Author: "Benoit Vacherie" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Benoit Vacherie"' showing total 44 results

Start Over Author "Benoit Vacherie"

44 results on '"Benoit Vacherie"'

1. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author: Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni
Subjects: General. Including nature conservation, geographical distribution, QH1-199.5
Abstract: Abstract A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.
Published: 2024
Full Text: View/download PDF

2. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author: Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni
Subjects: General. Including nature conservation, geographical distribution, QH1-199.5
Published: 2024
Full Text: View/download PDF

3. Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy

Author: Kevin Sugier, Benoit Vacherie, Astrid Cornils, Patrick Wincker, Jean-Louis Jamet, and Mohammed-Amin Madoui
Subjects: Chitin, Microscopy, Biology marine, Anatomy, Copepod, Oithona, Medicine, Biology (General), QH301-705.5
Abstract: Among copepods, which are the most abundant animals on Earth, the genus Oithona is described as one of the most numerous and plays a major role in the marine food chain and biogeochemical cycles, particularly through the excretion of chitin-coated fecal pellets. Despite the morphology of several Oithona species is well known, knowledge of its internal anatomy and chitin distribution is still limited. To answer this problem, Oithona nana and O. similis individuals were stained by Wheat Germ Agglutinin-Fluorescein IsoThioCyanate (WGA-FITC) and DiAmidino-2-PhenylIndole (DAPI) for fluorescence microscopy observations. The image analyses allowed a new description of the organization and chitin content of the digestive and reproductive systems of Oithona male and female. Chitin microfibrils were found all along the digestive system from the stomach to the hindgut with a higher concentration at the peritrophic membrane of the anterior midgut. Several midgut shrinkages were observed and proposed to be involved in faecal pellet shaping and motion. Amorphous chitin structures were also found to be a major component of the ducts and seminal vesicles and receptacles. The rapid staining protocol we proposed allowed a new insight into the Oithona internal anatomy and highlighted the role of chitin in the digestion and reproduction. This method could be applied to a wide range of copepods in order to perform comparative anatomy analyses.
Published: 2018
Full Text: View/download PDF

4. Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82.

Author: Sylvie Miquel, Eric Peyretaillade, Laurent Claret, Amélie de Vallée, Carole Dossat, Benoit Vacherie, El Hajji Zineb, Beatrice Segurens, Valerie Barbe, Pierre Sauvanet, Christel Neut, Jean-Frédéric Colombel, Claudine Medigue, Francisco J M Mojica, Pierre Peyret, Richard Bonnet, and Arlette Darfeuille-Michaud
Subjects: Medicine, Science
Abstract: BACKGROUND: Ileal lesions of Crohn's disease (CD) patients are abnormally colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells and macrophages. PRINCIPAL FINDINGS: We report here the complete genome sequence of E. coli LF82, the reference strain of adherent-invasive E. coli associated with ileal Crohn's disease. The LF82 genome of 4,881,487 bp total size contains a circular chromosome with a size of 4,773,108 bp and a plasmid of 108,379 bp. The analysis of predicted coding sequences (CDSs) within the LF82 flexible genome indicated that this genome is close to the avian pathogenic strain APEC_01, meningitis-associated strain S88 and urinary-isolated strain UTI89 with regards to flexible genome and single nucleotide polymorphisms in various virulence factors. Interestingly, we observed that strains LF82 and UTI89 adhered at a similar level to Intestine-407 cells and that like LF82, APEC_01 and UTI89 were highly invasive. However, A1EC strain LF82 had an intermediate killer phenotype compared to APEC-01 and UTI89 and the LF82 genome does not harbour most of specific virulence genes from ExPEC. LF82 genome has evolved from those of ExPEC B2 strains by the acquisition of Salmonella and Yersinia isolated or clustered genes or CDSs located on pLF82 plasmid and at various loci on the chromosome. CONCLUSION: LF82 genome analysis indicated that a number of genes, gene clusters and pathoadaptative mutations which have been acquired may play a role in virulence of AIEC strain LF82.
Published: 2010
Full Text: View/download PDF

5. The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese.

Author: Christophe Monnet, Valentin Loux, Jean-François Gibrat, Eric Spinnler, Valérie Barbe, Benoit Vacherie, Frederick Gavory, Edith Gourbeyre, Patricia Siguier, Michaël Chandler, Rayda Elleuch, Françoise Irlinger, and Tatiana Vallaeys
Subjects: Medicine, Science
Abstract: Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe(3+)/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.
Published: 2010
Full Text: View/download PDF

6. The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications.

Author: Hélène Falentin, Stéphanie-Marie Deutsch, Gwenaël Jan, Valentin Loux, Anne Thierry, Sandrine Parayre, Marie-Bernadette Maillard, Julien Dherbécourt, Fabien J Cousin, Julien Jardin, Patricia Siguier, Arnaud Couloux, Valérie Barbe, Benoit Vacherie, Patrick Wincker, Jean-François Gibrat, Claude Gaillardin, and Sylvie Lortal
Subjects: Medicine, Science
Abstract: BackgroundPropionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is also considered for its probiotic use. This species exhibits slow growth, low nutritional requirements, and hardiness in many habitats. It belongs to the taxonomic group of dairy propionibacteria, in contrast to the cutaneous species P. acnes. The genome of the type strain, P. freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027(T)), was sequenced with an 11-fold coverage.Methodology/principal findingsThe circular chromosome of 2.7 Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different insertion sequences (3.5% of the genome in base pairs). Using a proteomic approach, 490 of the 2439 predicted proteins were confirmed. The annotation revealed the genetic basis for the hardiness of P. freudenreichii, as the bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) as well as sequences involved in metabolism of various carbon sources, immunity against phages, duplicated chaperone genes and, interestingly, genes involved in the management of polyphosphate, glycogen and trehalose storage. The complete biosynthesis pathway for a bifidogenic compound is described, as well as a high number of surface proteins involved in interactions with the host and present in other probiotic bacteria. By comparative genomics, no pathogenicity factors found in P. acnes or in other pathogenic microbial species were identified in P. freudenreichii, which is consistent with the Generally Recognized As Safe and Qualified Presumption of Safety status of P. freudenreichii. Various pathways for formation of cheese flavor compounds were identified: the Wood-Werkman cycle for propionic acid formation, amino acid degradation pathways resulting in the formation of volatile branched chain fatty acids, and esterases involved in the formation of free fatty acids and esters.Conclusions/significanceWith the exception of its ability to degrade lactose, P. freudenreichii seems poorly adapted to dairy niches. This genome annotation opens up new prospects for the understanding of the P. freudenreichii probiotic activity.
Published: 2010
Full Text: View/download PDF

7. Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti.

Author: Arjan de Groot, Rémi Dulermo, Philippe Ortet, Laurence Blanchard, Philippe Guérin, Bernard Fernandez, Benoit Vacherie, Carole Dossat, Edmond Jolivet, Patricia Siguier, Michael Chandler, Mohamed Barakat, Alain Dedieu, Valérie Barbe, Thierry Heulin, Suzanne Sommer, Wafa Achouak, and Jean Armengaud
Subjects: Genetics, QH426-470
Abstract: To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment.
Published: 2009
Full Text: View/download PDF

8. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Author: Marie Touchon, Claire Hoede, Olivier Tenaillon, Valérie Barbe, Simon Baeriswyl, Philippe Bidet, Edouard Bingen, Stéphane Bonacorsi, Christiane Bouchier, Odile Bouvet, Alexandra Calteau, Hélène Chiapello, Olivier Clermont, Stéphane Cruveiller, Antoine Danchin, Médéric Diard, Carole Dossat, Meriem El Karoui, Eric Frapy, Louis Garry, Jean Marc Ghigo, Anne Marie Gilles, James Johnson, Chantal Le Bouguénec, Mathilde Lescat, Sophie Mangenot, Vanessa Martinez-Jéhanne, Ivan Matic, Xavier Nassif, Sophie Oztas, Marie Agnès Petit, Christophe Pichon, Zoé Rouy, Claude Saint Ruf, Dominique Schneider, Jérôme Tourret, Benoit Vacherie, David Vallenet, Claudine Médigue, Eduardo P C Rocha, and Erick Denamur
Subjects: Genetics, QH426-470
Abstract: The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.
Published: 2009
Full Text: View/download PDF

9. Chromosome-scale assembly of the yellow mealworm genome

Author: Fabrice Berro, Jean-Marc Aury, Yannick Moret, Caroline Belser, Evangelia Eleftheriou, Karine Labadie-Bretheau, Thomas Lefebvre, Mohammed-Amin Madoui, Sona Gasparian, Benoit Vacherie, Benjamin Istace, Benjamin Noel, Thierry Rigaud, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Plateforme de séquençage à haut débit (NGS), Département Plateforme (PF I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Ynsect, Evry, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and European Union’s Horizon 2020 research and innovation programme under the grant agreement No 837750 (project FARMYNG)
Subjects: 2. Zero hunger, Mealworm, 0303 health sciences, chromosome-scale assembly, Gene prediction, Chromosome, Genomics, General Medicine, Articles, Biology, biology.organism_classification, Genome, 03 medical and health sciences, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 0302 clinical medicine, Yellow Mealworm, Evolutionary biology, Proteome, genomics, Nanopore sequencing, Gene, 030217 neurology & neurosurgery, 030304 developmental biology, Research Article, Tenebrio molitor
Abstract: Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.
Published: 2022
Full Text: View/download PDF

10. Additional file 17 of Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

Author: Francois Thiaucourt, Manso-Silvan, Lucia, Woubit Salah, Barbe, Valérie, Benoit Vacherie, Jacob, Daniel, Breton, Marc, Dupuy, Virginie, Lomenech, Anne Marie, Blanchard, Alain, and Sirand-Pugnet, Pascal
Subjects: Data_FILES
Abstract: Authors’ original file for figure 9
Published: 2020
Full Text: View/download PDF

11. Additional file 2 of Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

Author: Francois Thiaucourt, Manso-Silvan, Lucia, Woubit Salah, Barbe, Valérie, Benoit Vacherie, Jacob, Daniel, Breton, Marc, Dupuy, Virginie, Lomenech, Anne Marie, Blanchard, Alain, and Sirand-Pugnet, Pascal
Subjects: heterocyclic compounds
Abstract: Additional file 2:"Comparison of related plasmid and ICE sequences in Mmc 95010". This figure describes the positions and sequences shared by the integrative conjugative elements copies and the plasmid that was characterized in the same strain. (PPT 288 KB)
Published: 2020
Full Text: View/download PDF

12. Additional file 9 of Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

Author: Francois Thiaucourt, Manso-Silvan, Lucia, Woubit Salah, Barbe, Valérie, Benoit Vacherie, Jacob, Daniel, Breton, Marc, Dupuy, Virginie, Lomenech, Anne Marie, Blanchard, Alain, and Sirand-Pugnet, Pascal
Subjects: Data_FILES
Abstract: Authors’ original file for figure 1
Published: 2020
Full Text: View/download PDF

13. Additional file 6 of Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

Author: Francois Thiaucourt, Manso-Silvan, Lucia, Woubit Salah, Barbe, Valérie, Benoit Vacherie, Jacob, Daniel, Breton, Marc, Dupuy, Virginie, Lomenech, Anne Marie, Blanchard, Alain, and Sirand-Pugnet, Pascal
Subjects: congenital, hereditary, and neonatal diseases and abnormalities, heterocyclic compounds
Abstract: Additional file 6:"Peculiar Mmc genomic locus encoding predicted surface proteins". This figure is a schematic representation of the locus and homologies with M. agalactiae or M. capricolum subsp. capricolum genes. (PPT 74 KB)
Published: 2020
Full Text: View/download PDF

14. Additional file of Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

Author: Francois Thiaucourt, Manso-Silvan, Lucia, Woubit Salah, Barbe, Valérie, Benoit Vacherie, Jacob, Daniel, Breton, Marc, Dupuy, Virginie, Lomenech, Anne Marie, Blanchard, Alain, and Sirand-Pugnet, Pascal
Abstract: Additional file of Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective
Published: 2020
Full Text: View/download PDF

15. Additional file 3 of Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

Author: Francois Thiaucourt, Manso-Silvan, Lucia, Woubit Salah, Barbe, Valérie, Benoit Vacherie, Jacob, Daniel, Breton, Marc, Dupuy, Virginie, Lomenech, Anne Marie, Blanchard, Alain, and Sirand-Pugnet, Pascal
Abstract: Additional file 3:"Comparison of plasmids from the mycoides cluster". This figure depicts the results of a three-way BLASTN comparison of three mycoplasma plasmid sequences using the Artemis Comparison Tool [71](PPT 144 KB)
Published: 2020
Full Text: View/download PDF

16. Additional file 5 of Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

Author: Francois Thiaucourt, Manso-Silvan, Lucia, Woubit Salah, Barbe, Valérie, Benoit Vacherie, Jacob, Daniel, Breton, Marc, Dupuy, Virginie, Lomenech, Anne Marie, Blanchard, Alain, and Sirand-Pugnet, Pascal
Subjects: digestive, oral, and skin physiology, education, heterocyclic compounds
Abstract: Additional file 5:"organization of a Mmc-specific lipoprotein gene clusters in the Mmc 95010 genome". This figure is a schematic representation of a lipoprotein family found in strain 95010 genome but not in the published MmmSC genomes. (PPT 506 KB)
Published: 2020
Full Text: View/download PDF

17. Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy

Author: Jean-Louis Jamet, Astrid Cornils, Kevin Sugier, Benoit Vacherie, Patrick Wincker, Mohammed-Amin Madoui, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0301 basic medicine, Zoology, lcsh:Medicine, Marine Biology, Chitin, macromolecular substances, Biology marine, General Biochemistry, Genetics and Molecular Biology, chemistry.chemical_compound, 03 medical and health sciences, Oithona, Fluorescence microscope, 0303 health sciences, Microscopy, biology, Aquatic and Marine Chemistry, General Neuroscience, lcsh:R, 030302 biochemistry & molecular biology, fungi, Hindgut, Midgut, General Medicine, Comparative anatomy, Biogeochemistry, biology.organism_classification, Copepod, Staining, 030104 developmental biology, chemistry, Anatomy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Digestion
Abstract: Among copepods, which are the most abundant animals on Earth, the genus Oithona is described as one of the most numerous and plays a major role in the marine food chain and biogeochemical cycles, particularly through the excretion of chitin-coated fecal pellets. Despite the morphology of several Oithona species is well known, knowledge of its internal anatomy and chitin distribution is still limited. To answer this problem, Oithona nana and O. similis individuals were stained by Wheat Germ Agglutinin-Fluorescein IsoThioCyanate (WGA-FITC) and DiAmidino-2-PhenylIndole (DAPI) for fluorescence microscopy observations. The image analyses allowed a new description of the organization and chitin content of the digestive and reproductive systems of Oithona male and female. Chitin microfibrils were found all along the digestive system from the stomach to the hindgut with a higher concentration at the peritrophic membrane of the anterior midgut. Several midgut shrinkages were observed and proposed to be involved in faecal pellet shaping and motion. Amorphous chitin structures were also found to be a major component of the ducts and seminal vesicles and receptacles. The rapid staining protocol we proposed allowed a new insight into the Oithona internal anatomy and highlighted the role of chitin in the digestion and reproduction. This method could be applied to a wide range of copepods in order to perform comparative anatomy analyses.
Published: 2018
Full Text: View/download PDF

18. Chitin distribution in the

Author: Kevin, Sugier, Benoit, Vacherie, Astrid, Cornils, Patrick, Wincker, Jean-Louis, Jamet, and Mohammed-Amin, Madoui
Subjects: Microscopy, Aquatic and Marine Chemistry, Oithona, fungi, Marine Biology, Chitin, macromolecular substances, Biogeochemistry, Anatomy, Biology marine, Copepod
Abstract: Among copepods, which are the most abundant animals on Earth, the genus Oithona is described as one of the most numerous and plays a major role in the marine food chain and biogeochemical cycles, particularly through the excretion of chitin-coated fecal pellets. Despite the morphology of several Oithona species is well known, knowledge of its internal anatomy and chitin distribution is still limited. To answer this problem, Oithona nana and O. similis individuals were stained by Wheat Germ Agglutinin-Fluorescein IsoThioCyanate (WGA-FITC) and DiAmidino-2-PhenylIndole (DAPI) for fluorescence microscopy observations. The image analyses allowed a new description of the organization and chitin content of the digestive and reproductive systems of Oithona male and female. Chitin microfibrils were found all along the digestive system from the stomach to the hindgut with a higher concentration at the peritrophic membrane of the anterior midgut. Several midgut shrinkages were observed and proposed to be involved in faecal pellet shaping and motion. Amorphous chitin structures were also found to be a major component of the ducts and seminal vesicles and receptacles. The rapid staining protocol we proposed allowed a new insight into the Oithona internal anatomy and highlighted the role of chitin in the digestion and reproduction. This method could be applied to a wide range of copepods in order to perform comparative anatomy analyses.
Published: 2017

19. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

Author: Fabrizio Stefani, Eric Karsenti, Olivier Jaillon, Claude Payri, Benoit Vacherie, Fabrice Not, Patrick Wincker, Flavia L. D. Nunes, Roberto Arrigoni, Valérie Barbe, Francesca Benzoni, Arrigoni, R, Vacherie, B, Benzoni, F, Stefani, F, Karsenti, E, Jaillon, O, Not, F, Nunes, F, Payri, C, Wincker, P, and Barbe, V
Subjects: 0301 basic medicine, Scleractinia, DNA, Ribosomal, DNA barcoding, Montipora, cnidarians, 03 medical and health sciences, Phylogenetics, systematic, RNA, Ribosomal, 18S, Genetics, Animals, Cluster Analysis, DNA Barcoding, Taxonomic, Acropora, cnidarian, systematics, Phylogeny, Ecology, Evolution, Behavior and Systematics, geography, geography.geographical_feature_category, biology, Phylogenetic tree, Ecology, hard corals, molecular evolution, fungi, Genetic Variation, Genes, rRNA, Sequence Analysis, DNA, Coral reef, Ribosomal RNA, Anthozoa, biology.organism_classification, hypervariable region, hard coral, 030104 developmental biology, gene structure and function, Nucleic Acid Conformation, Biotechnology
Abstract: Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.
Published: 2017
Full Text: View/download PDF

20. Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti†

Author: Sylvie Randazzo, Hosam Shams-Eldin, Karina Moubri-Ménage, Peter J. Krause, Kamel Hadj-Kaddour, Valérie Barbe, Françoise Debierre-Grockiego, Vincent Berry, Patrick Wincker, Stephane Delbecq, Sahar Usmani-Brown, Amina Dassouli, Aurelie Duclos, Yoann Augagneur, Vincent Ranwez, Choukri Ben Mamoun, Emmanuel Cornillot, Theo Schetters, Benoit Vacherie, Christian P. Vivarès, Frédéric Bringaud, Ralph T. Schwarz, Virginie Bres, B. Carcy, Benjamin Noel, André Gorenflot, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Internal Medecine, Yale (Department of Internal Medecine), Yale University School of Medicine, Infectiologie Santé Publique (ISP-311), Université de Tours-Institut National de la Recherche Agronomique (INRA), Vaccination Antiparasitaire : Laboratoire de Biologie Cellulaire et Moléculaire (LBCM), Université Montpellier 1 (UM1)-Université de Montpellier (UM), Institut für Virologie, Philipps University, Résonance magnétique des systèmes biologiques (RMSB), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Microbiology R&D Department, Intervet/Schering-Plough Animal Health (Microbiology R&D Department), Intervet/Schering-Plough Animal Health, Dynamique des interactions membranaires normales et pathologiques (DIMNP), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Cornillot, Emmanuel, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Yale School of Medicine [New Haven, Connecticut] (YSM), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Centre de résonance magnétique des systèmes biologiques (CRMSB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA)-Université de Tours, and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1)
Subjects: Mitochondrial DNA, Nuclear gene, Proteome, Glycosylphosphatidylinositols, animal diseases, Babesia microti, Genome, Apicomplexa, 03 medical and health sciences, eukaryote, parasitic diseases, Genetics, Clade, genome, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, biology, 030306 microbiology, Sequence Analysis, DNA, Genomics, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDE]Environmental Sciences, Protozoa, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Babesia microty, Genome, Protozoan
Abstract: International audience; We have sequenced the genome of the emerging human pathogen Babesia microti and compared it with that of other protozoa. B. microti has the smallest nuclear genome among all Apicomplexan parasites sequenced to date with three chromosomes encoding ∼3500 polypeptides, several of which are species specific. Genome-wide phylogenetic analyses indicate that B. microti is significantly distant from all species of Babesidae and Theileridae and defines a new clade in the phylum Apicomplexa. Furthermore, unlike all other Apicomplexa, its mitochondrial genome is circular. Genome-scale reconstruction of functional networks revealed that B. microti has the minimal metabolic requirement for intraerythrocytic protozoan parasitism. B. microti multigene families differ from those of other protozoa in both the copy number and organization. Two lateral transfer events with significant metabolic implications occurred during the evolution of this parasite. The genomic sequencing of B. microti identified several targets suitable for the development of diagnostic assays and novel therapies for human babesiosis.
Published: 2012
Full Text: View/download PDF

21. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

Author: Michael Wagner, Holger Daims, Thomas Rattei, Denis Le Paslier, Jaap S. Sinninghe Damsté, Eva Spieck, Hanna Koch, Eric Pelletier, Frank Maixner, Benoit Vacherie, and Sebastian Lücker
Subjects: Nitrite Reductases, Citric Acid Cycle, Molecular Sequence Data, Respiratory chain, Bacterial Physiological Phenomena, Enrichment culture, Evolution, Molecular, chemistry.chemical_compound, Bacterial Proteins, Amino Acid Sequence, Nitrites, Phylogeny, Multidisciplinary, Bacteria, Sequence Homology, Amino Acid, Sewage, biology, Reverse Transcriptase Polymerase Chain Reaction, Nitrospira moscoviensis, Planctomycetes, Gene Expression Regulation, Bacterial, Carbon Dioxide, Chromosomes, Bacterial, Biological Sciences, Comammox, biology.organism_classification, Biochemistry, Nitrite oxidoreductase, chemistry, Metagenome, Metagenomics, Oxidation-Reduction, Nitrospira, Genome, Bacterial
Abstract: Nitrospira are barely studied and mostly uncultured nitrite-oxidizing bacteria, which are, according to molecular data, among the most diverse and widespread nitrifiers in natural ecosystems and biological wastewater treatment. Here, environmental genomics was used to reconstruct the complete genome of “ Candidatus Nitrospira defluvii” from an activated sludge enrichment culture. On the basis of this first-deciphered Nitrospira genome and of experimental data, we show that Ca . N. defluvii differs dramatically from other known nitrite oxidizers in the key enzyme nitrite oxidoreductase (NXR), in the composition of the respiratory chain, and in the pathway used for autotrophic carbon fixation, suggesting multiple independent evolution of chemolithoautotrophic nitrite oxidation. Adaptations of Ca . N. defluvii to substrate-limited conditions include an unusual periplasmic NXR, which is constitutively expressed, and pathways for the transport, oxidation, and assimilation of simple organic compounds that allow a mixotrophic lifestyle. The reverse tricarboxylic acid cycle as the pathway for CO 2 fixation and the lack of most classical defense mechanisms against oxidative stress suggest that Nitrospira evolved from microaerophilic or even anaerobic ancestors. Unexpectedly, comparative genomic analyses indicate functionally significant lateral gene-transfer events between the genus Nitrospira and anaerobic ammonium-oxidizing planctomycetes, which share highly similar forms of NXR and other proteins reflecting that two key processes of the nitrogen cycle are evolutionarily connected.
Published: 2010
Full Text: View/download PDF

22. The complete mitochondrial genome of Acanthastrea maxima (Cnidaria, scleractinia, Lobophylliidae)

Author: Francesca Benzoni, Valérie Barbe, Roberto Arrigoni, Benoit Vacherie, Arrigoni, R, Vacherie, B, Benzoni, F, and Barbe, V
Subjects: 0301 basic medicine, Mitochondrial DNA, DNA, Mitochondrial, Homing endonuclease, 03 medical and health sciences, Genome Size, RNA, Transfer, Genetics, Animals, Molecular Biology, Genome size, Gene, Genomic organization, Base Composition, biology, Base Sequence, Intron, Nucleic acid sequence, Sequence Analysis, DNA, Ribosomal RNA, Anthozoa, Mitochondria, 030104 developmental biology, RNA, Ribosomal, Genome, Mitochondrial, biology.protein, Coral, genome organization, group I intron, mitogenome, threatened species, BIO/05 - ZOOLOGIA
Abstract: The complete nucleotide sequence of the mitochondrial genome of the scleractinian coral Acanthastrea maxima has been obtained, representing the first sequenced mitogenome of a member of the Lobophylliidae. The mitochondrial genome is 18,278 bp in length, the longest sequence among the robust corals sequenced mitogenome to date. The overall GC composition (33.7%) and the gene arrangement are similar to those of the other scleractinian corals, including 13 protein-coding genes, 2 rRNA genes (rnl and rns) and 2 tRNA genes (tRNA-Met and tRNA-Trp). All genes except tRNA-Trp, atp8, cox1, tRNA-Met and rnl are engulfed by a large group I intron in the nad5 gene. A second group I intron of 1077 bp in length is inserted in the cox1 gene and it encodes a putative homing endonuclease. There are four regions of gene overlaps totalling 22 bp and nine intergenic spacer regions for a total of 2220 bp, of which the cox3-cox2 region may correspond to the putative control region.
Published: 2016

23. Complete nucleotide sequence of the mitochondrial DNA from

Author: Patrick Wincker, Benoit Vacherie, Yvan Zivanovic, Hiroshi Fukuhara, and Monique Bolotin-Fukuhara
Subjects: 2. Zero hunger, Kluyveromyces lactis, Genetics, 0303 health sciences, Mitochondrial DNA, biology, Base pair, 030302 biochemistry & molecular biology, Nucleic acid sequence, General Medicine, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, Genome, 03 medical and health sciences, Transfer RNA, Genome size, Gene, 030304 developmental biology
Abstract: The total nucleotide sequence of the mitochondrial genome of the yeast Kluyveromyces lactis was determined. The DNA is a circular molecule of 40,291 base pairs, with 26.1% GC. It contains a set of protein- and RNA-coding genes equivalent to those of the Saccharomyces cerevisiae mitochondrial genome. The genome size is about one half of that of S. cerevisiae mitochondrial DNA. The difference in size is due essentially to a reduced proportion of intergenic and intronic sequences. The coding sequences occupy about one third of the genome, the rest being composed of AT-rich sequences and numerous short GC-rich clusters that are dispersed mostly in the non-coding regions and a few within coding sequences. The presence of these GC clusters is a characteristic feature common to K. lactis and S. cerevisiae mitochondrial DNA, although their sequence patterns are different. The absence of the NADH dehydrogenase subunit genes distinguishes this yeast and S. cerevisiae from the typically aerobic species. The genetic code appears to be that of the standard fungal mitochondrial genomes, with UGA as a tryptophan codon. There are only 22 transfer RNA genes, those corresponding to CUN and CGN codons being missing. CUN codons are absent in the protein-coding sequences. There are five CGN codons within the open reading frames, but they are located exclusively in the introns, rendering them untranslatable. Introns are found only the genes in KlCOX1 and LrRNA. The transcription promoter motif known in S. cerevisiae and several other yeast species is also present. All genes are transcribed from the same strand, except those on a single 7-kilobase pairs segment (EMBL Accession No. AY654900).
Published: 2005
Full Text: View/download PDF

24. The DNA sequence and analysis of human chromosome 14

Author: Roland Heilig, Ralph Eckenberg, Jean-Louis Petit, Núria Fonknechten, Corinne Da Silva, Laurence Cattolico, Michaël Levy, Valérie Barbe, Véronique de Berardinis, Abel Ureta-Vidal, Eric Pelletier, Virginie Vico, Véronique Anthouard, Lee Rowen, Anup Madan, Shizhen Qin, Hui Sun, Hui Du, Kymberlie Pepin, François Artiguenave, Catherine Robert, Corinne Cruaud, Thomas Brüls, Olivier Jaillon, Lucie Friedlander, Gaelle Samson, Philippe Brottier, Susan Cure, Béatrice Ségurens, Franck Anière, Sylvie Samain, Hervé Crespeau, Nissa Abbasi, Nathalie Aiach, Didier Boscus, Rachel Dickhoff, Monica Dors, Ivan Dubois, Cynthia Friedman, Michel Gouyvenoux, Rose James, Anuradha Madan, Barbara Mairey–Estrada, Sophie Mangenot, Nathalie Martins, Manuela Ménard, Sophie Oztas, Amber Ratcliffe, Tristan Shaffer, Barbara Trask, Benoit Vacherie, Chadia Bellemere, Caroline Belser, Marielle Besnard-Gonnet, Delphine Bartol–Mavel, Magali Boutard, Stéphanie Briez-Silla, Stephane Combette, Virginie Dufossé-Laurent, Carolyne Ferron, Christophe Lechaplais, Claudine Louesse, Delphine Muselet, Ghislaine Magdelenat, Emilie Pateau, Emmanuelle Petit, Peggy Sirvain-Trukniewicz, Arnaud Trybou, Nathalie Vega-Czarny, Elodie Bataille, Elodie Bluet, Isabelle Bordelais, Maria Dubois, Corinne Dumont, Thomas Guérin, Sébastien Haffray, Rachid Hammadi, Jacqueline Muanga, Virginie Pellouin, Dominique Robert, Edith Wunderle, Gilbert Gauguet, Alice Roy, Laurent Sainte-Marthe, Jean Verdier, Claude Verdier-Discala, LaDeana Hillier, Lucinda Fulton, John McPherson, Fumihiko Matsuda, Richard Wilson, Claude Scarpelli, Gábor Gyapay, Patrick Wincker, William Saurin, Francis Quétier, Robert Waterston, Leroy Hood, and Jean Weissenbach
Subjects: Chromosomes, Human, Pair 14, Base Composition, Multidisciplinary, Molecular Sequence Data, Immunity, Reproducibility of Results, Genomics, Sequence Analysis, DNA, Physical Chromosome Mapping, DNA, Mitochondrial, DNA, Ribosomal, Synteny, Mice, Open Reading Frames, Genes, Animals, Humans, Chromosomes, Artificial, CpG Islands, 5' Untranslated Regions, Pseudogenes, Microsatellite Repeats
Abstract: Chromosome 14 is one of five acrocentric chromosomes in the human genome. These chromosomes are characterized by a heterochromatic short arm that contains essentially ribosomal RNA genes, and a euchromatic long arm in which most, if not all, of the protein-coding genes are located. The finished sequence of human chromosome 14 comprises 87,410,661 base pairs, representing 100% of its euchromatic portion, in a single continuous segment covering the entire long arm with no gaps. Two loci of crucial importance for the immune system, as well as more than 60 disease genes, have been localized so far on chromosome 14. We identified 1,050 genes and gene fragments, and 393 pseudogenes. On the basis of comparisons with other vertebrate genomes, we estimate that more than 96% of the chromosome 14 genes have been annotated. From an analysis of the CpG island occurrences, we estimate that 70% of these annotated genes are complete at their 5' end.
Published: 2003
Full Text: View/download PDF

25. Complete Genome Sequence of the Piezophilic, Mesophilic, Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13(T.)

Author: Valérie Barbe, Benoit Vacherie, Bernard Ollivier, Boyang Ji, Didier Alazard, Marie-Laure Fardeau, Zoé Rouy, Sabine Leroy, Philippe N. Bertin, Gregory Gimenez, Alain Dolla, Nathalie Pradel, Amira Amrani, Emmanuel Talla, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie et Biotechnologie des Environements Chauds (MICROBIOTECH), Université de Provence - Aix-Marseille 1, Orange Labs [Cesson-Sévigné], Orange Labs, Institut TELECOM/TELECOM Lille1, Institut Mines-Télécom [Paris] (IMT), Department of Chemistry, University of Ngaoundéré, Interactions et Modulateurs de Réponses (IMR), Centre National de la Recherche Scientifique (CNRS), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Département de Chimie [Univ Ngaoundéré] (UN-FS), Faculté de Sciences [Univ Ngaoundéré] (UN-FS), Université de Ngaoundéré/University of Ngaoundéré [Cameroun] (UN)-Université de Ngaoundéré/University of Ngaoundéré [Cameroun] (UN), Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes ( URMITE ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR48, INSB-INSB-Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), CEA/DSV/FAR/IG/Genoscope Laboratoire de Génomique Comparative, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Microbiologie et Biotechnologie des Environements Chauds ( MICROBIOTECH ), Institut Mines-Télécom [Paris], University of Ngaoundere, Interactions et Modulateurs de Réponses ( IMR ), Centre National de la Recherche Scientifique ( CNRS ), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: Chimie analytique, méthode d'analyse, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Plasmid, séquençage, Genetics, PHYLOGENIE, échantillon, 14. Life underwater, Prokaryotes, BACTERIE MESOPHILE, Sulfate, Molecular Biology, 030304 developmental biology, bactérie, Whole genome sequencing, 0303 health sciences, SULFATOREDUCTION, acide gras, biology, 030306 microbiology, génome, Desulfovibrio hydrothermalis, biology.organism_classification, GENE, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, STRUCTURE GENETIQUE, chemistry, SEQUENCAGE, Analytical chemistry, Bacteria, Mesophile
Abstract: Desulfovibrio hydrothermalis AM13 T is a piezophilic, mesophilic, hydrogenotrophic sulfate-reducing bacterium collected from a deep-sea hydrothermal chimney on the East Pacific Rise (2,600 m depth, 13°N). We report the genome sequence of this bacterium, which includes a 3,702,934-bp chromosome and a circular plasmid of 5,328 bp.
Published: 2013
Full Text: View/download PDF

26. Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5T

Author: Benoit Vacherie, Alain Dolla, Philippe N. Bertin, Claudine Médigue, Agnès Hirschler-Réa, Bernard Ollivier, Odile Valette, Marie-Laure Fardeau, Valérie Barbe, Oulfat Amin, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie et Biotechnologie des Environements Chauds (MICROBIOTECH), Université de Provence - Aix-Marseille 1, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Interactions et Modulateurs de Réponses (IMR), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genetics, Whole genome sequencing, 0303 health sciences, Hot spring, Desulfotomaculum hydrothermale, biology, 030306 microbiology, biology.organism_classification, C content, Genome, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, chemistry, Prokaryotes, Sulfate, Molecular Biology, Bacteria, 030304 developmental biology
Abstract: Here, we report the draft genome sequence of Desulfotomaculum hydrothermale , a sulfate-reducing, spore-forming bacterium isolated from a Tunisian hot spring. The genome is composed of 2.7 Mb, with a G+C content of 49.48%, and it contains 2,643 protein-coding sequences.
Published: 2013
Full Text: View/download PDF

27. Genome sequence of Blastococcus saxobsidens DD2, a stone-inhabiting bacterium

Author: Maher Gtari, Elena Crotti, Daniele Daffonchio, Valérie Barbe, Benoit Vacherie, Petar Pujic, Bessem Chouaia, Faten Ghodhbane-Gtari, Lorenzo Brusetti, Jérôme Gury, Imen Essoussi, Claudine Médigue, Imen Nouioui, Imed Sbissi, Philippe Normand, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: Whole genome sequencing, 0303 health sciences, 030306 microbiology, Ecology, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biology, biology.organism_classification, Settore BIO/19 - Microbiologia Generale, Genome, Blastococcus saxobsidens, Microbiology, Actinobacteria, Genome Announcements, Calcarenite, 03 medical and health sciences, Genus, Molecular Biology, Botany, Stone sample, Bacteria, Genome, Bacterial, 030304 developmental biology
Abstract: International audience; Members of the genus Blastococcus have been isolated from sandstone monuments, as well as from sea, soil, plant, and snow samples. We report here the genome sequence of a member of this genus, Blastococcus saxobsidens strain DD2, isolated from below the surface of a Sardinian wall calcarenite stone sample.
Published: 2012
Full Text: View/download PDF

28. Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization

Author: Joseph Schacherer, Patrick Wincker, Emmanuel Talla, Jean Weissenbach, Benoit Vacherie, Valérie Barbe, Marie Laure Straub, Philippe Baret, Stéphanie Weiss, Christine Sacerdot, Guillaume Morel, Jacky de Montigny, Eric Pelletier, José Almeida Cruz, Julie Poulain, Sandrine Mallet, Laurence Despons, Gaelle Samson, Serge Casaregola, Guilhem Savel, Guy-Franck Richard, Zlatyo Uzunov, Véronique Leh Louis, Valérie Kugler, Noémie Jacques, Marc Lemaire, David James Sherman, Agnès Thierry, Tiphaine Martin, Claude Gaillardin, Anasua Sarkar, Marie Line Seret, Anne Friedrich, Eric Westhof, Paul P. Jung, Cécile Fairhead, Cécile Neuvéglise, Pascal Durrens, Claudine Bleykasten, Christian Marck, Bernard Dujon, Jean Luc Souciet, Claire Jubin, Université de Strasbourg (UNISTRA), Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AgroParisTech, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et de Technologies de Saclay (IBITECS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Architecture et Réactivité de l'ARN (ARN), Centre National de la Recherche Scientifique (CNRS)-Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Biologie systémique - Systems Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire des levures (YMG), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université de Strasbourg - UMR 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique (CNRS), This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computer framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program 'Génotypage et Génomique Comparée,' and the ACI IMPBIO 'Génolevures En Ligne.'We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia, SFRH/BD/33528/2008), ANR-05-BLAN-0331,GENARISE,How do genes arise ? Lessons and questions from the evolution of yeast genomes.(2005), UCL - SST/ELI/ELIA - Agronomy, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université Catholique de Louvain = Catholic University of Louvain (UCL), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Genome evolution, Biology, Investigations, genome evolution, HEMIASCOMYCETOUS YEASTS, Gene dosage, Genome, allopolyploidy, Loss of heterozygosity, SACCHAROMYCES-CEREVISIAE, 03 medical and health sciences, NUCLEOLAR DOMINANCE, CANDIDA-ALBICANS, DNA-SEQUENCES, EVOLUTION, GENE, GLYCEROL, HALOTOLERANT, SPECIATION, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene duplication, Genetics, Molecular Biology, Gene, hybridization, Genetics (clinical), [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, osmotolerant yeast P. sorbitophila, osmotolerant yeast P, Numt, loss of heterozygosity, GC-content
Abstract: the Consortium National de Recherche en Génomique (CNRG) to Génoscope, CNRS (GDR 2354, Génolevures), The computer framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program "Génotypage et Génomique Comparée," and the ACI IMPBIO "Génolevures En Ligne."; International audience; Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain.
Published: 2012
Full Text: View/download PDF

29. Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces

Author: Maher Gtari, Jérôme Gury, Petar Pujic, Benoit Vacherie, Bessem Chouaia, Elena Crotti, Daniele Daffonchio, Imen Essoussi, Ines Abbassi-Ghozzi, Faten Ghodhbane-Gtari, Alexandra Calteau, Lorenzo Brusetti, Valérie Barbe, Claudine Médigue, Imen Nouioui, Philippe Normand, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: DNA, Bacterial, Geologic Sediments, Operon, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Settore BIO/19 - Microbiologia Generale, Microbiology, 03 medical and health sciences, Molecular Biology, Actinomycetales, Gene, Soil Microbiology, 030304 developmental biology, Whole genome sequencing, Genetics, 0303 health sciences, Base Sequence, Strain (chemistry), biology, 030306 microbiology, Chromosome Mapping, Chromosome, Sequence Analysis, DNA, Ribosomal RNA, biology.organism_classification, Genome Announcements, Soil microbiology, Genome, Bacterial
Abstract: International audience; Here we report the full genome sequence of Modestobacter marinus strain BC501, an actinobacterial isolate that thrives on stone surfaces. The generated chromosome is circular, with a length of 5.57 Mb and a G+C content of 74.13%, containing 5,445 protein-coding genes, 48 tRNAs, and 3 ribosomal operons.
Published: 2012
Full Text: View/download PDF

30. Complete Genome Sequence of a Beneficial Plant Root-Associated Bacterium, Pseudomonas brassicacearum

Author: Philippe Ortet, Mohamed Barakat, Sylvain Fochesato, Valérie Barbe, Thierry Heulin, David Lalaouna, Wafa Achouak, Benoit Vacherie, Catherine Santaella, Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA))
Subjects: DNA, Bacterial, Molecular Sequence Data, Microbiology, Genome, Plant Roots, 03 medical and health sciences, Pseudomonas, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, Whole genome sequencing, 0303 health sciences, biology, 030306 microbiology, Nucleic acid sequence, Chromosome, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Genome project, Gene Expression Regulation, Bacterial, biology.organism_classification, Genome Announcements, Pseudomonas brassicacearum, Bacteria, Genome, Bacterial
Abstract: To shed light on the genetic equipment of the beneficial plant-associated bacterium Pseudomonas brassicacearum , we sequenced the whole genome of the strain NFM421. Its genome consists of one chromosome equipped with a repertoire of factors beneficial for plant growth. In addition, a complete type III secretion system and two complete type VI secretion systems were identified. We report here the first genome sequence of this species.
Published: 2011
Full Text: View/download PDF

31. Complete Genome Sequence of the Fish Pathogen Flavobacterium branchiophilum

Author: Eduardo P. C. Rocha, Eric Duchaud, Valentin Loux, Marie Touchon, Valérie Barbe, Benoit Vacherie, Jean-François Bernardet, Paul Barbier, Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Unité Mathématique Informatique et Génome (MIG), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), This work was supported in part by grant 07-GMGE from the Agence Nationale de la Recherche of France. P.B. is a Université Evry Val d'Essonne Ph.D. fellowshi, ANR-07-GMGE-0004,FLAVOPHYLOGENOMICS,Analyses phylogénomiques des bactéries pathogènes des poissons du genre Flavobacterium.(2007), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Unité de recherche Virologie et Immunologie Moléculaires (VIM), Unité de mathémathique informatique et génome, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA, Bacterial, Gene Transfer, Horizontal, Virulence Factors, Bacterial Toxins, Molecular Sequence Data, complete genome, Virulence, Flavobacterium psychrophilum, Biology, Flavobacterium, Applied Microbiology and Biotechnology, Genome, Fish Diseases, 03 medical and health sciences, RNA, Transfer, Gene Order, genomics, Animals, Evolutionary and Genomic Microbiology, 14. Life underwater, Adhesins, Bacterial, bacteria, Gene, Genome size, Catfishes, 030304 developmental biology, 2. Zero hunger, Genetics, Whole genome sequencing, Hungary, 0303 health sciences, Ecology, 030306 microbiology, microbiology, Sequence Analysis, DNA, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], RNA, Bacterial, RNA, Ribosomal, biotechnology and applied microbiology, Horizontal gene transfer, Genome, Bacterial, Food Science, Biotechnology, pathogen
Abstract: Members of the genus Flavobacterium occur in a variety of ecological niches and represent an interesting diversity of lifestyles. Flavobacterium branchiophilum is the main causative agent of bacterial gill disease, a severe condition affecting various cultured freshwater fish species worldwide, in particular salmonids in Canada and Japan. We report here the complete genome sequence of strain FL-15 isolated from a diseased sheatfish ( Silurus glanis ) in Hungary. The analysis of the F. branchiophilum genome revealed putative mechanisms of pathogenicity strikingly different from those of the other, closely related fish pathogen Flavobacterium psychrophilum , including the first cholera-like toxin in a non- Proteobacteria and a wealth of adhesins. The comparison with available genomes of other Flavobacterium species revealed a small genome size, large differences in chromosome organization, and fewer rRNA and tRNA genes, in line with its more fastidious growth. In addition, horizontal gene transfer shaped the evolution of F. branchiophilum , as evidenced by its virulence factors, genomic islands, and CRISPR (clustered regularly interspaced short palindromic repeats) systems. Further functional analysis should help in the understanding of host-pathogen interactions and in the development of rational diagnostic tools and control strategies in fish farms.
Published: 2011
Full Text: View/download PDF

32. Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis

Author: Pascal Touzet, Pierre Saumitou-Laprade, Valérie Barbe, Vincent Castric, Laurence Maréchal-Drouard, Aude Darracq, Patricia Lenoble, Sophie Oztas, Adeline Courseaux, Jean-Stéphane Varré, Benoit Vacherie, Génétique et évolution des populations végétales (GEPV), Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), Bioinformatics and Sequence Analysis (BONSAI), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0106 biological sciences, Mutation rate, Mitochondrial DNA, DNA, Plant, Lineage (evolution), Molecular Sequence Data, Genomics, Biology, phylogeny, DNA, Mitochondrial, Synteny, 01 natural sciences, Genome, Chromosomes, Plant, Evolution, Molecular, 03 medical and health sciences, Monophyly, Species Specificity, Phylogenetics, Genetics, rearrangements, Research Articles, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Base Sequence, Sequence Homology, Amino Acid, DNA, Chloroplast, Chromosome Mapping, Genetic Variation, Sequence Analysis, DNA, Genes, Mitochondrial, mitochondrial genomes, Genome, Mitochondrial, Mutation, Beta vulgaris, comparative genomic, Genome, Plant, 010606 plant biology & botany
Abstract: International audience; Despite their monophyletic origin, mitochondrial (mt) genomes of plants and animals have developed contrasted evolutionary paths over time. Animal mt genomes are generally small, compact and exhibit high mutation rates, while plant mt genomes exhibit low mutation rates, little compactness, larger sizes and highly rearranged structures. We present the (nearly) whole sequences of 5 new mt genomes in the Beta genus: 4 from Beta vulgaris and 1 from Beta macrocarpa, a sister-species belonging to the same Beta section. We pooled our results with two previously sequenced genomes of Beta vulgaris and studied genome diversity at the species level with an emphasis on cytoplasmic male sterilizing genomes (CMS). We showed that, contrarily to what was previously assumed, all three CMS genomes belong to a single sterile lineage. In addition, the CMSs seem to have undergone an acceleration of the rates of substitution and rearrangement. This study suggests that male sterility emergence might have been favored by faster rates of evolution, unless CMS itself caused faster evolution.
Published: 2011
Full Text: View/download PDF

33. Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

Author: Valérie Barbe, Marc Breton, Pascal Sirand-Pugnet, Anne Marie Lomenech, Lucia Manso-Silvan, François Thiaucourt, Woubit Salah, Benoit Vacherie, Alain Blanchard, Daniel J. Jacob, Virginie Dupuy, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Sciences et Technologies - Bordeaux 1, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université Sciences et Technologies - Bordeaux 1 (UB), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)
Subjects: Proteomics, ruminant, Subspecies, L73 - Maladies des animaux, Genome, Plasmid, Contagious bovine pleuropneumonia, Segmental Duplications, Genomic, Pathogen, génomique comparée, Chèvre, bactérie, Genetics, 0303 health sciences, Comparative Genomic Hybridization, biology, santé animale, Strain (biology), Goats, Mycoplasma mycoides, GENOMIQUE, Multigene Family, Horizontal gene transfer, Petits ruminants, Female, bactérie pathogène, CAPRI, Biotechnology, Research Article, Plasmids, DNA, Bacterial, lcsh:QH426-470, lcsh:Biotechnology, Lipoproteins, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, lcsh:TP248.13-248.65, medicine, Animals, pathologie animale, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, GENETIQUE, MYCOIDES SMALL COLONY, 030306 microbiology, génome, Genetic Variation, Molecular Sequence Annotation, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, lcsh:Genetics, DNA Transposable Elements, Genome, Bacterial
Abstract: Background The Mycoplasma mycoides cluster consists of five species or subspecies that are ruminant pathogens. One subspecies, Mycoplasma mycoides subspecies mycoides Small Colony (MmmSC), is the causative agent of contagious bovine pleuropneumonia. Its very close relative, Mycoplasma mycoides subsp. capri (Mmc), is a more ubiquitous pathogen in small ruminants causing mastitis, arthritis, keratitis, pneumonia and septicaemia and is also found as saprophyte in the ear canal. To understand the genetics underlying these phenotypic differences, we compared the MmmSC PG1 type strain genome, which was already available, with the genome of an Mmc field strain (95010) that was sequenced in this study. We also compared the 95010 genome with the recently published genome of another Mmc strain (GM12) to evaluate Mmc strain diversity. Results The MmmSC PG1 genome is 1,212 kbp and that of Mmc 95010 is ca. 58 kbp shorter. Most of the sequences present in PG1 but not 95010 are highly repeated Insertion Sequences (three types of IS) and large duplicated DNA fragments. The 95010 genome contains five types of IS, present in fewer copies than in PG1, and two copies of an integrative conjugative element. These mobile genetic elements have played a key role in genome plasticity, leading to inversions of large DNA fragments. Comparison of the two genomes suggested a marked decay of the PG1 genome that seems to be correlated with a greater number of IS. The repertoire of gene families encoding surface proteins is smaller in PG1. Several genes involved in polysaccharide metabolism and protein degradation are also absent from, or degraded in, PG1. Conclusions The genome of MmmSC PG1 is larger than that of Mmc 95010, its very close relative, but has less coding capacity. This is the result of large genetic rearrangements due to mobile elements that have also led to marked gene decay. This is consistent with a non-adaptative genomic complexity theory, allowing duplications or pseudogenes to be maintained in the absence of adaptive selection that would lead to purifying selection and genome streamlining over longer evolutionary times. These findings also suggest that MmmSC only recently adapted to its bovine host.
Published: 2011
Full Text: View/download PDF

34. The Arthrobacter arilaitensis Re117 Genome Sequence Reveals Its Genetic Adaptation to the Surface of Cheese

Author: Valérie Barbe, Rayda Elleuch, Jean-François Gibrat, Françoise Irlinger, Michael Chandler, Christophe Monnet, Edith Gourbeyre, Frederick Gavory, Benoit Vacherie, Patricia Siguier, Tatiana Vallaeys, Eric Spinnler, Valentin Loux, Génie et Microbiologie des Procédés Alimentaires (GMPA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Genescope, Université d'Évry-Val-d'Essonne (UEVE), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génie Enzymatique et de Microbiologie, Université de Sfax - University of Sfax, Ecosystèmes lagunaires - CC093, Université Montpellier 2 - Sciences et Techniques (UM2), Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Ecologie des systèmes marins côtiers (Ecosym), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Unité Mathématique Informatique et Génome (MIG), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Anatomy and Physiology, Applied Microbiology, fromage, Genome, Biochemistry, Plasmid, Cheese, Genome Sequencing, Bacterial Physiology, Amino Acids, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, chemistry.chemical_classification, Genetics, bactérie, 0303 health sciences, Multidisciplinary, biology, Fatty Acids, Chromosome Mapping, Genomics, Salt Tolerance, Chromosomes, Bacterial, Adaptation, Physiological, Amino acid, BACTERIA, Medicine, Carbohydrate Metabolism, Research Article, Biotechnology, DNA, Bacterial, Science, Iron, Molecular Sequence Data, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Microbiology, Synteny, 03 medical and health sciences, Species Specificity, Arthrobacter, Gene, Biology, 030304 developmental biology, Microbial Metabolism, Siderophore transport, 030306 microbiology, COMPLETE GENOME, génome, GENOMICS, cheese, Bacteriology, Sequence Analysis, DNA, Comparative Genomics, biology.organism_classification, Lipid Metabolism, Carbon, Metabolism, chemistry, Physiological Processes, Energy Metabolism, Bacteria, Genome, Bacterial
Abstract: Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe(3+)/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.
Published: 2010
Full Text: View/download PDF

35. The complete genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy actinobacterium with food and probiotic applications

Author: Valérie Barbe, Hélène Falentin, Arnaud Couloux, Patrick Wincker, Sandrine Parayre, Gwénaël Jan, Marie-Bernadette Maillard, Benoit Vacherie, Anne Thierry, Fabien J. Cousin, Patricia Siguier, Valentin Loux, Jean-François Gibrat, Julien Jardin, Julien Dherbécourt, Stéphanie-Marie Deutsch, Sylvie Lortal, Claude Gaillardin, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Unité Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité Mathématique Informatique et Génome (MIG), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Loux, Valentin, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Science, Propionibacterium, PROPIONIBACTERIUM, PROBIOTIQUE, GENOME, CHEESE, PROPIONIBACTERIE, APPLICATION, FROMAGE, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Genome, Microbiology, Microbiology/Applied Microbiology, 03 medical and health sciences, Generally recognized as safe, Gene, 030304 developmental biology, Comparative genomics, 0303 health sciences, Multidisciplinary, biology, 030306 microbiology, Propionibacterium freudenreichii, Probiotics, food and beverages, Genome project, biology.organism_classification, Genetics and Genomics/Gene Function, Actinobacteria, Genetics and Genomics/Genome Projects, Biochemistry, Food Microbiology, Medicine, Genome, Bacterial, Bacteria, Research Article
Abstract: BackgroundPropionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is also considered for its probiotic use. This species exhibits slow growth, low nutritional requirements, and hardiness in many habitats. It belongs to the taxonomic group of dairy propionibacteria, in contrast to the cutaneous species P. acnes. The genome of the type strain, P. freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027(T)), was sequenced with an 11-fold coverage.Methodology/principal findingsThe circular chromosome of 2.7 Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different insertion sequences (3.5% of the genome in base pairs). Using a proteomic approach, 490 of the 2439 predicted proteins were confirmed. The annotation revealed the genetic basis for the hardiness of P. freudenreichii, as the bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) as well as sequences involved in metabolism of various carbon sources, immunity against phages, duplicated chaperone genes and, interestingly, genes involved in the management of polyphosphate, glycogen and trehalose storage. The complete biosynthesis pathway for a bifidogenic compound is described, as well as a high number of surface proteins involved in interactions with the host and present in other probiotic bacteria. By comparative genomics, no pathogenicity factors found in P. acnes or in other pathogenic microbial species were identified in P. freudenreichii, which is consistent with the Generally Recognized As Safe and Qualified Presumption of Safety status of P. freudenreichii. Various pathways for formation of cheese flavor compounds were identified: the Wood-Werkman cycle for propionic acid formation, amino acid degradation pathways resulting in the formation of volatile branched chain fatty acids, and esterases involved in the formation of free fatty acids and esters.Conclusions/significanceWith the exception of its ability to degrade lactose, P. freudenreichii seems poorly adapted to dairy niches. This genome annotation opens up new prospects for the understanding of the P. freudenreichii probiotic activity.
Published: 2010
Full Text: View/download PDF

36. Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids

Author: Gildas Le Corguillé, Benoit Vacherie, Xavier Bailly, Gareth A. Pearson, Bernhard Gschloessl, Erwan Corre, Claire Jubin, Catherine Leblanc, Marta Valente, J. Mark Cock, Carla Viegas, Akira F. Peters, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université - Faculté de Médecine (SU FM), Sorbonne Université (SU), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), his work, performed within the framework of Marine Genomics Europe NoE 7 (EC contract N° GOCE-CT-2004-505403), was partially supported by the Brittany Regional Council (G. L. C. grant) and by FCT-FEDER (Portugal)., Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de Biologie François JACOB (JACOB), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay
Subjects: 0106 biological sciences, Evolution, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Phaeophyta, 010603 evolutionary biology, 01 natural sciences, Haptophyte, Evolution, Molecular, 03 medical and health sciences, DNA, Algal, Phylogenetics, Botany, Research article, QH359-425, Plastids, Plastid, Neighbour Join, Genome, Chloroplast, Bayesian Inference Analysis, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, biology, Base Sequence, Heterokont, Ectocarpus siliculosus, fungi, food and beverages, Chromosome Mapping, Sequence Analysis, DNA, Plastid Genome, biology.organism_classification, Plastid Protein, Chloroplast, Chloroplast DNA, Evolutionary biology, Fucus, Ectocarpales, Approximately Unbiased
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.
Published: 2009
Full Text: View/download PDF

37. Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti

Author: Carole Dossat, Suzanne Sommer, Benoit Vacherie, Rémi Dulermo, Edmond Jolivet, Patricia Siguier, Laurence Blanchard, Wafa Achouak, Bernard Fernandez, Philippe Ortet, Michael Chandler, Jean Armengaud, Philippe J Guerin, Valérie Barbe, Thierry Heulin, Alain Dedieu, Arjan de Groot, Mohamed Barakat, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Microbiologie Environnementale et Moléculaire (MEM), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-07-BLAN-0106,DEINOCOCCUS,Structure of the nucleoïd and radioresistance of Deinococcus radiodurans and Deinococcus deserti(2007), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, Cancer Research, Proteomes, Computational Biology/Comparative Sequence Analysis, Gene prediction, medicine.disease_cause, Genome, Africa, Northern, Genetics (clinical), 2. Zero hunger, Genetics, 0303 health sciences, Genetics and Genomics/Gene Expression, Genomics, Genome project, Deinococcus deserti, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Evolutionary Biology/Microbial Evolution and Genomics, Proteome, Genetics and Genomics/Gene Discovery, Deinococcus, Desert Climate, Genetics and Genomics/Comparative Genomics, Ecology/Environmental Microbiology, Research Article, lcsh:QH426-470, Ultraviolet Rays, Molecular Sequence Data, DNA repair, DNA polymerase, Biology, Microbiology, 03 medical and health sciences, Bacterial Proteins, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Microbiology/Environmental Microbiology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Bacterial genomics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Molecular Biology/Recombination, Whole genome sequencing, Comparative genomics, Molecular Biology/DNA Repair, 030306 microbiology, Database searching, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, lcsh:Genetics, Gamma Rays, Biophysics/Protein Chemistry and Proteomics, 13. Climate action, Genome, Bacterial, Genome annotation
Abstract: To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment., Author Summary D. deserti belongs to the Deinococcaceae, a family of bacteria characterized by an exceptional ability to withstand the lethal effects of DNA-damaging agents, including ionizing radiation, UV light, and desiccation. It was isolated from Sahara surface sands, an extreme and nutrient-poor environment, regularly exposed to intense UV radiation, cycles of extreme temperatures, and desiccation. The evolution of organisms that are able to survive acute irradiation doses of 15,000 Gy is difficult to explain given the apparent absence of highly radioactive habitats on Earth over geologic time. Thus, it seems more likely that the natural selection pressure for the evolution of radiation-resistant bacteria was chronic exposure to nonradioactive forms of DNA damage, in particular those promoted by desiccation. Here, we report the first complete genome sequence of a bacterium, D. deserti VCD115, isolated from hot, arid desert surface sand. Accurate genome annotation of its 3,455 genes was guided by extensive proteome analysis in which 1,348 proteins were uncovered after growth in standard conditions. Supplementary genes involved in manganese import, in nutrient import, and in DNA repair were identified and are likely important for survival and adaptation of D. deserti to its hostile environment.
Published: 2009
Full Text: View/download PDF

38. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

Author: Edouard Bingen, Olivier Clermont, Chantal Le Bouguénec, Zoé Rouy, Sophie Oztas, James R. Johnson, Anne-Marie Gilles, Erick Denamur, Marie Touchon, Olivier Tenaillon, David Vallenet, Valérie Barbe, Marie-Agnès Petit, Meriem El Karoui, Stéphane Bonacorsi, Dominique Schneider, Louis Garry, Eduardo P. C. Rocha, Alexandra Calteau, Antoine Danchin, Xavier Nassif, Ivan Matic, Vanessa Martinez-Jéhanne, Jérôme Tourret, Sophie Mangenot, Christophe Pichon, Jean Marc Ghigo, Claude Saint Ruf, Philippe Bidet, Claire Hoede, Eric Frapy, Christiane Bouchier, Simon Baeriswyl, Benoit Vacherie, Stéphane Cruveiller, Mathilde Lescat, Odile Bouvet, Carole Dossat, Claudine Médigue, Médéric Diard, Hélène Chiapello, Atelier de BioInformatique (ABI), Université Pierre et Marie Curie - Paris 6 (UPMC), Génomique évolutive des microbes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Ecologie et Evolution des Microorganismes (EEM), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génétique moléculaire, évolutive et médicale, IFR65-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris 7, Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Mathématique, Informatique, et Génomique, Institut National de la Recherche Agronomique (INRA), Génétique des Génomes Bactériens, Pathogénie des infections systémiques (UMR_S 570), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique des Biofilms, Veterans Affairs Medical Center, Department of Medecine, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Pathogénie Bactérienne des Muqueuses, Unité des Bactéries Lactiques et Pathogènes Opportunistes, Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Gagnon, Jean, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7)-Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme), Institut Pasteur [Paris], University of Minnesota [Twin Cities], IFR65-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Atelier de BioInformatique ( ABI ), Université Pierre et Marie Curie - Paris 6 ( UPMC ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Ecologie et Evolution des Microorganismes ( EEM ), Université Paris 13 ( UP13 ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), IFR65-Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hôpital Robert Debré-Université Paris Diderot - Paris 7 ( UPD7 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique ( INRA ), Pathogénie des infections systémiques ( UMR_S 570 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), University of Minnesota [Minneapolis], Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] ( LAPM ), and Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH : Escherichia coli, Cancer Research, MESH : Polymorphism, Genetic, MESH : Recombination, Genetic, MESH : Models, Genetic, MESH : Models, Biological, MESH: Genome, Bacterial, Genome, MESH: Genetics, Gene flow, MESH : Genetics, MESH: Models, Genetic, MESH: Phylogeny, bioinformatique, Phylogeny, Genetics (clinical), MESH: Evolution, Molecular, Recombination, Genetic, bactérie, 2. Zero hunger, Genetics, Likelihood Functions, 0303 health sciences, Phylogenetic tree, MESH: Escherichia coli, MESH: Genomics, Genomics, Genome project, Evolutionary Biology/Microbial Evolution and Genomics, MESH: DNA Transposable Elements, MESH : DNA Transposable Elements, MESH: Recombination, Genetic, escherichia coli, MESH : Likelihood Functions, Research Article, lcsh:QH426-470, MESH : Genome, Bacterial, Biology, Models, Biological, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, MESH: Polymorphism, Genetic, Escherichia coli, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Evolution, Molecular, Gene conversion, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Polymorphism, Genetic, Evolutionary Biology/Evolutionary and Comparative Genetics, Models, Genetic, 030306 microbiology, génome, MESH : Genomics, MESH: Models, Biological, MESH : Phylogeny, Microbiology/Medical Microbiology, lcsh:Genetics, DNA Transposable Elements, MESH: Likelihood Functions, MESH : Genome, Genome, Bacterial
Abstract: The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome., Author Summary Although abundant knowledge has been accumulated regarding the E. coli laboratory strain K-12, little is known about the evolutionary trajectories that have driven the high diversity observed among natural isolates of the species, which encompass both commensal and highly virulent intestinal and extraintestinal pathogenic strains. We have annotated or re-annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Although recombination rates are much higher than mutation rates, we were able to reconstruct a robust phylogeny based on the ∼2,000 genes common to all strains. Based on this phylogeny, we established the evolutionary scenario of gains and losses of thousands of specific genes, identifying functional classes under opposite selection pressures. This genome flux is confined to very few positions in the chromosome, which are the same for every genome. Notably, we identified few or no extraintestinal virulence-specific genes. We also defined a long-scale structure of recombination in the genome with lower recombination rates at the terminus of replication. These findings demonstrate that, despite a very high gene flow, genes can co-exist in an organised genome.
Published: 2009
Full Text: View/download PDF

39. Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila

Author: David Vallenet, Bruno Lemaitre, Claire Jubin, Claudine Médigue, Zoé Rouy, Nicolas Vodovar, Patrick Wincker, Aurélie Lajus, Béatrice Ségurens, Benoit Vacherie, Stéphane Cruveiller, Valérie Barbe, Laurence Cattolico, Jean Weissenbach, Frédéric Boccard, Carlos Acosta, Centre de génétique moléculaire (CGM), Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and CNRS (Programme Séquençage à grande échelle), IFR115, MRT/ACI IMPBio 2004 ‘MicroScope', N.V. was supported by a doctoral fellowship from the Association Vaincre la Mucoviscidose and the Association pour la Recherche sur le Cancer (ARC)
Subjects: Insecticides, Insecta, Molecular Sequence Data, Biomedical Engineering, Virulence, Bioengineering, MESH: Base Sequence, MESH: Genome, Bacterial, Applied Microbiology and Biotechnology, Genome, Microbiology, 03 medical and health sciences, Complete sequence, MESH: Insects, Bacterial Proteins, Pseudomonas, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, MESH: Pest Control, Biological, MESH: Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Pest Control, Biological, Pathogen, MESH: Bacterial Proteins, Soil Microbiology, 030304 developmental biology, 0303 health sciences, MESH: Molecular Sequence Data, Base Sequence, biology, 030306 microbiology, Chromosome Mapping, MESH: Pseudomonas, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Insecticides, MESH: Soil Microbiology, Pseudomonadales, Molecular Medicine, MESH: Chromosome Mapping, Pseudomonas entomophila, Genome, Bacterial, Biotechnology, Pseudomonadaceae
Abstract: Pseudomonas entomophila is an entomopathogenic bacterium that, upon ingestion, kills Drosophila melanogaster as well as insects from different orders. The complete sequence of the 5.9-Mb genome was determined and compared to the sequenced genomes of four Pseudomonas species. P. entomophila possesses most of the catabolic genes of the closely related strain P. putida KT2440, revealing its metabolically versatile properties and its soil lifestyle. Several features that probably contribute to its entomopathogenic properties were disclosed. Unexpectedly for an animal pathogen, P. entomophila is devoid of a type III secretion system and associated toxins but rather relies on a number of potential virulence factors such as insecticidal toxins, proteases, putative hemolysins, hydrogen cyanide and novel secondary metabolites to infect and kill insects. Genome-wide random mutagenesis revealed the major role of the two-component system GacS/GacA that regulates most of the potential virulence factors identified.
Published: 2006
Full Text: View/download PDF

40. Complete nucleotide sequence of the mitochondrial DNA from Kluyveromyces lactis

Author: Yvan, Zivanovic, Patrick, Wincker, Benoit, Vacherie, Monique, Bolotin-Fukuhara, Hiroshi, Fukuhara, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Sequence Analysis, DNA, MESH: Molecular Sequence Data, Base Sequence, MESH: RNA, Fungal, Molecular Sequence Data, MESH: DNA, Mitochondrial, RNA, Fungal, Sequence Analysis, DNA, MESH: Base Sequence, MESH: RNA, Transfer, DNA, Mitochondrial, MESH: Kluyveromyces, GC Rich Sequence, Kluyveromyces, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, RNA, Transfer, RNA, Ribosomal, MESH: Genome, Fungal, MESH: RNA, Ribosomal, MESH: GC Rich Sequence, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Genome, Fungal
Abstract: The total nucleotide sequence of the mitochondrial genome of the yeast Kluyveromyces lactis was determined. The DNA is a circular molecule of 40,291 base pairs, with 26.1% GC. It contains a set of protein- and RNA-coding genes equivalent to those of the Saccharomyces cerevisiae mitochondrial genome. The genome size is about one half of that of S. cerevisiae mitochondrial DNA. The difference in size is due essentially to a reduced proportion of intergenic and intronic sequences. The coding sequences occupy about one third of the genome, the rest being composed of AT-rich sequences and numerous short GC-rich clusters that are dispersed mostly in the non-coding regions and a few within coding sequences. The presence of these GC clusters is a characteristic feature common to K. lactis and S. cerevisiae mitochondrial DNA, although their sequence patterns are different. The absence of the NADH dehydrogenase subunit genes distinguishes this yeast and S. cerevisiae from the typically aerobic species. The genetic code appears to be that of the standard fungal mitochondrial genomes, with UGA as a tryptophan codon. There are only 22 transfer RNA genes, those corresponding to CUN and CGN codons being missing. CUN codons are absent in the protein-coding sequences. There are five CGN codons within the open reading frames, but they are located exclusively in the introns, rendering them untranslatable. Introns are found only the genes in KlCOX1 and LrRNA. The transcription promoter motif known in S. cerevisiae and several other yeast species is also present. All genes are transcribed from the same strand, except those on a single 7-kilobase pairs segment (EMBL Accession No. AY654900).
Published: 2005
Full Text: View/download PDF

41. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Author: Nicole Stange-Thomann, Michael Katinka, Michael Levy, Vincent Laudet, Olivier Jaillon, Cécile Fischer, Véronique de Berardinis, Zineb Skalli, Jill P. Mesirov, David M. Jaffe, Alain Bernot, Genís Parra, Simone Duprat, Claude Scarpelli, Daniel Kahn, Chad Nusbaum, Sophie Nicaud, Laurence Bouneau, Francis Quetier, Hugues Roest Crollius, Corinne Cruaud, Bruce W. Birren, Jérôme Gouzy, Kevin McKernan, Eric S. Lander, Nathalie Boudet, Vanina Castelli, Marc Robinson-Rechavi, Jean-Pierre Coutanceau, Béatrice Segurens, Michael C. Zody, Corinne Dasilva, Evan Mauceli, Paul A. McEwan, Manolis Kellis, Carole Dossat, Benoit Vacherie, Marcel Salanoubat, Roderic Guigó, Sheila Fisher, Christian Biémont, Stephanie Bosak, Jean Weissenbach, Véronique Anthouard, Jean-Nicolas Volff, William Saurin, Vincent Schächter, Julie Poulain, Catherine Ozouf-Costaz, Jean-Louis Petit, Laurence Cattolico, Guillaume Lardier, Charles Chapple, Sergi Castellano, Georges Lutfalla, Frédéric Brunet, Kerstin Lindblad-Toh, Philippe Brottier, Claire Jubin, Patrick Wincker, Jean-Marc Aury, Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche biologie moléculaire de la cellule, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Department of Atmospheric and Environmental Chemistry [Bothell], University of Washington-Bothell, Bayer Cropscience, Centre d'étude spatiale des rayonnements (CESR), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)
Subjects: Genome evolution, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Proteome, [SDV]Life Sciences [q-bio], Molecular Sequence Data, 2R hypothesis, Tetraodon nigroviridis, Fish Proteins, Synteny, Genome, Chromosomes, Evolution, Molecular, Gene Duplication, biology.animal, Animals, Chromosomes, Human, Humans, Urochordata, Tetraodon, Conserved Sequence, Mammals, Genetics, Base Composition, Multidisciplinary, Models, Genetic, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Fishes, Vertebrate, Sequence Analysis, DNA, Physical Chromosome Mapping, biology.organism_classification, Genes, Karyotyping, Vertebrates, Human genome
Abstract: International audience; Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests ∼900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
Published: 2004
Full Text: View/download PDF

42. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest

Author: Rüdiger Bode, Martin Mascher, Serge Casaregola, Anasua Sarkar, Guilhem Savel, Patrick Wincker, Valérie Barbe, Martin Giersberg, Marina Marcet-Houben, Keith Baronian, Nils Stein, Véronique Leh-Louis, Christine Sacerdot, Guy-Franck Richard, Jan Riechen, Ingrid Lafontaine, Jean Luc Souciet, Urs Hähnel, Eric Westhof, Joseph Schacherer, Uwe Scholz, Sebastian Worch, Sebastian Beier, Pascal Durrens, Erik Böer, Anke Trautwein-Schult, Christian Marck, Toni Gabaldón, Cécile Fairhead, Anja Hartmann, Claire Jubin, Bernard Dujon, Cécile Neuvéglise, Małgorzata Czernicka, Claudine Bleykasten, David James Sherman, Laurence Despons, Marie Laure Straub, Paul P. Jung, Marc Lemaire, Dagmara Jankowska, Tiphaine Martin, Benoit Vacherie, Emmanuel Talla, Agnès Thierry, José Almeida Cruz, André Goffeau, Gotthard Kunze, Claude Gaillardin, Philippe Baret, Guillaume Morel, Przemysław Piotr Gierski, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Yeast Genetics, Leibniz Institute of Plant Research (IPK), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona], Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et de Technologies de Saclay (IBITECS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université catholique de Louvain, Institut des Sciences de la Vie, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL), School of Biological Sciences, University of Canterbury, Institute of Biochemistry, Universität Greifswald - University of Greifswald, Université de Strasbourg (UNISTRA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Génétique moléculaire, génomique, microbiologie (GMGM), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire des levures (YMG), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program ' Génotypage et Génomique Comparée ' , the ACI IMPBIO ' Génolevures En Ligne ' and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia, SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161)., Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université Catholique de Louvain = Catholic University of Louvain (UCL), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Canterbury [Christchurch], International Institute of Molecular and Cell Biology [Warsaw] (IIMCB), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Kunze, Gotthard, Neuvéglise, Cécile, UCL - SST/ELI/ELIA - Agronomy, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: Yarrowia lipolytica, n-butanol, yeast, genome, tannic acid, metabolism, biotechnology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Technological development, Butyric acid, Applied Microbiology and Biotechnology, Genome, Blastobotrys, Saccharomycotina, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, N-butanol, 2. Zero hunger, 0303 health sciences, biology, Segmental duplications, Genomics, Phylogenetics, General Energy, Biochemistry, Biotechnology, Nitrogen, Saccharomyces cerevisiae, Biotecnologia agrícola, Computational biology, Management, Monitoring, Policy and Law, Biotechnological potentials, Arxula, Arxula adeninivorans, 03 medical and health sciences, Carbon and nitrogen, 030304 developmental biology, Saccharomycetes, Comparative genomics, Tannic acid, 030306 microbiology, Renewable Energy, Sustainability and the Environment, Protein, Research, Fundamental studies, Yarrowia, Llevats -- Genètica, biology.organism_classification, Yeast, Carbon, Metabolism, Genes, Organic acid
Abstract: Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant./nResults: The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. Conclusions: The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications. This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program “Génotypage et Génomique Comparée”, the ACI IMPBIO “Génolevures En Ligne” and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia; SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161). B.D. is a member of Institut Universitaire de France
Published: 2014
Full Text: View/download PDF

43. Male Differentiation in the Marine Copepod Oithona nana Reveals the Development of a New Nervous Ganglion and Lin12-Notch-Repeat Protein-Associated Proteolysis

Author: Kevin Sugier, Romuald Laso-Jadart, Benoît Vacherie, Jos Käfer, Laurie Bertrand, Karine Labadie, Nathalie Martins, Céline Orvain, Emmanuelle Petit, Patrick Wincker, Jean-Louis Jamet, Adriana Alberti, and Mohammed-Amin Madoui
Subjects: copepods, sexual differentiation, nervous system, Lin12-Notch-Repeat, Oithona, protein–protein interaction, Biology (General), QH301-705.5
Abstract: Copepods are among the most numerous animals, and they play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest density of copepods. The Oithona male paradox describes the activity states of males, which are obliged to alternate between immobile and mobile phases for ambush feeding and mate searching, respectively, while the female is less mobile and feeds less. To characterize the molecular basis of this sexual dimorphism, we combined immunofluorescence, genomics, transcriptomics, and protein–protein interaction approaches and revealed the presence of a male-specific nervous ganglion. Transcriptomic analysis showed male-specific enrichment for nervous system development-related transcripts. Twenty-seven Lin12-Notch Repeat domain-containing protein coding genes (LDPGs) of the 75 LDPGs identified in the genome were specifically expressed in males. Furthermore, some LDPGs coded for proteins with predicted proteolytic activity, and proteases-associated transcripts showed a male-specific enrichment. Using yeast double–hybrid assays, we constructed a protein–protein interaction network involving two LDPs with proteases, extracellular matrix proteins, and neurogenesis-related proteins. We also hypothesized possible roles of the LDPGs in the development of the lateral ganglia through helping in extracellular matrix lysis, neurites growth guidance, and synapses genesis.
Published: 2021
Full Text: View/download PDF

44. Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes

Author: Carmen Buchrieser, Laura Gomez-Valero, Benoit Vacherie, Christophe Rusniok, Valérie Barbe, Zoé Rouy, Claudine Médigue, Sophie Jarraud, Jerome Etienne, Biologie des bactéries intracellulaires, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Immunité infection vaccination (I2V), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de Référence des Legionella, Institut de Veille Sanitaire (INVS)-Université de Lyon, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and BMC, Ed.
Subjects: lcsh:QH426-470, Gene Transfer, Horizontal, lcsh:Biotechnology, Legionella pneumophila, Genome, Microbiology, 03 medical and health sciences, Plasmid, Phylogenetics, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Phylogeny, 030304 developmental biology, Synteny, Recombination, Genetic, 0303 health sciences, Polymorphism, Genetic, biology, 030306 microbiology, Sequence Analysis, DNA, biology.organism_classification, Biological Evolution, lcsh:Genetics, Horizontal gene transfer, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Protozoa, DNA microarray, Genome, Bacterial, Research Article, Biotechnology
Abstract: Background Legionella pneumophila is an intracellular pathogen of environmental protozoa. When humans inhale contaminated aerosols this bacterium may cause a severe pneumonia called Legionnaires' disease. Despite the abundance of dozens of Legionella species in aquatic reservoirs, the vast majority of human disease is caused by a single serogroup (Sg) of a single species, namely L. pneumophila Sg1. To get further insights into genome dynamics and evolution of Sg1 strains, we sequenced strains Lorraine and HL 0604 1035 (Sg1) and compared them to the available sequences of Sg1 strains Paris, Lens, Corby and Philadelphia, resulting in a comprehensive multigenome analysis. Results We show that L. pneumophila Sg1 has a highly conserved and syntenic core genome that comprises the many eukaryotic like proteins and a conserved repertoire of over 200 Dot/Icm type IV secreted substrates. However, recombination events and horizontal gene transfer are frequent. In particular the analyses of the distribution of nucleotide polymorphisms suggests that large chromosomal fragments of over 200 kbs are exchanged between L. pneumophila strains and contribute to the genome dynamics in the natural population. The many secretion systems present might be implicated in exchange of these fragments by conjugal transfer. Plasmids also play a role in genome diversification and are exchanged among strains and circulate between different Legionella species. Conclusion Horizontal gene transfer among bacteria and from eukaryotes to L. pneumophila as well as recombination between strains allows different clones to evolve into predominant disease clones and others to replace them subsequently within relatively short periods of time.
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

44 results on '"Benoit Vacherie"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources