooner and teams. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who graciously granted sampling permissionsPeer Reviewe
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Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans
'Springer Science and Business Media LLC', 2018Co-Authors: Seeleuthner Yoann, Acinas, Silvia G., Logares Ramiro, Mangot Jean-françois, Massana Ramon, Wincker PatrickAbstract:Seeleuthner, Yoann ... et al.-- This article is contribution number 63 of Tara Oceans.-- 10 pages, 4 figures, 1 table, data availability, supplementary material https://dx.doi.org/10.1038/s41467-017-02235-3Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecologyWe thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Governement ‘Investissement d’Avenir’ programs Oceanomics (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), Fund for Scientific Research-Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects ‘PHYTBACK/ANR-2010-1709-01’, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, TARA-GIRUS/ANR-09-PCS-GENM-218), EU FP7 (MicroB3/No. 287589, IHMS/HEALTH-F4-2010-261376), ERC Advanced Grant Award to CB (Diatomite: 294823), US NSF grant DEB-1031049 to M.E.S. and R.S., FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)Peer Reviewe
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A global ocean atlas of eukaryotic genes
'Springer Science and Business Media LLC', 2018Co-Authors: Carradec Quentin, Acinas, Silvia G., Wincker PatrickAbstract:Carradec, Quentin ... et al.-- This article is contribution number 62 of Tara Oceans.-- 13 pages, 6 figures, data availability, supplementary material https://dx.doi.org/10.1038/s41467-017-02342-1While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistryWe thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Governement ‘Investissement d’Avenir’ programs Oceanomics (ANR-11-BTBR-0008), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001–02), and FRANCE GENOMIQUE (ANR-10-INBS-09), Fund for Scientific Research—Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects ‘PHYTBACK/ANR-2010–1709–01’, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, TARA-GIRUS/ANR-09-PCS-GENM-218), EU FP7 (MicroB3/No.287589), ERC Advanced Grant Award (Diatomite: 294823), the LouisD foundation of the Institut de France, a Radcliffe Institute Fellowship from Harvard University to CB, JSPS/MEXT KAKENHI (Nos. 26430184, 16H06437, 16H06429, 16K21723, 16KT0020), The Canon Foundation (No. 203143100025), agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner, and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org). We also acknowledge C. Scarpelli for support in high-performance computing. Computations were performed using the platine, titane and curie HPC machine provided through GENCI grants (t2011076389, t2012076389, t2013036389, t2014036389, t2015036389, and t2016036389)Peer Reviewe
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Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition
'Springer Science and Business Media LLC', 2017Co-Authors: Alberti Adriana, Acinas, Silvia G., Cornejo-castillo, Francisco M., Ferrera Isabel, Royo-llonch Marta, Logares Ramiro, Fernández-gómez Beatriz, Wincker PatrickAbstract:Alberti, Adriana ... et al.-- 20 pages, 6 figures, 2 tablesA unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystemsWe thank the commitment of the following people and sponsors: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Government 'Investissements d'Avenir' programmes OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08), Agence Nationale de la Recherche, European Union FP7 (MicroB3/No.287589) and the U.S. National Science Foundation awards DEB-1031049, OCE-0623288, OCE-821374 and OCE-1019242 (to M.E.S. and R.S.) and OCE-1335810 (to R.S.). Additional funding was provided by Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS and by Japan Society for the Promotion of Science (JSPS)/KAKENHI (grant numbers 26430184, 16H06429, 16K21723 and 16H06437). We also thank the support and commitment of agnès b. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the Eléctricité de France (EDF) Foundation, Fondation pour la recherche sur la biodiversité (FRB), the Foundation Prince Albert II de Monaco, the Tara Foundation, its schooner and teamsPeer Reviewe
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Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton
'Springer Science and Business Media LLC', 2014Co-Authors: Von Dassow Peter, Wincker Patrick, Da Silva Corinne, John Uwe, Ogata Hiroyuki, Probert Ian, Bendif, El Mahdi, Kege, Jessica U., Audic Stephane, Claverie Jean-michelAbstract:© International Society for Microbial Ecology, 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 1365–1377, doi:10.1038/ismej.2014.221.Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.This research was supported by a Marie Curie International Incoming Fellowship FUNSEXDEPHYND to PvD within the 7th European Community Framework Programme, FONDECYT Projects 1110575 (to PvD) and 312004 (to DM-F), the French Agence Nationale de la Recherche/Investissements d’Avenir Grants POSEIDON and OCEANOMICS (Grant No. ANR-11-BTBR-0008 to CdV and IP), the European ERA-net program BiodivERsA under the BioMarks project (to EMB), funding from NASA and NSF (Grants NNX11AF55G and EF-0424599 to DMG and SD), the Genoscope 2007-2008 sequencing initiative and the PACES research program of the Alfred Wegener Helmholtz Institute Helmhotz Centre for Polar and Marine Research