120 results on '"Corre E"'
Search Results
2. Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies.
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Doré, H, Guyet, U, Leconte, J, Farrant, GK, Alric, B, Ratin, M, Ostrowski, M, Ferrieux, M, Brillet-Guéguen, L, Hoebeke, M, Siltanen, J, Le Corguillé, G, Corre, E, Wincker, P, Scanlan, DJ, Eveillard, D, Partensky, F, Garczarek, L, Doré, H, Guyet, U, Leconte, J, Farrant, GK, Alric, B, Ratin, M, Ostrowski, M, Ferrieux, M, Brillet-Guéguen, L, Hoebeke, M, Siltanen, J, Le Corguillé, G, Corre, E, Wincker, P, Scanlan, DJ, Eveillard, D, Partensky, F, and Garczarek, L
- Abstract
The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change.
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- 2023
3. Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts.
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Blanchard, JL, Doré, H, Leconte, J, Guyet, U, Breton, S, Farrant, GK, Demory, D, Ratin, M, Hoebeke, M, Corre, E, Pitt, FD, Ostrowski, M, Scanlan, DJ, Partensky, F, Six, C, Garczarek, L, Blanchard, JL, Doré, H, Leconte, J, Guyet, U, Breton, S, Farrant, GK, Demory, D, Ratin, M, Hoebeke, M, Corre, E, Pitt, FD, Ostrowski, M, Scanlan, DJ, Partensky, F, Six, C, and Garczarek, L
- Abstract
Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of "who is where" by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage
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- 2022
4. Deciphering the infectious process of Colletotrichum lupini in lupin through transcriptomic and proteomic analysis
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Dubrulle G., Picot A., Madec S., Corre E., Pawtowski A., Baroncelli R., Zivy M., Balliau T., Le Floch G., Pensec F., Dubrulle G., Picot A., Madec S., Corre E., Pawtowski A., Baroncelli R., Zivy M., Balliau T., Le Floch G., and Pensec F.
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Anthracnose disease ,Pathogenicity factor ,Proteome ,Transcriptome - Abstract
The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other Colletotrichum species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the Colletotrichum acutatum species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of Colletotrichum spp. during the onset of plant infection.
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- 2020
5. Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses
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Dupont, Samuel, Lokmer, A., Corre, E., Auguet, Jean-christophe, Petton, Bruno, Toulza, E., Montagnani, Caroline, Tanguy, G., Pecqueur, D., Salmeron, C., Guillou, L., Desnues, C., La Scola, B., Bou Khalil, J., De Lorgeril, Julien, Mitta, Guillaume, Gueguen, Yannick, Escoubas, Jean Michel, Dupont, Samuel, Lokmer, A., Corre, E., Auguet, Jean-christophe, Petton, Bruno, Toulza, E., Montagnani, Caroline, Tanguy, G., Pecqueur, D., Salmeron, C., Guillou, L., Desnues, C., La Scola, B., Bou Khalil, J., De Lorgeril, Julien, Mitta, Guillaume, Gueguen, Yannick, and Escoubas, Jean Michel
- Abstract
Background The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. Results We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease. To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a natural environment either before or during a disease outbreak. Using metabarcoding and shotgun metagenomics, we demonstrate that hemolymph can be considered as an ecological niche hosting bacterial, protist and viral communities, each of them shaped by different factors and distinct from the corresponding communities in the surrounding seawater. Overall, we found that hemolymph microbiota is more strongly shaped by the environment than by host genetic background. Co-occurrence network analyses suggest a disruption of the microbial network after transplantation into natural environment during both non-infectious and infectious periods. Whereas we could not identify a common microbial community signature for healthy animals, OsHV-1 μVar virus dominated the hemolymph virome during the disease outbreak, without significant modifications of other microbiota components. Conclusion Our study shows that oyster hemolymph is a complex ecosystem containing diverse bacteria, protists and viruses, whose composition and dynamics are primarily determined by the environment. However, all of these are also shaped by oyster genetic backgrounds, indicating they indeed interact with the oyster host and are therefore not only of transi
- Published
- 2020
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6. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.
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Garczarek L, Guyet U, Doré H, Farrant GK, Hoebeke M, Brillet-Guéguen L, Bisch A, Ferrieux M, Siltanen J, Corre E, Le Corguillé G, Ratin M, Pitt FD, Ostrowski M, Conan M, Siegel A, Labadie K, Aury J-M, Wincker P, Scanlan DJ, Partensky F, Garczarek L, Guyet U, Doré H, Farrant GK, Hoebeke M, Brillet-Guéguen L, Bisch A, Ferrieux M, Siltanen J, Corre E, Le Corguillé G, Ratin M, Pitt FD, Ostrowski M, Conan M, Siegel A, Labadie K, Aury J-M, Wincker P, Scanlan DJ, and Partensky F
- Abstract
Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.
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- 2020
7. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria.
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Doré H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, Pitt FD, Ostrowski M, Six C, Brillet-Guéguen L, Hoebeke M, Bisch A, Le Corguillé G, Corre E, Labadie K, Aury J-M, Wincker P, Choi DH, Noh JH, Eveillard D, Scanlan DJ, Partensky F, Garczarek L, Doré H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, Pitt FD, Ostrowski M, Six C, Brillet-Guéguen L, Hoebeke M, Bisch A, Le Corguillé G, Corre E, Labadie K, Aury J-M, Wincker P, Choi DH, Noh JH, Eveillard D, Scanlan DJ, Partensky F, and Garczarek L
- Abstract
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates lik
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- 2020
8. A de novo approach to disentangle partner identity and function in holobiont systems
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Meng, A., Marchet, C., Corre, E., Peterlongo, P., Alberti, A., Da Silva, C., Wincker, P., Pelletier, E., Probert, I., Decelle, Johan, Le Crom, S., Not, F., Bittner, L., Meng, A., Marchet, C., Corre, E., Peterlongo, P., Alberti, A., Da Silva, C., Wincker, P., Pelletier, E., Probert, I., Decelle, Johan, Le Crom, S., Not, F., and Bittner, L.
- Abstract
BackgroundStudy of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept.ResultsWe considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner’s transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited.ConclusionsIn contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or po
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- 2018
9. Chloropicophyceae, a new class of picophytoplanktonic prasinophytes.
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Lopes dos-Santos, Antonina, Pollina, T., Gourvil, P., Corre, E., Marie, D., Garrido, José Luis, Rodríguez Hernández, Francisco José, Noël, M.H., Vaulot, Daniel, Eikrem, Wenche, Lopes dos-Santos, Antonina, Pollina, T., Gourvil, P., Corre, E., Marie, D., Garrido, José Luis, Rodríguez Hernández, Francisco José, Noël, M.H., Vaulot, Daniel, and Eikrem, Wenche
- Abstract
Prasinophytes are a paraphyletic group of nine lineages of green microalgae that are currently classified either at the class or order level or as clades without formal taxonomic description. Prasinophyte clade VII comprises picoplanktonic algae that are important components of marine phytoplankton communities, particularly in moderately oligotrophic waters. Despite first being cultured in the 1960s, this clade has yet to be formally described. Previous phylogenetic analyses using the 18S rRNA gene divided prasinophyte clade VII into three lineages, termed A, B and C, the latter formed by a single species, Picocystis salinarum, that to date has only been found in saline lakes. Strains from lineages A and B cannot be distinguished by light microscopy and have very similar photosynthetic pigment profiles corresponding to the prasino-2A pigment group. We obtained phenotypic and genetic data on a large set of prasinophyte clade VII culture strains that allowed us to clarify the taxonomy of this important marine group. We describe two novel classes, the Picocystophyceae and the Chloropicophyceae, the latter containing two novel genera, Chloropicon and Chloroparvula, and eight new species of marine picoplanktonic green algae
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- 2017
10. Responses of the arcto-boreal krill species Thysanoessa inermis to variations in water temperature: coupling Hsp70 isoform expressions with metabolism
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Huenerlage, Kim, Cascella, Kévin, Corre, E., Toomey, L., Lee, C.Y., Buchholz, Friedrich, Toullec, Jean-Yves, Huenerlage, Kim, Cascella, Kévin, Corre, E., Toomey, L., Lee, C.Y., Buchholz, Friedrich, and Toullec, Jean-Yves
- Abstract
Recent studies have indicated a metabolic temperature sensitivity in both the arcto-boreal krill species Thysanoessa inermis and Thysanoessa raschii that may determine these species' abundance and population persistence at lower latitudes (up to 40° N). T. inermis currently dominates the krill community in the Barents Sea and in the high Arctic Kongsfjord. We aimed to increase the knowledge on the upper thermal limit found in the latter species by estimating the CT50 value (19.7 °C) (critical temperature at which 50 % of animals are reactive) and by linking metabolic rate measurements with molecular approaches. Optical oxygen sensors were used to measure respiration rates in steps of 2 °C (from 0 to 16 °C). To follow the temperature-mediated mechanisms of passive response, i.e., as a proxy for molecular stress, molecular chaperone heat shock protein 70 (Hsp70) sequences were extracted from a transcriptome assembly, and the gene expression kinetics were monitored during an acute temperature exposure to 6 or 10 °C with subsequent recovery at 4 °C. Our results showed upregulation of hsp70 genes, especially the structurally constitutive and mitochondrial isoforms. These findings confirmed the temperature sensitivity of T. inermis and showed that the thermal stress took place before reaching the upper temperature limit estimated by respirometry at 12 °C. This study provides a baseline for further investigations into the thermal tolerances of arcto-boreal Thysanoessa spp. and comparisons with other krill species under different climatic regimes, especially Antarctica.
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- 2016
11. The Ectocarpus genome and brown algal genomics
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Cock, J.M., Sterck, L., Ahmed, S., Allen, A. E., Amoutzias, G., Anthouard, V., Artiguenave, F., Arun, A., Aury, J. M., Badger, J. H., Beszteri, B., Billiau, K., Bonnet, E., Bothwell, J. H., Bowler, C., Boyen, C., Brownlee, C., Carrano, C. J., Charrier, B., Cho, G. Y., Coelho, S. M., Collen, J., Le Corguille, G., Corre, E., Dartevelle, L., Da Silva, C., Delage, L., Delaroque, N., Dittami, S. M., Doulbeau, Sylvie, Elias, M., Farnham, G., Gachon, C. M. M., Godfroy, O., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Kuepper, F. C., Lang, D., Le Bail, A., Luthringer, R., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P. J., Macaisne, N., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C. A., Nelson, D. R., Nyvall-Collen, P., Peters, A. F., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D.C., Scornet, D., Segurens, B., Strittmatter, M., Tonon, T., Tregear, James, Valentin, K., Von Dassow, P., Yamagishi, T., Rouze, P., Van de Peer, Y., Wincker, P., and Piganeau, G. (ed.)
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IRON-DEFICIENCY ,EVOLUTIONARY HISTORY ,PLANT MICRORNAS ,SILICULOSUS ,TOPOISOMERASE-VI ,fungi ,food and beverages ,DIATOM THALASSIOSIRA-PSEUDONANA ,PROTEIN FAMILY ,LAMINARIA-DIGITATA ,CHLAMYDOMONAS-REINHARDTII ,PHAEOPHYCEAE ,NORTH-ATLANTIC - Abstract
Brown algae are important organisms both because of their key ecological roles in coastal ecosystems and because of the remarkable biological features that they have acquired during their unusual evolutionary history. The recent sequencing of the complete genome of the filamentous brown alga Ectocarpus has provided unprecedented access to the molecular processes that underlie brown algal biology. Analysis of the genome sequence, which exhibits several unusual structural features, identified genes that are predicted to play key roles in several aspects of brown algal metabolism, in the construction of the multicellular bodyplan and in resistance to biotic and abiotic stresses. Information from the genome sequence is currently being used in combination with other genomic, genetic and biochemical tools to further investigate these and other aspects of brown algal biology at the molecular level. Here, we review some of the major discoveries that emerged from the analysis of the Ectocarpus genome sequence, with a particular focus on the unusual genome structure, inferences about brown algal evolution and novel aspects of brown algal metabolism.
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- 2012
12. The Ectocarpus genome and the independent evolution of multicellularity in brown algae
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Cock, J.M., Sterck, L., Rouzé, P., Scornet, D., Allen, A.E., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J.-M., Badger, J.H., Beszteri, B., Billiau, K., Bonnet, E., Bothwell, J.H., Bowler, C., Boyen, C., Brownlee, C., Carrano, C.J., Charrier, B., Cho, G.Y., Coelho, S.M., Collén, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S.M., Doulbeau, S., Elias, M., Farnham, G., Gachon, C.M.M., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F.C., Lang, D., Le Bail, A., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P.J., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C.A., Nelson, D.R., Nyvall-Collén, P., Peters, A.F., Pommier, C., Potin, Ph., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D.C., Segurens, B., Strittmatter, M., Tonon, T., Tregear, J.W., Valentin, K., von Dassow, P., Yamagishi, T., Van de Peer, Y., and Wincker, P.
- Abstract
Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related1. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1).We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic2 approaches to explore these and other aspects of brown algal biology further.
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- 2010
13. Comparative Transcriptome of Wild Type and Selected Strains of the Microalgae Tisochrysis lutea Provides Insights into the Genetic Basis, Lipid Metabolism and the Life Cycle
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Carrier, Gregory, Garnier, Matthieu, Le Cunff, Loic, Bougaran, Gael, Probert, Ian, De Vargas, Colomban, Corre, E, Cadoret, Jean-paul, Saint-jean, Bruno, Carrier, Gregory, Garnier, Matthieu, Le Cunff, Loic, Bougaran, Gael, Probert, Ian, De Vargas, Colomban, Corre, E, Cadoret, Jean-paul, and Saint-jean, Bruno
- Abstract
The applied exploitation of microalgae cultures has to date almost exclusively involved the use of wild type strains, deposited over decades in dedicated culture collections. Concomitantly, the concept of improving algae with selection programs for particular specific purposes is slowly emerging. Studying since a decade an economically and ecologically important haptophyte Tisochrysis lutea (Tiso), we took advantage of the availability of wild type (Tiso-Wt) and selected (Tiso-S2M2) strains to conduct a molecular variations study. This endeavour presented substantial challenges: the genome assembly was not yet available, the life cycle unknown and genetic diversity of Tiso-Wt poorly documented. This study brings the first molecular data in order to set up a selection strategy for that microalgae. Following high-throughput Illumina sequencing, transcriptomes of Tiso-Wt and Tiso-S2M2 were de novo assembled and annotated. Genetic diversity between both strains was analyzed and revealed a clear conservation, while a comparison of transcriptomes allowed identification of polymorphisms resulting from the selection program. Of 34,374 transcripts, 291 were differentially expressed and 165 contained positional polymorphisms (SNP, Indel). We focused on lipid over-accumulation of the Tiso-S2M2 strain and 8 candidate genes were identified by combining analysis of positional polymorphism, differential expression levels, selection signature and by study of putative gene function. Moreover, genetic analysis also suggests the existence of a sexual cycle and genetic recombination in Tisochrysis lutea.
- Published
- 2014
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14. The Ectocarpus genome and the independent evolution of multicellularity in the brown algae
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Cock, J. M., Sterck, L., Rouze, P., Scorne, D., Allen, A. E., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J. M., Badger, J. H., Beszteri, Bank, Billiau, K., Bonnet, E., Bothwell, J. H. F., Bowler, C., Boyen, C., Brownlee, C., Carrano, C. J., Charrier, B., Youn Cho, G., Coelho, S. M., Collén, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S. M., Doulbeau, S., Elias, M., Farnham, C., Gachon, C. M. M., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F. C., Lang, D., Le Bail, A., Leblan, C., Lerouge, P., Lohr, M., López-González, P. J., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C. A., Nelson, D. R., Nyvall-Collén, Pi, Peters, A. F., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S. A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D. C., Séguren, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, Klaus-Ulrich, von Dassow, P., Yamagishi, T., Van de Peer, Y., Wincker, P., Cock, J. M., Sterck, L., Rouze, P., Scorne, D., Allen, A. E., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J. M., Badger, J. H., Beszteri, Bank, Billiau, K., Bonnet, E., Bothwell, J. H. F., Bowler, C., Boyen, C., Brownlee, C., Carrano, C. J., Charrier, B., Youn Cho, G., Coelho, S. M., Collén, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S. M., Doulbeau, S., Elias, M., Farnham, C., Gachon, C. M. M., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F. C., Lang, D., Le Bail, A., Leblan, C., Lerouge, P., Lohr, M., López-González, P. J., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C. A., Nelson, D. R., Nyvall-Collén, Pi, Peters, A. F., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S. A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D. C., Séguren, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, Klaus-Ulrich, von Dassow, P., Yamagishi, T., Van de Peer, Y., and Wincker, P.
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- 2010
15. ATP Binding Cassette transporters associated with chemoresistance: transcriptional profiling in extreme cohorts and their prognostic impact in a cohort of 281 acute myeloid leukemia patients
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Marzac, C., primary, Garrido, E., additional, Tang, R., additional, Fava, F., additional, Hirsch, P., additional, De Benedictis, C., additional, Corre, E., additional, Lapusan, S., additional, Lallemand, J.-Y., additional, Marie, J.-P., additional, Jacquet, E., additional, and Legrand, O., additional
- Published
- 2011
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16. Long-term immune deficiency after allogeneic stem cell transplantation: B-cell deficiency is associated with late infections
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Corre, E., primary, Carmagnat, M., additional, Busson, M., additional, de Latour, R. P., additional, Robin, M., additional, Ribaud, P., additional, Toubert, A., additional, Rabian, C., additional, and Socie, G., additional
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- 2010
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17. Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels
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Corre Erwan, Dossat Carole, Lecompte Odile, Ripp Raymond, Boutet Isabelle, Tanguy Arnaud, and Lallier François H
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Bathymodiolus azoricus ,symbiosis ,gene expression ,environment ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The deep-sea hydrothermal vent mussel Bathymodiolus azoricus harbors thiotrophic and methanotrophic symbiotic bacteria in its gills. While the symbiotic relationship between this hydrothermal mussel and these chemoautotrophic bacteria has been described, the molecular processes involved in the cross-talking between symbionts and host, in the maintenance of the symbiois, in the influence of environmental parameters on gene expression, and in transcriptome variation across individuals remain poorly understood. In an attempt to understand how, and to what extent, this double symbiosis affects host gene expression, we used a transcriptomic approach to identify genes potentially regulated by symbiont characteristics, environmental conditions or both. This study was done on mussels from two contrasting populations. Results Subtractive libraries allowed the identification of about 1000 genes putatively regulated by symbiosis and/or environmental factors. Microarray analysis showed that 120 genes (3.5% of all genes) were differentially expressed between the Menez Gwen (MG) and Rainbow (Rb) vent fields. The total number of regulated genes in mussels harboring a high versus a low symbiont content did not differ significantly. With regard to the impact of symbiont content, only 1% of all genes were regulated by thiotrophic (SOX) and methanotrophic (MOX) bacteria content in MG mussels whereas 5.6% were regulated in mussels collected at Rb. MOX symbionts also impacted a higher proportion of genes than SOX in both vent fields. When host transcriptome expression was analyzed with respect to symbiont gene expression, it was related to symbiont quantity in each field. Conclusions Our study has produced a preliminary description of a transcriptomic response in a hydrothermal vent mussel host of both thiotrophic and methanotrophic symbiotic bacteria. This model can help to identify genes involved in the maintenance of symbiosis or regulated by environmental parameters. Our results provide evidence of symbiont effect on transcriptome regulation, with differences related to type of symbiont, even though the relative percentage of genes involved remains limited. Differences observed between the vent site indicate that environment strongly influences transcriptome regulation and impacts both activity and relative abundance of each symbiont. Among all these genes, those participating in recognition, the immune system, oxidative stress, and energy metabolism constitute new promising targets for extended studies on symbiosis and the effect of environmental parameters on the symbiotic relationships in B. azoricus.
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- 2011
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18. Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids
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Corre Erwan, Gschloessl Bernhard, Viegas Carla, Valente Marta, Pearson Gareth, Le Corguillé Gildas, Bailly Xavier, Peters Akira F, Jubin Claire, Vacherie Benoit, Cock J Mark, and Leblanc Catherine
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Evolution ,QH359-425 - Abstract
Abstract Background Heterokont algae, together with cryptophytes, haptophytes and some alveolates, possess red-algal derived plastids. The chromalveolate hypothesis proposes that the red-algal derived plastids of all four groups have a monophyletic origin resulting from a single secondary endosymbiotic event. However, due to incongruence between nuclear and plastid phylogenies, this controversial hypothesis remains under debate. Large-scale genomic analyses have shown to be a powerful tool for phylogenetic reconstruction but insufficient sequence data have been available for red-algal derived plastid genomes. Results The chloroplast genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus, have been fully sequenced. These species represent two distinct orders of the Phaeophyceae, which is a major group within the heterokont lineage. The sizes of the circular plastid genomes are 139,954 and 124,986 base pairs, respectively, the size difference being due principally to the presence of longer inverted repeat and intergenic regions in E. siliculosus. Gene contents of the two plastids are similar with 139-148 protein-coding genes, 28-31 tRNA genes, and 3 ribosomal RNA genes. The two genomes also exhibit very similar rearrangements compared to other sequenced plastid genomes. The tRNA-Leu gene of E. siliculosus lacks an intron, in contrast to the F. vesiculosus and other heterokont plastid homologues, suggesting its recent loss in the Ectocarpales. Most of the brown algal plastid genes are shared with other red-algal derived plastid genomes, but a few are absent from raphidophyte or diatom plastid genomes. One of these regions is most similar to an apicomplexan nuclear sequence. The phylogenetic relationship between heterokonts, cryptophytes and haptophytes (collectively referred to as chromists) plastids was investigated using several datasets of concatenated proteins from two cyanobacterial genomes and 18 plastid genomes, including most of the available red algal and chromist plastid genomes. Conclusion The phylogenetic studies using concatenated plastid proteins still do not resolve the question of the monophyly of all chromist plastids. However, these results support both the monophyly of heterokont plastids and that of cryptophyte and haptophyte plastids, in agreement with nuclear phylogenies.
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- 2009
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19. P-gp activity is a critical resistance factor against AVE9633 and DM4 cytotoxicity in leukaemia cell lines, but not a major mechanism of chemoresistance in cells from acute myeloid leukaemia patients
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Fava Fanny, Morjani Hamid, Marjanovic Zora, Zuany-Amorim Claudia, Faussat Anne-Marie, Perrot Jean-Yves, Cohen Simy, Tang Ruoping, Corre Elise, Legrand Ollivier, and Marie Jean-Pierre
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background AVE9633 is a new immunoconjugate comprising a humanized monoclonal antibody, anti-CD33 antigen, linked through a disulfide bond to the maytansine derivative DM4, a cytotoxic agent and potent tubulin inhibitor. It is undergoing a phase I clinical trial. Chemoresistance to anti-mitotic agents has been shown to be related, in part, to overexpression of ABC proteins. The aim of the present study was to investigate the potential roles of P-gp, MRP1 and BCRP in cytotoxicity in AVE9633-induced acute myeloid leukaemia (AML). Methods This study used AML cell lines expressing different levels of P-gp, MRP1 or BCRP proteins and twenty-five samples from AML patients. Expression and functionality of the transporter protein were analyzed by flow cytometry. The cytotoxicity of the drug was evaluated by MTT and apoptosis assays. Results P-gp activity, but not MRP1 and BCRP, attenuated AVE9633 and DM4 cytotoxicity in myeloid cell lines. Zosuquidar, a potent specific P-gp inhibitor, restored the sensitivity of cells expressing P-gp to both AVE9633 and DM4. However, the data from AML patients show that 10/25 samples of AML cells (40%) were resistant to AVE9633 or DM4 (IC50 > 500 nM), and this was not related to P-gp activity (p-Value: 0.7). Zosuquidar also failed to re-establish drug sensitivity. Furthermore, this resistance was not correlated with CD33 expression (p-Value: 0.6) in those cells. Conclusion P-gp activity is not a crucial mechanism of chemoresistance to AVE9633. For patients whose resistance to conventional anthracycline AML regimens is related to ABC protein expression, a combination with AVE9633 could be beneficial. Other mechanisms such as microtubule alteration could play an important role in chemoresistance to AVE9633.
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- 2009
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20. Candidate genes involved in biosynthesis and degradation of the main extracellular matrix polysaccharides of brown algae and their probable evolutionary history.
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Mazéas L, Bouguerba-Collin A, Cock JM, Denoeud F, Godfroy O, Brillet-Guéguen L, Barbeyron T, Lipinska AP, Delage L, Corre E, Drula E, Henrissat B, Czjzek M, Terrapon N, and Hervé C
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- Alginates metabolism, Genomics methods, Phaeophyceae genetics, Phaeophyceae metabolism, Phylogeny, Polysaccharides biosynthesis, Polysaccharides metabolism, Extracellular Matrix metabolism, Evolution, Molecular
- Abstract
Background: Brown algae belong to the Stramenopiles phylum and are phylogenetically distant from plants and other multicellular organisms. This independent evolutionary history has shaped brown algae with numerous metabolic characteristics specific to this group, including the synthesis of peculiar polysaccharides contained in their extracellular matrix (ECM). Alginates and fucose-containing sulphated polysaccharides (FCSPs), the latter including fucans, are the main components of ECMs. However, the metabolic pathways of these polysaccharides remain poorly described due to a lack of genomic data., Results: An extensive genomic dataset has been recently released for brown algae and their close sister species, for which we previously performed an expert annotation of key genes involved in ECM-carbohydrate metabolisms. Here we provide a deeper analysis of this set of genes using comparative genomics, phylogenetics analyses, and protein modelling. Two key gene families involved in both the synthesis and degradation of alginate were suggested to have been acquired by the common ancestor of brown algae and their closest sister species Schizocladia ischiensis. Our analysis indicates that this assumption can be extended to additional metabolic steps, and thus to the whole alginate metabolic pathway. The pathway for the biosynthesis of fucans still remains biochemically unresolved and we also investigate putative fucosyltransferase genes that may harbour a fucan synthase activity in brown algae., Conclusions: Our analysis is the first extensive survey of carbohydrate-related enzymes in brown algae, and provides a valuable resource for future research into the glycome and ECM of brown algae. The expansion of specific families related to alginate metabolism may have represented an important prerequisite for the evolution of developmental complexity in brown algae. Our analysis questions the possible occurrence of FCSPs outside brown algae, notably within their closest sister taxon and in other Stramenopiles such as diatoms. Filling this knowledge gap in the future will help determine the origin and evolutionary history of fucan synthesis in eukaryotes., (© 2024. The Author(s).)
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- 2024
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21. Transcriptomic responses of Antarctic clam Laternula elliptica to nanoparticles, at single and combined exposures reveal ecologically relevant biomarkers.
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Rondon R, Valdés C, Cosseau C, Bergami E, Cárdenas CA, Balbi T, Pérez-Toledo C, Garrido I, Perrois G, Chaparro C, Corre E, Corsi I, and González-Aravena M
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- Animals, Antarctic Regions, Biomarkers metabolism, Polystyrenes toxicity, Environmental Monitoring methods, Bivalvia drug effects, Bivalvia genetics, Titanium toxicity, Nanoparticles toxicity, Transcriptome drug effects, Water Pollutants, Chemical toxicity
- Abstract
In recent years micro- and nanoplastics and metal-oxide nanomaterials have been found in several environmental compartments. The Antarctic soft clam Laternula elliptica is an endemic Antarctic species having a wide distribution in the Southern Ocean. Being a filter-feeder, it could act as suitable bioindicator of pollution from nanoparticles also considering its sensitivity to various sources of stress. The present study aims to assess the impact of polystyrene nanoparticles (PS-NP) and the nanometal titanium-dioxide (n-TiO
2 ) on genome-wide transcript expression of L. elliptica either alone and in combination and at two toxicological relevant concentrations (5 and 50 µg/L) during 96 h exposure. Transcript-target qRT-PCR was performed with the aim to identify suitable biomarkers of exposure and effects. As expected, at the highest concentration tested, the clustering was clearer between control and exposed clams. A total of 221 genes resulted differentially expressed in exposed clams and control ones, and 21 of them had functional annotation such as ribosomal proteins, antioxidant, ion transport (osmoregulation), acid-base balance, immunity, lipid metabolism, cell adhesion, cytoskeleton, apoptosis, chromatin condensation and cell signaling. At functional level, relevant transcripts were shared among some treatments and could be considered as general stress due to nanoparticle exposure. After applying transcript-target approach duplicating the number of clam samples, four ecologically relevant transcripts were revealed as biomarkers for PS-NP, n-TiO2 and their combination at 50 µg/L, that could be used for monitoring clams' health status in different Antarctic localities., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2024
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22. A combination of 5-azacytidine and nivolumab is a potentially effective rescue therapy in relapsed/refractory AITL.
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Ricard L, Cervera P, Stocker N, Corre E, Van de Wyngaert Z, Banet A, Marjanovic Z, Dulery R, Bravetti C, Joly AC, Baylatry MT, and Coppo P
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- Humans, Female, Male, Aged, Middle Aged, Neoplasm Recurrence, Local drug therapy, Lymphoma, T-Cell, Peripheral drug therapy, Lymphoma, T-Cell, Peripheral mortality, Treatment Outcome, Aged, 80 and over, Drug Resistance, Neoplasm, Immune Checkpoint Inhibitors therapeutic use, Immune Checkpoint Inhibitors adverse effects, Nivolumab therapeutic use, Azacitidine therapeutic use, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Antineoplastic Combined Chemotherapy Protocols adverse effects
- Abstract
Introduction: Angioimmunoblastic T-cell lymphoma (AITL) is a peripheral T-cell lymphoma characterized by a T follicular helper cell phenotype expressing PD-1 (programmed cell death-1). AITL exhibits a poor response to conventional chemotherapy, with a median 5-year overall survival of 44% and a progression-free survival of 32%. Relapse is common, resulting in a median overall survival of 6 months. Recurrent mutations are detected in genes regulating DNA methylation, including TET2, DNMT3A, and IDH2 variants, along with the prevalent RHOA G17V mutation. In this context, patients treated with the hypomethylating agent 5-azacytidine achieved overall response and complete response rates of 75% and 41%, respectively. We hypothesized that targeted therapies combining anti-PD-1 checkpoint blockers with hypomethylating agents could be efficient in AITL patients and less toxic than standard chemotherapy., Methods: Here, we report the efficacy of a regimen combining 5-azacytidine and nivolumab in nine relapsed or refractory AITL patients., Results: This regimen was well-tolerated, especially in elderly patients. The overall response rate was 78%, including four partial responses (44%) and three complete responses (33%). Allogeneic hematopoietic stem cell transplantation was performed in two patients who reached complete response., Discussion: These preliminary favorable results may serve as a basis for further investigation in prospective studies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Ricard, Cervera, Stocker, Corre, Van de Wyngaert, Banet, Marjanovic, Dulery, Bravetti, Joly, Baylatry and Coppo.)
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- 2024
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23. Differential prognostic values of the three AKT isoforms in acute myeloid leukemia.
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Corre E, Soum C, Pfeifer R, Bessière C, Dailhau S, Marbœuf C, Meggetto F, Touriol C, Récher C, Bousquet M, and Pyronnet S
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- Humans, Core Binding Factor Alpha 2 Subunit genetics, Mutation, Phosphatidylinositol 3-Kinases genetics, Prognosis, Protein Isoforms genetics, Protein Isoforms metabolism, Leukemia, Myeloid, Acute genetics, Proto-Oncogene Proteins c-akt genetics, Proto-Oncogene Proteins c-akt metabolism
- Abstract
The PI3K-AKT-mTOR pathway lies at the confluence of signaling pathways in which various components are subjected to activating genetic alterations in acute myeloid leukemia (AML), thus contributing to oncogenesis. Three AKT isoforms exist in humans. However, whether one isoform predominates in AML remains unknown. This study reveals that AKT3 behaves very distinctly than AKT1 or AKT2 in both normal myeloid differentiation and AML. During normal differentiation, AKT3 is preferentially expressed in hematopoietic stem cells whilst AKT1 becomes preferentially expressed as cells differentiate into granulocytes or monocytes. AKT2 expression remains unchanged. In AML, AKT3 expression varies widely among patient samples and is counterintuitively high in mature/monocytic leukemia. Furthermore, a low level of AKT3 expression is strongly correlated to genetic alterations associated with a better outcome (NPM1 mutations and RUNX1-RUNX1T1 translocation), while a high level is correlated to alterations associated to a bad outcome (RUNX1 mutations; and SRSF2, U2AF1, SF3B1, ASXL1 and BCOR mutations occurring frequently in MDS and MPN). Consistently, a high AKT3 expression level appears as a very strong predictor of poor survival. Curiously, although modestly varying among AML samples, a high AKT1 expression shows in contrast as a strong predictor of a better patient outcome. These data suggest that AKT3 and AKT1 expressions have strong, yet opposite, prognostic values., (© 2024. The Author(s).)
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- 2024
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24. Comparative Population Transcriptomics Provide New Insight into the Evolutionary History and Adaptive Potential of World Ocean Krill.
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Choquet M, Lenner F, Cocco A, Toullec G, Corre E, Toullec JY, and Wallberg A
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- Animals, Phylogeny, Transcriptome, Gene Expression Profiling, Genomics, Antarctic Regions, Euphausiacea genetics
- Abstract
Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
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- 2023
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25. The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species.
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Lipinska AP, Krueger-Hadfield SA, Godfroy O, Dittami SM, Ayres-Ostrock L, Bonthond G, Brillet-Guéguen L, Coelho S, Corre E, Cossard G, Destombe C, Epperlein P, Faugeron S, Ficko-Blean E, Beltrán J, Lavaut E, Le Bars A, Marchi F, Mauger S, Michel G, Potin P, Scornet D, Sotka EE, Weinberger F, Cabral de Oliveira M, Guillemin ML, Plastino EM, and Valero M
- Subjects
- Ecosystem, Genomics, Genome, Gracilaria genetics, Rhodophyta genetics
- Abstract
Macroalgal (seaweed) genomic resources are generally lacking as compared with other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole-genome assemblies for two species (Gracilaria chilensis and Gracilaria gracilis), a draft genome assembly of Gracilaria caudata, and genome annotation of the previously published Gracilaria vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
- Published
- 2023
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26. Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies.
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Doré H, Guyet U, Leconte J, Farrant GK, Alric B, Ratin M, Ostrowski M, Ferrieux M, Brillet-Guéguen L, Hoebeke M, Siltanen J, Le Corguillé G, Corre E, Wincker P, Scanlan DJ, Eveillard D, Partensky F, and Garczarek L
- Subjects
- Seawater microbiology, Ecosystem, Ferric Compounds metabolism, Oceans and Seas, Metagenome, Multigene Family, Nitrogen metabolism, Phosphorus metabolism, Phylogeny, Synechococcus genetics, Synechococcus metabolism, Prochlorococcus genetics
- Abstract
The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change., (© 2023. The Author(s).)
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- 2023
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27. SulfAtlas, the sulfatase database: state of the art and new developments.
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Stam M, Lelièvre P, Hoebeke M, Corre E, Barbeyron T, and Michel G
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- Humans, Phylogeny, Databases, Factual, Sulfatases genetics, Sulfatases chemistry
- Abstract
SulfAtlas (https://sulfatlas.sb-roscoff.fr/) is a knowledge-based resource dedicated to a sequence-based classification of sulfatases. Currently four sulfatase families exist (S1-S4) and the largest family (S1, formylglycine-dependent sulfatases) is divided into subfamilies by a phylogenetic approach, each subfamily corresponding to either a single characterized specificity (or few specificities in some cases) or to unknown substrates. Sequences are linked to their biochemical and structural information according to an expert scrutiny of the available literature. Database browsing was initially made possible both through a keyword search engine and a specific sequence similarity (BLAST) server. In this article, we will briefly summarize the experimental progresses in the sulfatase field in the last 6 years. To improve and speed up the (sub)family assignment of sulfatases in (meta)genomic data, we have developed a new, freely-accessible search engine using Hidden Markov model (HMM) for each (sub)family. This new tool (SulfAtlas HMM) is also a key part of the internal pipeline used to regularly update the database. SulfAtlas resource has indeed significantly grown since its creation in 2016, from 4550 sequences to 162 430 sequences in August 2022., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2023
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28. metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.
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Zafeiropoulos H, Beracochea M, Ninidakis S, Exter K, Potirakis A, De Moro G, Richardson L, Corre E, Machado J, Pafilis E, Kotoulas G, Santi I, Finn RD, Cox CJ, and Pavloudi C
- Subjects
- Workflow, Metagenomics, Computational Biology, Metagenome, Software, Genomics
- Abstract
Background: Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner., Findings: Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case., Conclusions: metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data., (© The Author(s) 2023. Published by Oxford University Press GigaScience.)
- Published
- 2022
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29. Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts.
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Doré H, Leconte J, Guyet U, Breton S, Farrant GK, Demory D, Ratin M, Hoebeke M, Corre E, Pitt FD, Ostrowski M, Scanlan DJ, Partensky F, Six C, and Garczarek L
- Subjects
- Phylogeography, Seawater microbiology, Phylogeny, Oceans and Seas, Phytoplankton, Synechococcus genetics
- Abstract
Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21
st , 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus , Synechococcus , and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of "who is where" by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.- Published
- 2022
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30. Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella.
- Author
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Thomas-Bulle C, Bertrand D, Nagarajan N, Copley RR, Corre E, Hourdez S, Bonnivard É, Claridge-Chang A, and Jollivet D
- Subjects
- Acclimatization, Adaptation, Physiological, Animals, Genomics, Selection, Genetic, Polychaeta genetics
- Abstract
Background: The transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to separate of vent populations, promoting local adaptation and contributing to bursts of speciation and species specialization. The tube-dwelling worms Alvinella pompejana called the Pompeii worm and its sister species A. caudata live syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution., Results: We explored genomic patterns of divergence in the early and late stages of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations of Alvinella pompejana (early stage of separation) and between A. pompejana and its syntopic species Alvinella caudata (late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes of A. pompejana and A. caudata are clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement., Conclusion: Our analyses highlight the non-negligible role of natural selection on both the early and late stages of speciation in the iconic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed light on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time., (© 2022. The Author(s).)
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- 2022
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31. Structural and Functional Characterization of Orcokinin B-like Neuropeptides in the Cuttlefish ( Sepia officinalis ).
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Endress M, Zatylny-Gaudin C, Leprince J, Lefranc B, Corre E, Le Corguillé G, Bernay B, Leduc A, Rangama J, Mouret L, Lafont AG, Bondon A, and Henry J
- Subjects
- Amino Acid Sequence, Animals, Decapodiformes, Female, Neuropeptides, Sepia
- Abstract
The cuttlefish ( Sepia officinalis ) is a Cephalopod mollusk that lives in the English Channel and breeds in coastal spawning grounds in spring. A previous work showed that the control of egg-laying is monitored by different types of regulators, among which neuropeptides play a major role. They are involved in the integration of environmental cues, and participate in the transport of oocytes in the genital tract and in the secretion of capsular products. This study addresses a family of neuropeptides recently identified and suspected to be involved in the control of the reproduction processes. Detected by mass spectrometry and immunocytochemistry in the nerve endings of the accessory sex glands of the females and ovary, these neuropeptides are also identified in the hemolymph of egg-laying females demonstrating that they also have a hormone-like role. Released in the hemolymph by the sub-esophageal mass, a region that innervates the genital tract and the neurohemal area of the vena cava, in in vitro conditions these neuropeptides modulated oocyte transport and capsular secretion. Finally, in silico analyses indicated that these neuropeptides, initially called FLGamide, had extensive structural homology with orcokinin B, which motivated their name change.
- Published
- 2022
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32. [Resistance to BRAF inhibitors: A lesson from clinical observations].
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Dahmani C, Corre E, Dandou S, Mangé A, Radulescu O, Coopman PJ, Cuq P, and Larive RM
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- Cell Line, Tumor, Drug Resistance, Neoplasm genetics, Humans, MAP Kinase Signaling System, Mutation, Protein Kinase Inhibitors pharmacology, Protein Kinase Inhibitors therapeutic use, Neoplasms drug therapy, Neoplasms genetics, Neoplasms metabolism, Proto-Oncogene Proteins B-raf genetics, Proto-Oncogene Proteins B-raf metabolism
- Abstract
The MAPK/ERK pathway is an essential intracellular signaling pathway. Its deregulation is involved in tumor transformation and progression. The discovery of activating mutations of BRAF in various cancers has opened new therapeutic avenues with BRAF protein kinase inhibitors. Depending on the type of cancers, these inhibitors have shown either insufficient efficacy due to primary resistance of tumor cells or transient efficacy due to the development of acquired resistance. In this review, we revisit the discoveries that led to the development of BRAF inhibitors and detail the molecular and cellular mechanisms of resistance in cancers treated with these inhibitors. Understanding these mechanisms is crucial for developing more efficient therapeutic strategies., (© 2022 médecine/sciences – Inserm.)
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- 2022
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33. Inter-Specific Genetic Exchange Despite Strong Divergence in Deep-Sea Hydrothermal Vent Gastropods of the Genus Alviniconcha .
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Castel J, Hourdez S, Pradillon F, Daguin-Thiébaut C, Ballenghien M, Ruault S, Corre E, Tran Lu Y A, Mary J, Gagnaire PA, Bonhomme F, Breusing C, Broquet T, and Jollivet D
- Subjects
- Animals, DNA, Mitochondrial genetics, Electron Transport Complex IV genetics, Phylogeny, Snails, Hydrothermal Vents
- Abstract
Deep hydrothermal vents are highly fragmented and unstable habitats at all temporal and spatial scales. Such environmental dynamics likely play a non-negligible role in speciation. Little is, however, known about the evolutionary processes that drive population-level differentiation and vent species isolation and, more specifically, how geography and habitat specialisation interplay in the species history of divergence. In this study, the species range and divergence of Alviniconcha snails that occupy active Western Pacific vent fields was assessed by using sequence variation data of the mitochondrial Cox1 gene, RNAseq, and ddRAD-seq. Combining morphological description and sequence datasets of the three species across five basins, we confirmed that A. kojimai , A. boucheti , and A. strummeri , while partially overlapping over their range, display high levels of divergence in the three genomic compartments analysed that usually encompass values retrieved for reproductively isolated species with divergences rang from 9% to 12.5% (mtDNA) and from 2% to 3.1% (nuDNA). Moreover, the three species can be distinguished on the basis of their external morphology by observing the distribution of bristles and the shape of the columella. According to this sampling, A. boucheti and A. kojimai form an east-to-west species abundance gradient, whereas A. strummeri is restricted to the Futuna Arc/Lau and North Fiji Basins. Surprisingly, population models with both gene flow and population size heterogeneities among genomes indicated that these three species are still able to exchange genes due to secondary contacts at some localities after a long period of isolation.
- Published
- 2022
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34. Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas.
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Ferrieux M, Dufour L, Doré H, Ratin M, Guéneuguès A, Chasselin L, Marie D, Rigaut-Jalabert F, Le Gall F, Sciandra T, Monier G, Hoebeke M, Corre E, Xia X, Liu H, Scanlan DJ, Partensky F, and Garczarek L
- Abstract
Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ferrieux, Dufour, Doré, Ratin, Guéneuguès, Chasselin, Marie, Rigaut-Jalabert, Le Gall, Sciandra, Monier, Hoebeke, Corre, Xia, Liu, Scanlan, Partensky and Garczarek.)
- Published
- 2022
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35. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR.
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Waterhouse RM, Adam-Blondon AF, Agosti D, Baldrian P, Balech B, Corre E, Davey RP, Lantz H, Pesole G, Quast C, Glöckner FO, Raes N, Sandionigi A, Santamaria M, Addink W, Vohradsky J, Nunes-Jorge A, Willassen NP, and Lanfear J
- Subjects
- Computational Biology, Europe, Biodiversity, Biological Science Disciplines
- Abstract
Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity., Competing Interests: No competing interests were disclosed., (Copyright: © 2021 Waterhouse RM et al.)
- Published
- 2021
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36. Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp.
- Author
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Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai R, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouzé P, Van de Peer Y, Wincker P, Rombauts S, Porcel BM, and Guillou L
- Published
- 2021
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37. Marine Synechococcus picocyanobacteria: Light utilization across latitudes.
- Author
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Six C, Ratin M, Marie D, and Corre E
- Subjects
- Adaptation, Physiological genetics, Adaptation, Physiological physiology, Bacterial Proteins genetics, Cold Temperature, Ecosystem, Ecotype, Light, Metagenome genetics, Metagenomics methods, Photosynthesis genetics, Photosynthesis physiology, Seawater, Synechococcus genetics, Synechococcus physiology
- Abstract
The most ubiquitous cyanobacteria, Synechococcus , have colonized different marine thermal niches through the evolutionary specialization of lineages adapted to different ranges of temperature seawater. We used the strains of Synechococcus temperature ecotypes to study how light utilization has evolved in the function of temperature. The tropical Synechococcus (clade II) was unable to grow under 16 °C but, at temperatures >25 °C, induced very high growth rates that relied on a strong synthesis of the components of the photosynthetic machinery, leading to a large increase in photosystem cross-section and electron flux. By contrast, the Synechococcus adapted to subpolar habitats (clade I) grew more slowly but was able to cope with temperatures <10 °C. We show that growth at such temperatures was accompanied by a large increase of the photoprotection capacities using the orange carotenoid protein (OCP). Metagenomic analyzes revealed that Synechococcus natural communities show the highest prevalence of the ocp genes in low-temperature niches, whereas most tropical clade II Synechococcus have lost the gene. Moreover, bioinformatic analyzes suggested that the OCP variants of the two cold-adapted Synechococcus clades I and IV have undergone evolutionary convergence through the adaptation of the molecular flexibility. Our study points to an important role of temperature in the evolution of the OCP. We, furthermore, discuss the implications of the different metabolic cost of these physiological strategies on the competitiveness of Synechococcus in a warming ocean. This study can help improve the current hypotheses and models aimed at predicting the changes in ocean carbon fluxes in response to global warming., Competing Interests: The authors declare no competing interest.
- Published
- 2021
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38. Publisher Correction: Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams.
- Author
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Leduc A, Chaouni S, Pouzoulet F, De Marzi L, Megnin-Chanet F, Corre E, Stefan D, Habrand JL, Sichel F, and Laurent C
- Published
- 2021
- Full Text
- View/download PDF
39. Marine Transcriptomics Analysis for the Identification of New Antimicrobial Peptides.
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Houyvet B, Bouchon-Navaro Y, Bouchon C, Corre E, and Zatylny-Gaudin C
- Subjects
- Animals, Antimicrobial Peptides pharmacology, Bacteria drug effects, Bacteria growth & development, Erythrocytes drug effects, Fish Proteins pharmacology, Gene Expression Profiling, Hemolysis drug effects, Humans, Transcriptome, Anti-Bacterial Agents pharmacology, Antimicrobial Peptides genetics, Fish Proteins genetics, Perciformes genetics
- Abstract
Antimicrobial peptides (AMPs) participate in the immune system to avoid infection, are present in all living organisms and can be used as drugs. Fish express numerous AMP families including defensins, cathelicidins, liver-expressed antimicrobial peptides (LEAPs), histone-derived peptides, and piscidins (a fish-specific AMP family). The present study demonstrates for the first time the occurrence of several AMPs in lionfish ( Pterois volitans ). Using the lionfish transcriptome, we identified four transcript sequences encoding cysteine-rich AMPs and two new transcripts encoding piscidin-like peptides. These AMPs are described for the first time in a species of the Scorpaenidae family. A functional approach on new pteroicidins was carried out to determine antimicrobial sequences and potential uses, with a view to using some of these AMPs for human health or in aquaculture.
- Published
- 2021
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40. Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines.
- Author
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Karimi E, Geslain E, Belcour A, Frioux C, Aïte M, Siegel A, Corre E, and Dittami SM
- Abstract
Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases., Competing Interests: The authors declare there are no competing interests., (©2021 Karimi et al.)
- Published
- 2021
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41. High-throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally.
- Author
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Couton M, Baud A, Daguin-Thiébaut C, Corre E, Comtet T, and Viard F
- Abstract
High-throughput sequencing of amplicons (HTSA) has been proposed as an effective approach to evaluate taxonomic and genetic diversity at the same time. However, there are still uncertainties as to how the results produced by different bioinformatics treatments impact the conclusions drawn on biodiversity and population genetics indices.We evaluated the ability of six bioinformatics pipelines to recover taxonomic and genetic diversity from HTSA data obtained from controlled assemblages. To that end, 20 assemblages were produced using 354 colonies of Botrylloides spp., sampled in the wild in ten marinas around Brittany (France). We used DNA extracted from preservative ethanol (ebDNA) after various time of storage (3, 6, and 12 months), and from a bulk of preserved specimens (bulkDNA). DNA was amplified with primers designed for targeting this ascidian genus. Results obtained from HTSA data were compared with Sanger sequencing on individual zooids (i.e., individual barcoding).Species identification and relative abundance determined with HTSA data from either ebDNA or bulkDNA were similar to those obtained with traditional individual barcoding. However, after 12 months of storage, the correlation between HTSA and individual-based data was lower than after shorter durations. The six bioinformatics pipelines were able to depict accurately the genetic diversity using standard population genetics indices (H
S and FST ), despite producing false positives and missing rare haplotypes. However, they did not perform equally and dada2 was the only pipeline able to retrieve all expected haplotypes.This study showed that ebDNA is a nondestructive alternative for both species identification and haplotype recovery, providing storage does not last more than 6 months before DNA extraction. Choosing the bioinformatics pipeline is a matter of compromise, aiming to retrieve all true haplotypes while avoiding false positives. We here recommend to process HTSA data using dada2, including a chimera-removal step. Even if the possibility to use multiplexed primer sets deserves further investigation to expand the taxonomic coverage in future similar studies, we showed that primers targeting a particular genus allowed to reliably analyze this genus within a complex community., Competing Interests: None declared., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)- Published
- 2021
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42. Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams.
- Author
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Leduc A, Chaouni S, Pouzoulet F, De Marzi L, Megnin-Chanet F, Corre E, Stefan D, Habrand JL, Sichel F, and Laurent C
- Subjects
- Animals, Body Weight radiation effects, Dose-Response Relationship, Radiation, Gene Expression Profiling, Gene Expression Regulation radiation effects, Gene Ontology, Keratins metabolism, Mice, Inbred C57BL, Protein Interaction Maps genetics, RNA, Messenger genetics, RNA, Messenger metabolism, RNA, Untranslated genetics, RNA, Untranslated metabolism, Mice, Protons, Skin metabolism, Skin radiation effects, Transcriptome genetics, Whole-Body Irradiation
- Abstract
Proton therapy allows to avoid excess radiation dose on normal tissues. However, there are some limitations. Indeed, passive delivery of proton beams results in an increase in the lateral dose upstream of the tumor and active scanning leads to strong differences in dose delivery. This study aims to assess possible differences in the transcriptomic response of skin in C57BL/6 mice after TBI irradiation by active or passive proton beams at the dose of 6 Gy compared to unirradiated mice. In that purpose, total RNA was extracted from skin samples 3 months after irradiation and RNA-Seq was performed. Results showed that active and passive delivery lead to completely different transcription profiles. Indeed, 140 and 167 genes were differentially expressed after active and passive scanning compared to unirradiated, respectively, with only one common gene corresponding to RIKEN cDNA 9930021J03. Moreover, protein-protein interactions performed by STRING analysis showed that 31 and 25 genes are functionally related after active and passive delivery, respectively, with no common gene between both types of proton delivery. Analysis showed that active scanning led to the regulation of genes involved in skin development which was not the case with passive delivery. Moreover, 14 ncRNA were differentially regulated after active scanning against none for passive delivery. Active scanning led to 49 potential mRNA-ncRNA pairs with one ncRNA mainly involved, Gm44383 which is a miRNA. The 43 genes potentially regulated by the miRNA Gm44393 confirmed an important role of active scanning on skin keratin pathway. Our results demonstrated that there are differences in skin gene expression still 3 months after proton irradiation versus unirradiated mouse skin. And strong differences do exist in late skin gene expression between scattered or scanned proton beams. Further investigations are strongly needed to understand this discrepancy and to improve treatments by proton therapy.
- Published
- 2021
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43. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox.
- Author
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Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, and Delsuc F
- Subjects
- Animals, High-Throughput Nucleotide Sequencing veterinary, Nanopore Sequencing veterinary, Foxes classification, Foxes genetics, Genetic Variation, Genome, Hyaenidae classification, Hyaenidae genetics
- Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox ( Otocyon megalotis ) and the aardwolf ( Proteles cristatus ), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status ( P. cristatus and P. septentrionalis ) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species., Competing Interests: RA, MT, CS, NA, AK, EC, BN, FD No competing interests declared, (© 2021, Allio et al.)
- Published
- 2021
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44. Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes.
- Author
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Dorrell RG, Villain A, Perez-Lamarque B, Audren de Kerdrel G, McCallum G, Watson AK, Ait-Mohamed O, Alberti A, Corre E, Frischkorn KR, Pierella Karlusich JJ, Pelletier E, Morlon H, Bowler C, and Blanc G
- Subjects
- Chloroplasts genetics, DNA Fingerprinting methods, Genome genetics, Symbiosis genetics, Cyanobacteria genetics, Diatoms genetics, Gene Transfer, Horizontal genetics, Phylogeny
- Abstract
Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution., Competing Interests: The authors declare no competing interest.
- Published
- 2021
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45. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.
- Author
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Garczarek L, Guyet U, Doré H, Farrant GK, Hoebeke M, Brillet-Guéguen L, Bisch A, Ferrieux M, Siltanen J, Corre E, Le Corguillé G, Ratin M, Pitt FD, Ostrowski M, Conan M, Siegel A, Labadie K, Aury JM, Wincker P, Scanlan DJ, and Partensky F
- Subjects
- Bacterial Proteins genetics, Geography, Likelihood Functions, Phylogeny, User-Computer Interface, Aquatic Organisms genetics, Cyanobacteria genetics, Data Curation, Databases, Genetic, Genome, Bacterial, Information Systems
- Abstract
Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2021
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46. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp.
- Author
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Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai R, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouzé P, Van de Peer Y, Wincker P, Rombauts S, Porcel BM, and Guillou L
- Subjects
- Base Sequence, Evolution, Molecular, Introns physiology, Biological Evolution, DNA, Protozoan analysis, Dinoflagellida cytology, Dinoflagellida genetics, Organelles physiology, Protozoan Proteins analysis
- Abstract
Background: Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization., Results: We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions., Conclusion: These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
- Published
- 2021
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- View/download PDF
47. Efficacy of subcutaneous preemptive rituximab in immune-mediated thrombotic thrombocytopenic purpura: Experience from the first 12 cases.
- Author
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Delrue M, Baylatry MT, Joly AC, Corre E, Marjanovic Z, El-Khoury-Hanna N, Féger F, Suner L, Veyradier A, Stépanian A, and Coppo P
- Subjects
- Adult, Female, Humans, Injections, Subcutaneous, Male, Middle Aged, Purpura, Thrombocytopenic, Idiopathic blood, Purpura, Thrombocytopenic, Idiopathic prevention & control, Purpura, Thrombotic Thrombocytopenic blood, Purpura, Thrombotic Thrombocytopenic prevention & control, Rituximab administration & dosage
- Published
- 2021
- Full Text
- View/download PDF
48. Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection.
- Author
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Kayal E, Alves-de-Souza C, Farhat S, Velo-Suarez L, Monjol J, Szymczak J, Bigeard E, Marie D, Noel B, Porcel BM, Corre E, Six C, and Guillou L
- Abstract
Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya . We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Kayal, Alves-de-Souza, Farhat, Velo-Suarez, Monjol, Szymczak, Bigeard, Marie, Noel, Porcel, Corre, Six and Guillou.)
- Published
- 2020
- Full Text
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49. Erratum for Jouault et al., "Alterocin, an Antibiofilm Protein Secreted by Pseudoalteromonas sp. Strain 3J6".
- Author
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Jouault A, Gobet A, Simon M, Portier E, Perennou M, Corre E, Gaillard F, Vallenet D, Michel G, Fleury Y, Bazire A, and Dufour A
- Published
- 2020
- Full Text
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50. Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis.
- Author
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Dubrulle G, Picot A, Madec S, Corre E, Pawtowski A, Baroncelli R, Zivy M, Balliau T, Le Floch G, and Pensec F
- Abstract
The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other Colletotrichum species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the Colletotrichum acutatum species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of Colletotrichum spp. during the onset of plant infection.
- Published
- 2020
- Full Text
- View/download PDF
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