Author: "Delphine, Naquin" - Searchworks@Jio Institute Digital Library Search Results

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1. Sulfur starvation-induced autophagy in Saccharomyces cerevisiae involves SAM-dependent signaling and transcription activator Met4

Author: Magali Prigent, Hélène Jean-Jacques, Delphine Naquin, Stéphane Chédin, Marie-Hélène Cuif, Renaud Legouis, and Laurent Kuras
Subjects: Science
Abstract: Abstract Autophagy is a key lysosomal degradative mechanism allowing a prosurvival response to stresses, especially nutrient starvation. Here we investigate the mechanism of autophagy induction in response to sulfur starvation in Saccharomyces cerevisiae. We found that sulfur deprivation leads to rapid and widespread transcriptional induction of autophagy-related (ATG) genes in ways not seen under nitrogen starvation. This distinctive response depends mainly on the transcription activator of sulfur metabolism Met4. Consistently, Met4 is essential for autophagy under sulfur starvation. Depletion of either cysteine, methionine or SAM induces autophagy flux. However, only SAM depletion can trigger strong transcriptional induction of ATG genes and a fully functional autophagic response. Furthermore, combined inactivation of Met4 and Atg1 causes a dramatic decrease in cell survival under sulfur starvation, highlighting the interplay between sulfur metabolism and autophagy to maintain cell viability. Thus, we describe a pathway of sulfur starvation-induced autophagy depending on Met4 and involving SAM as signaling sulfur metabolite.
Published: 2024
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2. Maternal inheritance of functional centrioles in two parthenogenetic nematodes

Author: Aurélien Perrier, Nadège Guiglielmoni, Delphine Naquin, Kevin Gorrichon, Claude Thermes, Sonia Lameiras, Alexander Dammermann, Philipp H. Schiffer, Maia Brunstein, Julie C. Canman, and Julien Dumont
Subjects: Science
Abstract: Abstract Centrioles are the core constituent of centrosomes, microtubule-organizing centers involved in directing mitotic spindle assembly and chromosome segregation in animal cells. In sexually reproducing species, centrioles degenerate during oogenesis and female meiosis is usually acentrosomal. Centrioles are retained during male meiosis and, in most species, are reintroduced with the sperm during fertilization, restoring centriole numbers in embryos. In contrast, the presence, origin, and function of centrioles in parthenogenetic species is unknown. We found that centrioles are maternally inherited in two species of asexual parthenogenetic nematodes and identified two different strategies for maternal inheritance evolved in the two species. In Rhabditophanes diutinus, centrioles organize the poles of the meiotic spindle and are inherited by both the polar body and embryo. In Disploscapter pachys, the two pairs of centrioles remain close together and are inherited by the embryo only. Our results suggest that maternally-inherited centrioles organize the embryonic spindle poles and act as a symmetry-breaking cue to induce embryo polarization. Thus, in these parthenogenetic nematodes, centrioles are maternally-inherited and functionally replace their sperm-inherited counterparts in sexually reproducing species.
Published: 2024
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3. Transgressive phenotypes from outbreeding between the Trichoderma reesei hyper producer RutC30 and a natural isolate

Author: Laetitia Chan Ho Tong, Etienne Jourdier, Delphine Naquin, Fadhel Ben Chaabane, Thiziri Aouam, Gwladys Chartier, Itzel Castro González, Antoine Margeot, and Frederique Bidard
Subjects: Trichoderma reesei, sexual reproduction, cellulases, transgressive phenotype, outbreeding, Microbiology, QR1-502
Abstract: ABSTRACT Trichoderma reesei, the main filamentous fungus used for industrial cellulase production, was long considered to be asexual. The recent discovery of the mating type locus in the natural isolate QM6a and the possibility to cross this sterile female strain with a fertile natural female strain opened up a new avenue for strain optimization. We crossed the hyperproducer RutC30 with a compatible female ascospore-derived isolate of the wild-type strain CBS999.97 and analyzed about 300 offspring. A continuous distribution of secreted protein levels was observed in the progeny, confirming the involvement of several mutated loci in the hyperproductive phenotype. A bias toward MAT1-2 strains was identified for higher producers, but not directly linked to the Mating-type locus itself. Transgressive phenotypes were observed in terms of both productivity and secretome quality, with offspring that outperform their parents for three enzymatic activities. Genomic sequences of the 10 best producers highlighted the genetic diversity generated and the involvement of parental alleles in hyperproduction and fertility.IMPORTANCEThe filamentous fungus Trichoderma reesei produces cellulolytic enzymes that are essential for the hydrolysis of lignocellulosic biomass into monomerics sugars. The filamentous fungus T. reesei produces cellulolytic enzymes that are essential for the hydrolysis of lignocellulosic biomass into monomerics sugars, which can in turn be fermented to produce second-generation biofuels and bioproducts. Production performance improvement, which is essential to reduce production cost, relies on classical mutagenesis and genetic engineering techniques. Although sexual reproduction is a powerful tool for improving domesticated species, it is often difficult to apply to industrial fungi since most of them are considered asexual. In this study, we demonstrated that outbreeding is an efficient strategy to optimize T. reesei. Crossing between a natural isolate and a mutagenized strain generated a biodiverse progeny with some offspring displaying transgressive phenotype for cellulase activities.
Published: 2024
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4. Dissimilar gene repertoires of Dickeya solani involved in the colonization of lesions and roots of Solanum tuberosum

Author: Kévin Robic, Euphrasie Munier, Géraldine Effantin, Joy Lachat, Delphine Naquin, Erwan Gueguen, and Denis Faure
Subjects: blackleg disease, Tn-seq, soft rot, Solanum tuberosrum, root colonization, Plant culture, SB1-1110
Abstract: Dickeya and Pectobacterium species are necrotrophic pathogens that macerate stems (blackleg disease) and tubers (soft rot disease) of Solanum tuberosum. They proliferate by exploiting plant cell remains. They also colonize roots, even if no symptoms are observed. The genes involved in pre-symptomatic root colonization are poorly understood. Here, transposon-sequencing (Tn-seq) analysis of Dickeya solani living in macerated tissues revealed 126 genes important for competitive colonization of tuber lesions and 207 for stem lesions, including 96 genes common to both conditions. Common genes included acr genes involved in the detoxification of plant defense phytoalexins and kduD, kduI, eda (=kdgA), gudD, garK, garL, and garR genes involved in the assimilation of pectin and galactarate. In root colonization, Tn-seq highlighted 83 genes, all different from those in stem and tuber lesion conditions. They encode the exploitation of organic and mineral nutrients (dpp, ddp, dctA, and pst) including glucuronate (kdgK and yeiQ) and synthesis of metabolites: cellulose (celY and bcs), aryl polyene (ape), and oocydin (ooc). We constructed in-frame deletion mutants of bcsA, ddpA, apeH, and pstA genes. All mutants were virulent in stem infection assays, but they were impaired in the competitive colonization of roots. In addition, the ΔpstA mutant was impaired in its capacity to colonize progeny tubers. Overall, this work distinguished two metabolic networks supporting either an oligotrophic lifestyle on roots or a copiotrophic lifestyle in lesions. This work revealed novel traits and pathways important for understanding how the D. solani pathogen efficiently survives on roots, persists in the environment, and colonizes progeny tubers.
Published: 2023
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5. Systematic comparison of small RNA library preparation protocols for next-generation sequencing

Author: Cloelia Dard-Dascot, Delphine Naquin, Yves d’Aubenton-Carafa, Karine Alix, Claude Thermes, and Erwin van Dijk
Subjects: Small RNA, Bias, Library preparation, Next-generation sequencing, NGS, 2’-O-methyl RNA, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Next-generation sequencing technologies have revolutionized the study of small RNAs (sRNAs) on a genome-wide scale. However, classical sRNA library preparation methods introduce serious bias, mainly during adapter ligation steps. Several types of sRNA including plant microRNAs (miRNA), piwi-interacting RNAs (piRNA) in insects, nematodes and mammals, and small interfering RNAs (siRNA) in insects and plants contain a 2’-O-methyl (2’-OMe) modification at their 3′ terminal nucleotide. This inhibits 3′ adapter ligation and makes library preparation particularly challenging. To reduce bias, the NEBNext kit (New England Biolabs) uses polyethylene glycol (PEG), the NEXTflex V2 kit (BIOO Scientific) uses both randomised adapters and PEG, and the novel SMARTer (Clontech) and CATS (Diagenode) kits avoid ligation altogether. Here we compared these methods with Illumina’s classical TruSeq protocol regarding the detection of normal and 2’ OMe RNAs. In addition, we modified the TruSeq and NEXTflex protocols to identify conditions that improve performance. Results Among the five kits tested with their respective standard protocols, the SMARTer and CATS kits had the lowest levels of bias but also had a strong formation of side products, and as a result performed relatively poorly with biological samples; NEXTflex detected the largest numbers of different miRNAs. The use of a novel type of randomised adapters called MidRand-Like (MRL) adapters and PEG improved the detection of 2’ OMe RNAs both in the TruSeq as well as in the NEXTflex protocol. Conclusions While it is commonly accepted that biases in sRNA library preparation protocols are mainly due to adapter ligation steps, the ligation-free protocols were not the best performing methods. Our modified versions of the TruSeq and NEXTflex protocols provide an improved tool for the study of 2’ OMe RNAs.
Published: 2018
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6. Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics

Author: Abdoul-Razak Tidjani, Jean-Noël Lorenzi, Maxime Toussaint, Erwin van Dijk, Delphine Naquin, Olivier Lespinet, Cyril Bontemps, and Pierre Leblond
Subjects: Streptomyces, conjugation, gene transfer, plasticity, population, Microbiology, QR1-502
Abstract: ABSTRACT In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations. IMPORTANCE Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.
Published: 2019
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7. Genomics in the long-read sequencing era

Author: Erwin L. van Dijk, Delphine Naquin, Kévin Gorrichon, Yan Jaszczyszyn, Rania Ouazahrou, Claude Thermes, Céline Hernandez, 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), and National Center of Human Genomics Research (CNRGH)
Subjects: [SDV]Life Sciences [q-bio], Genetics
Abstract: International audience
Published: 2023
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8. Impact of the severity of negative energy balance on gene expression in the subcutaneous adipose tissue of periparturient primiparous Holstein dairy cows: Identification of potential novel metabolic signals for the reproductive system.

Author: Namya Mellouk, Christelle Rame, Delphine Naquin, Yan Jaszczyszyn, Jean-Luc Touzé, Eric Briant, Daniel Guillaume, Theodoros Ntallaris, Patrice Humblot, and Joëlle Dupont
Subjects: Medicine, Science
Abstract: The severity of negative energy balance (NEB) in high-producing dairy cows has a high incidence among health diseases. The cow's energy status during early lactation critically affects metabolic and reproductive parameters. The first objective of this study was to investigate by RNA-seq analysis and RT-qPCR the gene expression profile in white adipose tissue and by gene ontology and upstream regulation tools the relationships with energy metabolism and reproduction in two groups of primiparous dairy cows with extreme NEB statuses (NEB < -9 Mcal/day vs. NEB > -9 Mcal/day) around parturition. The second objective was to determine the potential involvement of a new adipokine identified as a candidate for the regulation of ovarian function in our RNA-seq analysis by using bovine primary granulosa culture, thymidine incorporation to determine cell proliferation and ELISA assays to measure progesterone secretion. The RNA-seq analysis revealed that 514 genes were over-expressed and 695 were under-expressed in the adipose tissue of cows with severe NEB (SNEB) and cows with moderate NEB (MNEB) during the -4 and 16 wkpp period. In addition, 491 genes were over-expressed and 705 genes were under-expressed in the adipose tissue of SNEB cows compared to MNEB cows. Among these differently expressed genes (DEGs), 298 were related to metabolic functions and 264 to reproductive traits. A set of 19 DEGs were validated by RT-qPCR, including CCL21 (C-C motif chemokine ligand 21). Moreover, CCL21, a gene known to be secreted by adipose tissue, was chosen for further analysis in plasma and ovaries. The use of next-generation sequencing technologies allowed us to characterise the transcriptome of white adipose tissue from primiparous cows with different levels of NEB during lactation. This study highlighted the alteration of the expression of genes related to lipid metabolism, including CCL21, which is released in the bloodstream and associated with the in vitro regulation of ovarian functions.
Published: 2019
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9. Pervasive transcription enhances the accessibility of H-NS-silenced promoters and generates bistability in

Author: Nara, Figueroa-Bossi, María Antonia, Sánchez-Romero, Patricia, Kerboriou, Delphine, Naquin, Clara, Mendes, Philippe, Bouloc, Josep, Casadesús, and Lionello, Bossi
Subjects: DNA-Binding Proteins, Bacterial Proteins, Transcription, Genetic, Virulence, Salmonella, Gene Expression Regulation, Bacterial, Gene Silencing, Single-Cell Analysis, Promoter Regions, Genetic
Abstract: In
Published: 2023

10. Construction of a Transposon Mutant Library in the Pathogen Agrobacterium tumefaciens C58 and Identification of Genes Involved in Gall Niche Exploitation and Colonization

Author: Marta Torres, Almudena Gonzalez-Mula, Delphine Naquin, and Denis Faure
Published: 2022
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11. Construction of a Transposon Mutant Library in the Pathogen Agrobacterium tumefaciens C58 and Identification of Genes Involved in Gall Niche Exploitation and Colonization

Author: Marta, Torres, Almudena, Gonzalez-Mula, Delphine, Naquin, and Denis, Faure
Abstract: Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease on a wide range of host species by transferring and integrating a part of its own DNA (T-DNA) into the plant genome. The genes responsible of the above-mentioned processes are well characterized. However, a large number of the mechanisms involved in exploitation and colonization of the galls (also named plant tumors) remain unknown. Due to recent development of "transposon-sequencing" (Tn-Seq) techniques, a high-throughput screening and identification of the different genes involved in such mechanisms is now possible. In this chapter, we describe the detailed methodology used to construct a transposon library in A. tumefaciens and to conduct a Tn-Seq approach to discover genes involved in plant tumor exploitation and colonization.
Published: 2022

12. Pervasive transcription enhances the accessibility of H-NS-silenced promoters and generates bistability in Salmonella virulence gene expression

Author: Nara Figueroa-Bossi, María Antonia Sánchez-Romero, Patricia Kerboriou, Delphine Naquin, Clara Mendes, Philippe Bouloc, Josep Casadesús, Lionello Bossi, Université Paris-Saclay, 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), Departamento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain., ANR-15-CE11-0024,IntegRhoMe,Toward an Integrated View of Transcription Terminator Rho Functions and Mechanisms(2015), Universidad de Sevilla. Departamento de Microbiología y Parasitología, Universidad de Sevilla. Departamento de Genética, Agence Nationale de la Recherche. France, Ministerio de Ciencia e Innovación (MICIN). España, and Agencia Estatal de Investigación. España
Subjects: H-NS, Multidisciplinary, bistability, Silencing, pervasive transcription, silencing, Pervasive transcription, Pathogenicity Islands, Bistability, pathogenicity islands, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract: In Escherichia coli and Salmonella, many genes silenced by the nucleoid structuring protein H-NS are activated upon inhibiting Rho-dependent transcription termination. This response is poorly understood and difficult to reconcile with the view that H-NS acts mainly by blocking transcription initiation. Here we have analyzed the basis for the up-regulation of H-NS–silenced Salmonella pathogenicity island 1 (SPI-1) in cells depleted of Rho-cofactor NusG. Evidence from genetic experiments, semiquantitative 50 rapid amplification of complementary DNA ends sequencing (5’ RACE-Seq), and chromatin immunoprecipitation sequencing (ChIP-Seq) shows that transcription originating from spurious antisense promoters, when not stopped by Rho, elongates into a H-NS–bound regulatory region of SPI-1, displacing H-NS and rendering the DNA accessible to the master regulator HilD. In turn, HilD’s ability to activate its own transcription triggers a positive feedback loop that results in transcriptional activation of the entire SPI-1. Significantly, single-cell analyses revealed that this mechanism is largely responsible for the coexistence of two subpopulations of cells that either express or do not express SPI-1 genes. We propose that cell-to-cell differences produced by stochastic spurious transcription, combined with feedback loops that perpetuate the activated state, can generate bimodal gene expression patterns in bacterial populations. Agence Nationale de la Recherche de Francia - ANR-15-CE11-0024-03 Ministerio de Ciencia e Innovación y Agencia Estatal de Investigación, de España y Fondo Regional Europeo - PID2020-116995RB-I00
Published: 2022
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13. Plesiomonas shigelloides, an Atypical Enterobacterales with aVibrio-Related Secondary Chromosome

Author: Yazid Adam, Pierre Brezellec, Elena Espinosa, Amelie Besombes, Delphine Naquin, Evelyne Paly, Christophe Possoz, Erwin van Dijk, Francois-Xavier Barre, and Jean-Luc Ferat
Subjects: Proteomics, Genetics, Plesiomonas, Chromosomes, Bacterial, Genome, Bacterial, Ecology, Evolution, Behavior and Systematics, Vibrio
Abstract: About 10% of bacteria have a multichromosome genome with a primary replicon of bacterial origin, called the chromosome, and other replicons of plasmid origin, the chromids. Studies on multichromosome bacteria revealed potential points of coordination between the replication/segregation of chromids and the progression of the cell cycle. For example, replication of the chromid of Vibrionales (called Chr2) is initiated upon duplication of a sequence carried by the primary chromosome (called Chr1), in such a way that replication of both replicons is completed synchronously. Also, Chr2 uses the Chr1 as a scaffold for its partition in the daughter cells. How many of the features detected so far are required for the proper integration of a secondary chromosome in the cell cycle? How many more features remain to be discovered? We hypothesized that critical features for the integration of the replication/segregation of a given chromid within the cell cycle program would be conserved independently of the species in which the chromid has settled. Hence, we searched for a chromid related to that found in Vibrionales outside of this order. We identified one in Plesiomonas shigelloides, an aquatic and pathogenic enterobacterium that diverged early within the clade of Enterobacterales. Our results suggest that the chromids present in P. shigelloides and Vibrionales derive from a common ancestor. We initiated in silico genomic and proteomic comparative analyses of P. shigelloides, Vibrionales, and Enterobacterales that enabled us to establish a list of features likely involved in the maintenance of the chromid within the host cell cycle.
Published: 2022
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14. Unraveling the stratification of an iron-oxidizing microbial mat by metatranscriptomics.

Author: Achim Quaiser, Xavier Bodi, Alexis Dufresne, Delphine Naquin, André-Jean Francez, Alexandra Dheilly, Sophie Coudouel, Mathieu Pedrot, and Philippe Vandenkoornhuyse
Subjects: Medicine, Science
Abstract: A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria affiliated to the genus Leptothrix, dominated the community in the upper layers of the mat. Surprisingly, type I methanotrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem.
Published: 2014
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15. Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

Author: Julien Fumey, Cédric Cabau, Corentin Dechaud, Sylvie Rétaux, Louis Bernatchez, Peter Møller, Magali Naville, Christophe Klopp, Claude Thermes, Erik García-Machado, Maxime Policarpo, Jean-Nicolas Volff, Philippe Lafargeas, Didier Casane, Delphine Naquin, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-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), 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), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Institut de Biologie Intégrative et des Systèmes [Québec] (IBIS), Centro de Investigaciones Marinas, Universidad de La Habana, Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE92-0019,EVOBOOSTER,Impact des éléments transposables sur les réseaux de régulation génique : application aux voies biologiques à évolution rapide chez les poissons(2016), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)
Subjects: 0106 biological sciences, genetic structures, Pseudogene, [SDV]Life Sciences [q-bio], Population, relaxed selection, AcademicSubjects/SCI01180, 010603 evolutionary biology, 01 natural sciences, Genome, Lucifuga, 03 medical and health sciences, Cave, Loss of Function Mutation, Circadian Clocks, Genetics, Animals, Sinocyclocheilus, Selection, Genetic, education, Molecular Biology, Gene, molecular dating, Ecology, Evolution, Behavior and Systematics, Discoveries, Vision, Ocular, Zebrafish, eye-specific genes, 030304 developmental biology, cavefishes, 0303 health sciences, geography, education.field_of_study, geography.geographical_feature_category, biology, Pigmentation, Fossorial, AcademicSubjects/SCI01130, Fishes, biology.organism_classification, Moles, Caves, machine learning, Evolutionary biology, pseudogenization, Pseudogenes
Abstract: Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.
Published: 2021
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16. Agrobacterium tumefaciens fitness genes involved in the colonization of plant tumors and roots

Author: Yves Dessaux, Audren Jiquel, Etienne Jeanne, Denis Faure, Delphine Naquin, Marta Torres, Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physiology, Agrobacterium, Plant Tumors, Tn-Seq, Virulence, Plant Science, tomato, maize, Plant Roots, Iron assimilation, 03 medical and health sciences, Pseudomonas protegens, Solanum lycopersicum, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gall, biocontrol, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, gall, biology, 030306 microbiology, fungi, food and beverages, Agrobacterium tumefaciens, biology.organism_classification, root, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Carbon, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, poplar
Abstract: International audience; Agrobacterium tumefaciens colonizes the galls (plant tumors) it causes, and the roots of host and nonhost plants.Transposon-sequencing (Tn-Seq) was used to discover A.tumefaciens genes involved in reproductive success (fitness genes) on Solanum lycopersicum and Populus trichocarpa tumors and S.lycopersicum and Zea mays roots.The identified fitness genes represent 3–8% of A. tumefaciens genes and contribute to carbon and nitrogen metabolism, synthesis and repair of DNA, RNA and proteins and envelope-associated functions. Competition assays between 12 knockout mutants and wild-type confirmed the involvement of 10 genes (trpB, hisH, metH, cobN, ntrB, trxA, nrdJ, kamA, exoQ, wbbL) in A.tumefaciens fitness under both tumor and root conditions. The remaining two genes (fecA, noxA) were important in tumors only. None of these mutants was nonpathogenic, but four (hisH, trpB, exoQ, ntrB) exhibited impaired virulence. Finally, we used this knowledge to search for chemical and biocontrol treatments that target some of the identified fitness pathways and report reduced tumorigenesis and impaired establishment of A.tumefaciens on tomato roots using tannic acid or Pseudomonas protegens, which affect iron assimilation.This work revealed A.tumefaciens pathways that contribute to its competitive survival in plants and highlights a strategy to identify plant protection approaches against this pathogen.
Published: 2021
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17. Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

Author: Delphine Naquin, Corentin Dechaud, Maxime Policarpo, Philippe Lafargeas, Didier Casane, Christophe Klopp, Jean-Nicolas Volff, Julien Fumey, Erik García-Machado, Cédric Cabau, Claude Thermes, Peter Møller, Magali Naville, Louis Bernatchez, and Sylvie Rétaux
Subjects: education.field_of_study, biology, Evolutionary biology, Pseudogene, Population, Fossorial, Sinocyclocheilus, education, biology.organism_classification, Genome, Gene, Loss function, Lucifuga
Abstract: Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxing functional constraints. Gene decay can serve as a read-out of this evolutionary process. Animals living in the dark are outstanding models, in particular cavefishes as hundreds of species evolved independently during very different periods of time in absence of light. Here, we sought to understand some general principals on the extent and tempo of decay of several gene sets in cavefishes. The analysis of the genomes of two Cuban species belonging to the genusLucifugaprovides evidence for the most massive loss of eye genes reported so far in cavefishes. Comparisons with a recently-evolved cave population ofAstyanax mexicanusand three species belonging to the tetraploid Chinese genusSinocyclocheilusrevealed the combined effects of the level of eye regression, time and genome ploidy on the number of eye pseudogenes. In sharp contrast, most circadian clock and pigmentation genes appeared under strong selection. In cavefishes for which complete genomes are available, the limited extent of eye gene decay and the very small number of loss of function (LoF) mutations per pseudogene suggest that eye degeneration is never very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several eye pseudogenes carrying many LoF mutations in ancient fossorial mammals. Our analyses support the hypothesis that blind fishes cannot thrive more than a few millions of years in cave ecosystems.
Published: 2020
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18. Genome Sequences of 11 Conspecific

Author: Abdoul-Razak, Tidjani, Jean-Noël, Lorenzi, Maxime, Toussaint, Erwin, van Dijk, Delphine, Naquin, Olivier, Lespinet, Cyril, Bontemps, and Pierre, Leblond
Subjects: Genome Sequences
Abstract: The genomes of 11 conspecific Streptomyces strains, i.e., from the same species and inhabiting the same ecological niche, were sequenced and assembled. This data set offers an ideal framework to assess the genome evolution of Streptomyces species in their ecological context.
Published: 2019

19. Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics

Author: Cyril Bontemps, Jean-Noël Lorenzi, Delphine Naquin, Abdoul-Razak Tidjani, Pierre Leblond, Olivier Lespinet, Maxime Toussaint, Erwin van Dijk, Dynamique des Génomes et Adaptation Microbienne (DynAMic), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), 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), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: DNA, Bacterial, Gene Transfer, Horizontal, [SDV]Life Sciences [q-bio], Population, population, Ecological and Evolutionary Science, Biology, Microbiology, Genome, Streptomyces, 03 medical and health sciences, Virology, Indel, education, gene transfer, Gene, Phylogeny, 030304 developmental biology, Comparative genomics, 0303 health sciences, education.field_of_study, 030306 microbiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Variation, 15. Life on land, Chromosomes, Bacterial, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, QR1-502, Biosynthetic Pathways, Actinobacteria, Evolutionary biology, Genes, Bacterial, plasticity, Conjugation, Genetic, Multigene Family, Horizontal gene transfer, Gene pool, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial, Research Article, conjugation, Multilocus Sequence Typing, Plasmids
Abstract: Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods., In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.
Published: 2019
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20. The biotroph Agrobacterium tumefaciens thrives in tumors by exploiting a wide spectrum of plant host metabolites

Author: Peter Mergaert, Florian Lamouche, Delphine Naquin, Léo Mathias, Denis Faure, Almudena Gonzalez-Mula, Joy Lachat, 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), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), 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), Plateforme Génomique Environnementale et Fonctionnelle (GEF), Observatoire des Sciences de l'Univers de Rennes (OSUR), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA), PhD2014‐2016, Université Paris-Saclay, SE2016‐2017, Centre National de la Recherche Scientifique, ANR‐10‐LABX‐0040‐SPS, Labex, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Sucrose, MICROBIO, binding, Physiology, Metabolite, [SDV]Life Sciences [q-bio], Mutant, Plant Tumors, Hydroxybutyrates, Plant Science, PBI, 01 natural sciences, virulence factor, chemistry.chemical_compound, transcriptomics, Solanum lycopersicum, gamma-Aminobutyric Acid, 2. Zero hunger, gaba, high specificity, Plant Stems, Agrobacterium tumefaciens, plant pathogen, fitness, Biochemistry, NGS, Host-Pathogen Interactions, Metabolome, PF, biotroph, transposon-sequencing (Tn-seq), pathogen agrobacterium, Nitrogen, Biology, quorum-sensing signal, 03 medical and health sciences, Metabolomics, ecological niche, Gene, genome, Gene Library, structural basis, sequence, biology.organism_classification, gene-expression, Reverse genetics, Carbon, Citric acid cycle, 030104 developmental biology, chemistry, Genes, Bacterial, Mutation, DNA Transposable Elements, Transcriptome, 010606 plant biology & botany
Abstract: International audience; Agrobacterium tumefaciens is a niche-constructing biotroph that exploits host plant metabolites. We combined metabolomics, transposon-sequencing (Tn-seq), transcriptomics and reverse genetics to characterize A. tumefaciens pathways involved in the exploitation of resources from the Solanum lycopersicum host plant. Metabolomics of healthy stems and plant tumors revealed the common (e.g., sucrose, glutamate) and enriched (e.g., opines, GABA, GHB, pyruvate) metabolites that A. tumefaciens could use as nutrients. Transposon-sequencing and transcriptomics pinpointed the genes that are crucial and/or up-regulated when the pathogen grew on either sucrose (pgi, kdgA, pycA, cisY) or GHB (blcAB, pckA, eno, gpsA) as a carbon source. While sucrose assimilation involved the Entner-Doudoroff and tricarboxylic acid (TCA) pathways, GHB degradation required the blc genes, tricarboxylic acid cycle and gluconeogenesis. The tumor-enriched metabolite pyruvate is at the node connecting these pathways. Using reverse genetics, we showed that the blc, pckA and pycA loci were important for aggressiveness (tumor weight), proliferation (bacterial charge) and/or fitness (competition between the constructed mutants and wild-type) of A. tumefaciens in plant tumors. This work highlighted how a biotroph mobilizes its central metabolism for exploiting a wide diversity of resources in plant host. It further shows the complementarity of functional genome-wide scans by transcriptomics and transposon-sequencing to decipher the lifestyle of a plant pathogen. This article is protected by copyright. All rights reserved.
Published: 2019
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21. CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data.

Author: Delphine Naquin, Yves d'Aubenton-Carafa, Claude Thermes, and Maud Silvain
Published: 2014
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22. Impact of the severity of negative energy balance on gene expression in the subcutaneous adipose tissue of periparturient primiparous Holstein dairy cows: Identification of potential novel metabolic signals for the reproductive system

Author: Theodoros Ntallaris, Yan Jaszczyszyn, Christelle Ramé, Daniel Guillaume, Namya Mellouk, Patrice Humblot, Jean-Luc Touzé, Joëlle Dupont, Delphine Naquin, Eric Briant, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-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), 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), Unité Expérimentale de Physiologie Animale de l‘Orfrasiére (UE PAO), Institut National de la Recherche Agronomique (INRA), Swedish University of Agricultural Sciences (SLU), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physiology, [SDV]Life Sciences [q-bio], Adipose tissue, Gene Expression, White adipose tissue, Severity of Illness Index, Biochemistry, Epithelium, Transcriptome, Endocrinology, Reproductive Physiology, Animal Cells, Lactation, Gene expression, Medicine and Health Sciences, RNA-Seq, Lipid Hormones, Progesterone, 0303 health sciences, Multidisciplinary, 04 agricultural and veterinary sciences, Progesterone secretion, Lipids, Body Fluids, Dairying, medicine.anatomical_structure, Blood, Adipose Tissue, Medicine, Animal Nutritional Physiological Phenomena, Female, Anatomy, Cellular Types, Research Article, Genetics and Breeding, Science, Subcutaneous Fat, Adipokine, Biology, Blood Plasma, Andrology, 03 medical and health sciences, Metabolic Diseases, Weight Loss, medicine, Genetics, Animals, Genitalia, 030304 developmental biology, Granulosa Cells, Chemokine CCL21, Endocrine Physiology, Body Weight, 0402 animal and dairy science, Biology and Life Sciences, Lipid metabolism, Epithelial Cells, Cell Biology, Lipid Metabolism, 040201 dairy & animal science, Hormones, Biological Tissue, Metabolism, Gene Expression Regulation, Cattle, Lutein Cells, Energy Metabolism, Biomarkers
Abstract: International audience; The severity of negative energy balance (NEB) in high-producing dairy cows has a high incidence among health diseases. The cow's energy status during early lactation critically affects metabolic and reproductive parameters. The first objective of this study was to investigate by RNA-seq analysis and RT-qPCR the gene expression profile in white adipose tissue and by gene ontology and upstream regulation tools the relationships with energy metabolism and reproduction in two groups of primiparous dairy cows with extreme NEB statuses (NEB \textless -9 Mcal/day vs. NEB \textgreater -9 Mcal/day) around parturition. The second objective was to determine the potential involvement of a new adipokine identified as a candidate for the regulation of ovarian function in our RNA-seq analysis by using bovine primary granulosa culture, thymidine incorporation to determine cell proliferation and ELISA assays to measure progesterone secretion. The RNA-seq analysis revealed that 514 genes were over-expressed and 695 were under-expressed in the adipose tissue of cows with severe NEB (SNEB) and cows with moderate NEB (MNEB) during the -4 and 16 wkpp period. In addition, 491 genes were over-expressed and 705 genes were under-expressed in the adipose tissue of SNEB cows compared to MNEB cows. Among these differently expressed genes (DEGs), 298 were related to metabolic functions and 264 to reproductive traits. A set of 19 DEGs were validated by RT-qPCR, including CCL21 (C-C motif chemokine ligand 21). Moreover, CCL21, a gene known to be secreted by adipose tissue, was chosen for further analysis in plasma and ovaries. The use of next-generation sequencing technologies allowed us to characterise the transcriptome of white adipose tissue from primiparous cows with different levels of NEB during lactation. This study highlighted the alteration of the expression of genes related to lipid metabolism, including CCL21, which is released in the bloodstream and associated with the in vitro regulation of ovarian functions.
Published: 2019
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23. Lifestyle of the biotroph Agrobacterium tumefaciens in the ecological niche constructed on its host plant

Author: Catherine Grandclément, Delphine Naquin, Almudena Gonzalez-Mula, Laurent Soulère, Denis Faure, Yves Queneau, Mohammed Ahmar, Julien Lang, Yves Dessaux, 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), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), 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)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), 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), University Paris-Sud, CNRS [SE-2012], French National Research Agency (ANR) [ANR-12-BSV8-0003 (SENSOR), ANR-11-BSV7- 019 (ECORUM)], ANR-11-BSV7-0019,ECORUM,Signification écologique du quorum quenching dans les environnements rhizosphère et plantes(2011), ANR-12-BSV8-0003,sensor,Analyse structure-fonction de senseurs de pathogène fixant des composés de tumeurs de plante(2012), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, tumor, Physiology, Agrobacterium, Nitrogen, [SDV]Life Sciences [q-bio], Iron, Arabidopsis, opine, Opine, Plant Science, Arginine, quorum-sensing, 03 medical and health sciences, Ti plasmid, Plasmid, Bacterial Proteins, niche exploitation, Cell Wall, Plant Tumors, plasmid, Plant defense against herbivory, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, horizontal transfer, Ecosystem, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Chemotaxis, Agrobacterium tumefaciens, Gene Expression Regulation, Bacterial, biology.organism_classification, Plants, Genetically Modified, Carbon, Cell biology, 030104 developmental biology, Host-Pathogen Interactions, Mutation, Sugar Phosphates, Genome, Bacterial
Abstract: International audience; Agrobacterium tumefaciens constructs an ecological niche in its host plant by transferring the T-DNA from its Ti plasmid into the host genome and by diverting the host metabolism. We combined transcriptomics and genetics for understanding the A. tumefaciens lifestyle when it colonizes Arabidopsis thaliana tumors. Transcriptomics highlighted: a transition from a motile to sessile behavior that mobilizes some master regulators (Hfq, CtrA, DivK and PleD); a remodeling of some cell surface components (O-antigen, succinoglucan, curdlan, att genes, putative fasciclin) and functions associated with plant defense (Ef-Tu and flagellin pathogen-associated molecular pattern-response and glycerol-3-phosphate and nitric oxide signaling); and an exploitation of a wide variety of host resources, including opines, amino acids, sugars, organic acids, phosphate, phosphorylated compounds, and iron. In addition, construction of transgenic A. thaliana lines expressing a lactonase enzyme showed that Ti plasmid transfer could escape host-mediated quorum-quenching. Finally, construction of knock-out mutants in A. tumefaciens showed that expression of some At plasmid genes seemed more costly than the selective advantage they would have conferred in tumor colonization. We provide the first overview of A. tumefaciens lifestyle in a plant tumor and reveal novel signaling and trophic interplays for investigating host-pathogen interactions.
Published: 2018
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24. The Third Revolution in Sequencing Technology

Author: Delphine Naquin, Erwin van Dijk, Yan Jaszczyszyn, Claude Thermes, 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), and 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)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], real-time, dna methylation, Computational biology, Third generation sequencing, Biology, Genome, DNA sequencing, Structural variation, 03 medical and health sciences, symbols.namesake, human genome, Exome Sequencing, Genetics, Humans, nanopore, third-generation sequencing, Sanger sequencing, disease, synthetic long-read sequencing, structural variation, High-Throughput Nucleotide Sequencing, single-molecule real-time sequencing, DNA, Sequence Analysis, DNA, 030104 developmental biology, long-read sequencing, nanopore sequencing, surveillance, symbols, n-6-adenine, next-generation sequencing, Human genome, single-molecule, Nanopore sequencing, transcriptome, Single molecule real time sequencing
Abstract: International audience; Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete genome sequences to be deciphered for the first time. A second revolution came when next-generation sequencing (NGS) technologies appeared, which made genome sequencing much cheaper and faster. However, NGS methods have several drawbacks and pitfalls, most notably their short reads. Recently, third-generation/long-read methods appeared, which can produce genome assemblies of unprecedented quality. Moreover, these technologies can directly detect epigenetic modifications on native DNA and allow whole-transcript sequencing without the need for assembly. This marks the third revolution in sequencing technology. Here we review and compare the various long-read methods. We discuss their applications and their respective strengths and weaknesses and provide future perspectives.
Published: 2018
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25. The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family

Author: Solenn Cordonnier, Oscar Lima, Armel Salmon, Sophie Michon-Coudouel, Julie Ferreira de Carvalho, Abdelkader Aïnouche, Guillaume Martin, Malika L. Aïnouche, Mathieu Rousseau-Gueutin, Delphine Naquin, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Plateforme Génomique Environnementale et Fonctionnelle (GEF), Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Region Bretagne, grant no. 333709, European Project, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: 0106 biological sciences, Phylogénie, repeated plastid sequences, Lineage (evolution), Plant Science, Polymerase Chain Reaction, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, Lupinus luteus, Lupinus, sequence divergence, Chloroplaste, European yellow lupine, Phylogeny, functional gene transfer, Genetics, Papilionoidae, 0303 health sciences, biology, chloroplast genome evolution, Fabaceae, legume, Genistoid clade, 36-kb inversion, Chloroplast DNA, plastome hotspots, Séquence nucléotidique, structural plastid rearrangement, F60 - Physiologie et biochimie végétale, Molecular Sequence Data, 010603 evolutionary biology, Fabaceae phylogeny, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, lineage-specific marker, food, Phylogenetics, Plastid, Genome, Chloroplast, Transfert de gène, 030304 developmental biology, Génome, Sequence Analysis, DNA, Original Articles, flip-flop recombination, biology.organism_classification, food.food, Acide aminé, inverted repeats
Abstract: support from the 'Plate-forme Génomique Environnementale et Fonctionnelle' (OSUR: INEE-CNRS) and the Genouest Bioinformatic Plateform (University of Rennes 1); International audience; † Background and Aims To date chloroplast genomes are available only for members of the non-protein amino acidaccumulating clade (NPAAA) Papilionoid lineages in the legume family (i.e. Millettioids, Robinoids and the 'inverted repeat-lacking clade', IRLC). It is thus very important to sequence plastomes from other lineages in order to better understand the unusual evolution observed in this model flowering plant family. To this end, the plastome of a lupine species, Lupinus luteus, was sequenced to represent the Genistoid lineage, a noteworthy but poorly studied legume group. † Methods The plastome of L. luteus was reconstructed using Roche-454 and Illumina next-generation sequencing. Its structure, repetitive sequences, gene content and sequence divergence were compared with those of other Fabaceae plastomes. PCR screening and sequencing were performed in other allied legumes in order to determine the origin of a large inversion identified in L. luteus. † Key Results The first sequenced Genistoid plastome (L. luteus: 155 894 bp) resulted in the discovery of a 36-kb inversion, embedded within the already known 50-kb inversion in the large single-copy (LSC) region of the Papilionoideae. This inversion occurs at the base or soon after the Genistoid emergence, and most probably resulted from a flip-flop recombination between identical 29-bp inverted repeats within two trnS genes. Comparative analyses of the chloroplast gene content of L. luteus vs. Fabaceae and extra-Fabales plastomes revealed the loss of the plastid rpl22 gene, and its functional relocation to the nucleus was verified using lupine transcriptomic data. An investigation into the evolutionary rate of coding and non-coding sequencesamong legume plastomes resulted in the identification of remarkably variable regions. †Conclusions This study resulted in the discovery of a novel, major 36-kb inversion, specific to the Genistoids. Chloroplast mutational hotspots were also identified, which contain novel and potentially informative regions for molecular evolutionary studies at various taxonomic levels in the legumes. Taken together, the results provide new insights into the evolutionary landscape of the legume plastome.
Published: 2014
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26. Systematic comparison of small RNA library preparation protocols for next-generation sequencing

Author: Cloelia Dard-Dascot, Delphine Naquin, Yves d’Aubenton-Carafa, Karine Alix, Erwin van Dijk, Claude Thermes, Plateforme de séquençage à haut débit (NGS), Département Plateforme (PF I2BC), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-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), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Van Dijk, Erwin, 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), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), ProdInra, Archive Ouverte, Institut de Biologie Intégrative de la Cellule, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), National Center for Scientific Research (CNRS), French Alternative Energies and Atomic Energy Commission (CEA), Paris-Sud University, Plateforme de séquençage à haut débit ( NGS ), Département Plateforme ( PF I2BC ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), and Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS )
Subjects: 0301 basic medicine, Small RNA, Library preparation, lcsh:QH426-470, lcsh:Biotechnology, [SDV]Life Sciences [q-bio], Piwi-interacting RNA, Computational biology, Biology, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, Adapter (genetics), New england, Bias, lcsh:TP248.13-248.65, microRNA, Genetics, Animals, Humans, small RNA, Gene Library, [ SDV ] Life Sciences [q-bio], Sequence Analysis, RNA, Methodology Article, Computational Biology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Plants, [SDV] Life Sciences [q-bio], MicroRNAs, lcsh:Genetics, 030104 developmental biology, Next-generation sequencing, NGS, 2 '-O-methyl RNA, BIAS, 030220 oncology & carcinogenesis, Nucleic Acid Conformation, 2’-O-methyl RNA, next-generation sequencing, DNA microarray, Biotechnology
Abstract: Background Next-generation sequencing technologies have revolutionized the study of small RNAs (sRNAs) on a genome-wide scale. However, classical sRNA library preparation methods introduce serious bias, mainly during adapter ligation steps. Several types of sRNA including plant microRNAs (miRNA), piwi-interacting RNAs (piRNA) in insects, nematodes and mammals, and small interfering RNAs (siRNA) in insects and plants contain a 2’-O-methyl (2’-OMe) modification at their 3′ terminal nucleotide. This inhibits 3′ adapter ligation and makes library preparation particularly challenging. To reduce bias, the NEBNext kit (New England Biolabs) uses polyethylene glycol (PEG), the NEXTflex V2 kit (BIOO Scientific) uses both randomised adapters and PEG, and the novel SMARTer (Clontech) and CATS (Diagenode) kits avoid ligation altogether. Here we compared these methods with Illumina’s classical TruSeq protocol regarding the detection of normal and 2’ OMe RNAs. In addition, we modified the TruSeq and NEXTflex protocols to identify conditions that improve performance. Results Among the five kits tested with their respective standard protocols, the SMARTer and CATS kits had the lowest levels of bias but also had a strong formation of side products, and as a result performed relatively poorly with biological samples; NEXTflex detected the largest numbers of different miRNAs. The use of a novel type of randomised adapters called MidRand-Like (MRL) adapters and PEG improved the detection of 2’ OMe RNAs both in the TruSeq as well as in the NEXTflex protocol. Conclusions While it is commonly accepted that biases in sRNA library preparation protocols are mainly due to adapter ligation steps, the ligation-free protocols were not the best performing methods. Our modified versions of the TruSeq and NEXTflex protocols provide an improved tool for the study of 2’ OMe RNAs. Electronic supplementary material The online version of this article (10.1186/s12864-018-4491-6) contains supplementary material, which is available to authorized users.
Published: 2015
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27. Suppression of Dwarf and irregular xylem Phenotypes Generates Low-Acetylated Biomass Lines in Arabidopsis

Author: Valérie Lefebvre, Jacques Trouverie, Marie-Noelle Fortabat, Mylène Durand-Tardif, Aloïse Ducamp, Emilie Gineau, Catherine Lapierre, Grégory Mouille, Alexia Guillebaux, Stéphane Herbette, Christine Horlow, Matthieu Bensussan, Delphine Naquin, Aurélie Baldy, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre de génétique moléculaire UPR 3404, Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut Jean-Pierre Bourgin ( IJPB ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier ( PIAF ), Institut National de la Recherche Agronomique ( INRA ) -Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ), Ecophysiologie Végétale, Agronomie et Nutritions ( EVA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Caen Normandie ( UNICAEN ), and Normandie Université ( NU ) -Normandie Université ( NU )
Subjects: Physiology, [SDV]Life Sciences [q-bio], Mutant, Molecular Sequence Data, Arabidopsis, Dwarfism, Plant Science, Phloem, Suppression, Genetic, Acetyltransferases, Cell Wall, Xylem, Genetics, Vascular cambium, medicine, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biomass, Cellulose, Glucuronidase, biology, [ SDV ] Life Sciences [q-bio], Arabidopsis Proteins, fungi, Wild type, Membrane Proteins, Water, food and beverages, Acetylation, Articles, biology.organism_classification, medicine.disease, Cell biology, Phenotype, Ethyl Methanesulfonate, Mutation, Plant Vascular Bundle
Abstract: eskimo1-5 (esk1-5) is a dwarf Arabidopsis (Arabidopsis thaliana) mutant that has a constitutive drought syndrome and collapsed xylem vessels, along with low acetylation levels in xylan and mannan. ESK1 has xylan O-acetyltransferase activity in vitro. We used a suppressor strategy on esk1-5 to screen for variants with wild-type growth and low acetylation levels, a favorable combination for ethanol production. We found a recessive mutation in the KAKTUS (KAK) gene that suppressed dwarfism and the collapsed xylem character, the cause of decreased hydraulic conductivity in the esk1-5 mutant. Backcrosses between esk1-5 and two independent knockout kak mutants confirmed suppression of the esk1-5 effect. kak single mutants showed larger stem diameters than the wild type. The KAK promoter fused with a reporter gene showed activity in the vascular cambium, phloem, and primary xylem in the stem and hypocotyl. However, suppression of the collapsed xylem phenotype in esk1 kak double mutants was not associated with the recovery of cell wall O-acetylation or any major cell wall modifications. Therefore, our results indicate that, in addition to its described activity as a repressor of endoreduplication, KAK may play a role in vascular development. Furthermore, orthologous esk1 kak double mutants may hold promise for ethanol production in crop plants.
Published: 2015
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28. First Complete Genome Sequence of a Salmonella enterica subsp. enterica Serovar Derby Strain Associated with Pork in France

Author: Emilie Esnault, Valérie Rose, Edouard Hirchaud, Delphine Naquin, Annaëlle Kerouanton, Martine Denis, 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), and 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)
Subjects: Gel electrophoresis, Serotype, Whole genome sequencing, biology, Strain (biology), [SDV]Life Sciences [q-bio], biology.organism_classification, Microbiology, Salmonella enterica, Genetics, Pulsed-field gel electrophoresis, Salmonella enterica subsp. enterica, Prokaryotes, Molecular Biology
Abstract: In France, Salmonella enterica subsp. enterica serovar Derby is one of the most often isolated serovars in pigs. Here, we describe the draft genome sequence of a strain isolated from a pig. This strain had the most frequent pulsed-field gel electrophoresis (PFGE) and antimicrobial patterns (S, SSU, T) usually observed in pig production in France. Those patterns have been also highlighted in human isolates.
Published: 2015
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29. Unraveling the stratification of an iron-oxidizing microbial mat by metatranscriptomics

Author: André-Jean Francez, Sophie Coudouel, Achim Quaiser, Philippe Vandenkoornhuyse, Xavier Bodi, Delphine Naquin, Alexis Dufresne, Mathieu Pédrot, Alexandra Dheilly, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre de Recherches de Gif-sur-Yvette (FRC3115), non renseigné, Plateforme Génomique Environnementale et Fonctionnelle (GEF), Observatoire des Sciences de l'Univers de Rennes (OSUR), Géosciences Rennes (GR), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)
Subjects: Marine and Aquatic Sciences, lcsh:Medicine, RNA, Ribosomal, 16S, Microbial mat, lcsh:Science, Phylogeny, Freshwater Ecology, Genetics, Multidisciplinary, Ecology, biology, Biodiversity, Genomics, Functional Genomics, Community Ecology, Oxygenases, Leptothrix, Transcriptome Analysis, Methane, Oxidation-Reduction, Ecosystem Functioning, Research Article, Freshwater Environments, Sequence analysis, Iron, Microbial Consortia, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Microbiology, Ecosystems, Microbial Ecology, Phylogenetics, Community Structure, Ecosystem, Base Sequence, Sequence Analysis, RNA, Gene Expression Profiling, Ecology and Environmental Sciences, lcsh:R, Biology and Life Sciences, Computational Biology, Aquatic Environments, Ribosomal RNA, Genome Analysis, biology.organism_classification, Archaea, Microbial population biology, Earth Sciences, Pyrosequencing, lcsh:Q, Metagenomics
Abstract: International audience; A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria affiliated to the genus Leptothrix, dominated the community in the upper layers of the mat. Surprisingly, type I methanotrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem.
Published: 2014
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30. Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61

Author: Patrice Francois, Jacques Schrenzel, Hélène Falentin, Sébastien Nouaille, Delphine Naquin, Valentin Loux, Pascal Le Bourgeois, Dominique Lavenier, Sergine Even, David Hernandez, Pascal Loubière, Yves Le Loir, Frédérique Barloy-Hubler, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Unité Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), UMR 6026 Interactions cellulaires et Moléculaires , Campus de Beaulieu, Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), 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), Genomic Research Laboratory, Geneva University Hospital (HUG), Agence Nationale de la Recherche ALIA Project NABAB (no. ANR-08-ALIA-011)., Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Unité Mathématique Informatique et Génome (MIG), Interactions cellulaires et moléculaires (ICM), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), 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), ANR-08-ALIA-0011,NABAB,Stratégie Non AntiBiotique Anti-Bactéries pathogènes : exploration des capacités inhibitrices des écosystèmes naturels contre les contaminations à S. aureus en contexte laitier(2008), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: Dairy industry, fromage, Genome, Microbiology, 03 medical and health sciences, Plasmid, lactococcus lactis, séquençage, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Genetics, souche, Prokaryotes, Molecular Biology, fermentation, 030304 developmental biology, 2. Zero hunger, Whole genome sequencing, ddc:616, 0303 health sciences, biology, 030306 microbiology, Strain (biology), génome, Lactococcus lactis, biology.organism_classification, Lactococcus lactis subsp. lactis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, diversité génétique, bacteria, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: Lactococcus lactis is widely used in the dairy industry. We report the draft genome sequence of L. lactis subsp. lactis bv. diacetylactis LD61, an industrial and extensively studied strain. In contrast to the closely related and plasmidless strain IL1403, LD61 contains 6 plasmids, and the genome sequence provides additional information related to adaptation to the dairy environment.
Published: 2014
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31. Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

Author: C. A. da Silva, Julien Boutte, Armel Salmon, Patrick Wincker, Malika L. Aïnouche, Sophie Michon-Coudouel, Delphine Naquin, Julie Poulain, J. Ferreira de Carvalho, Alexandra Dheilly, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Plateforme Génomique Environnementale et Fonctionnelle (GEF), Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Projet GENOSPART (Genoscope), ARED EVOSPART grant, LIA 'Ecological Genomics of Polyploidy', Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), 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), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique
Subjects: 0106 biological sciences, Genetic Speciation, Locus (genetics), transcriptome assembly, Poaceae, Spartina alterniflora, Plant Roots, Polymorphism, Single Nucleotide, 01 natural sciences, Genome, DNA sequencing, invasive species, Contig Mapping, 03 medical and health sciences, Gene density, Genetics, Genetics (clinical), polyploidy, Gene Library, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Expressed sequence tag, Spartina, biology, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Salt-Tolerant Plants, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, Plant Leaves, RNA, Plant, Wetlands, chloridoideae, Original Article, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Transcriptome, Spartina maritima, Genome, Plant, 010606 plant biology & botany
Abstract: Plateforme BioGenouest 'Environmental and Functional Genomics'; Genouest Bioinformatics Plateform; International audience; Spartina species have a critical ecological role in salt marshes and represent an excellent system to investigate recurrent polyploid speciation. Using the 454 GS-FLX pyrosequencer, we assembled and annotated the first reference transcriptome (from roots and leaves) for two related hexaploid Spartina species that hybridize in Western Europe, the East American invasive Spartina alterniflora and the Euro-African S. maritima. The de novo read assembly generated 38 478 consensus sequences and 99% found an annotation using Poaceae databases, representing a total of 16 753 non-redundant genes. Spartina expressed sequence tags were mapped onto the Sorghum bicolor genome, where they were distributed among the subtelomeric arms of the 10 S. bicolor chromosomes, with high gene density correlation. Normalization of the complementary DNA library improved the number of annotated genes. Ecologically relevant genes were identified among GO biological function categories in salt and heavy metal stress response, C4 photosynthesis and in lignin and cellulose metabolism. Expression of some of these genes had been found to be altered by hybridization and genome duplication in a previous microarray-based study in Spartina. As these species are hexaploid, up to three duplicated homoeologs may be expected per locus. When analyzing sequence polymorphism at four different loci in S. maritima and S. alterniflora, we found up to four haplotypes per locus, suggesting the presence of two expressed homoeologous sequences with one or two allelic variants each. This reference transcriptome will allow analysis of specific Spartina genes of ecological or evolutionary interest, estimation of homoeologous gene expression variation using RNAseq and further gene expression evolution analyses in natural populations.
Published: 2013
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32. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Author: Dent Earl, Jacob O. Kitzman, Iain MacCallum, James R. Knight, Jacques Corbeil, Elenie Godzaridis, Cristian Del Fabbro, Paul J. Kersey, Martin Hunt, Octávio S. Paulo, Joseph Fass, Isaac Ho, Michael C. Schatz, Erich D. Jarvis, Dominique Lavenier, Simone Scalabrin, Thomas D. Otto, Nicolas Maillet, Siu-Ming Yiu, Timothy I. Shaw, David B. Jaffe, Henry Song, Ruibang Luo, Steve Goldstein, David Haussler, Francisco Pina-Martins, Richard A. Gibbs, Adam M. Phillippy, Michael Bechner, Ganeshkumar Ganapathy, Stephen Richards, Riccardo Vicedomini, Shuangye Yin, François Laviolette, Yingrui Li, T. Roderick Docking, Binghang Liu, Carson Qu, Wen-Chi Chou, Hao Zhang, Nuno A. Fonseca, Dariusz Przybylski, Bruno Vieira, Yue Liu, Matthew D. MacManes, Sébastien Boisvert, Yujian Shi, Jared T. Simpson, Sergey Kazakov, Sergey Koren, Jarrod Chapman, Giles Hall, Paul Baranay, Sante Gnerre, Shiguo Zhou, Rayan Chikhi, Filipe J. Ribeiro, Jason T. Howard, Zhenyu Li, Pavel Fedotov, Jay Shendure, J. Graham Ruby, Joseph B. Hiatt, Benedict Paten, Ian F Korf, David C. Schwartz, Keith Bradnam, Jianying Yuan, Alexey Sergushichev, Jun Wang, Hamidreza Chitsaz, Daniel S. Rokhsar, Inanc Birol, Huaiyang Jiang, Kim C. Worley, Anton Alexandrov, Zemin Ning, Delphine Naquin, Michael Place, Matthias Haimel, Guojie Zhang, Guillaume Chapuis, Fedor Tsarev, Scott J. Emrich, Shaun D. Jackman, Sergey Melnikov, Xiang Qin, Ted Sharpe, Francesco Vezzi, Tak-Wah Lam, Richard Durbin, Genome Center [UC Davis], University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), National Research University of Information Technologies, Mechanics and Optics [St. Petersburg] (ITMO), Computational Biology and Bioinformatics [New Haven], Yale University [New Haven], Laboratory for Molecular and Computational Genomics [Madison], University of Wisconsin-Madison, Genome Sciences Centre [Vancouver] (GSC), British Columbia Cancer Agency, Infectious Diseases Research Center [Québec], Université Laval [Québec] (ULaval), Faculté de médecine de l'Université Laval [Québec] (ULaval), DOE Joint Genome Institute [Walnut Creek], Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Dependability Interoperability and perfOrmance aNalYsiS Of networkS (DIONYSOS), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-RÉSEAUX, TÉLÉCOMMUNICATION ET SERVICES (IRISA-D2), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Department of computer science [Detroit], Wayne State University [Detroit], Institute of Bioinformatics [Athens], University of Georgia [USA], Institute of Aging Research [Boston], Hebrew SeniorLife [Boston], Department of Molecular Medicine [Québec], Institute of Applied Genomics [Udine] (IGA), Institute of Applied Genomics, The Wellcome Trust Sanger Institute [Cambridge], Howard Hughes Medical Institute [Santa Cruz] (HHMI), Howard Hughes Medical Institute (HHMI)-University of California [Santa Cruz] (UC Santa Cruz), Department of Computer Science and Engineering [South Bend], University of Notre Dame [Indiana] (UND), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, CRACS & Inesc TEC [Porto], Universidade do Porto = University of Porto, Medical Center [Durham], Duke University [Durham], Human Genome Sequencing Center [Houston] (HGSC), Baylor College of Medicine (BCM), Baylor University-Baylor University, Broad Institute [Cambridge], Harvard University-Massachusetts Institute of Technology (MIT), Faculty of Medicine, Department of Genome Sciences [Seattle] (GS), University of Washington [Seattle], 454 Life Sciences [Branford], 454 Life Sciences, National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, Center for Bioinformatics and Computational Biology [Maryland] (CBCB), University of Maryland [College Park], University of Maryland System-University of Maryland System, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory [Hong Kong], The University of Hong Kong (HKU), Invariant Preserving SOlvers (IPSO), Institut de Recherche Mathématique de Rennes (IRMAR), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, 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 de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), 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)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Department of Computer Science and Software Engineering [Québec], Beijing Genomics Institute [Shenzhen] (BGI), Berkeley California Institute for Quantitative Biosciences [Berkeley], University of California (UC), Computational Biology & Population Genomics Group [Lisboa], Centre for Environmental Biology, New York Genome Center [New York], New York Genome Center, Department of Molecular and Cell Biology, Department of Biochemistry and Biophysics, Howard Hughes Medical Institute (HHMI), Simons Center for Quantitative Biology [Cold Spring Harbor], Cold Spring Harbor Laboratory, Department of Epidemiology and Biostatistics [Athens], University of Georgia [USA]-College of Public Health, Science for Life Laboratory [Solna], Royal Institute of Technology [Stockholm] (KTH ), Department of Mathematics and Computer Science [Udine], Università degli Studi di Udine - University of Udine [Italie], University of California-University of California, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Howard Hughes Medical Institute (HHMI)-University of California [Santa Cruz] (UCSC), Universidade do Porto, Harvard University [Cambridge]-Massachusetts Institute of Technology (MIT), AGROCAMPUS OUEST, 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 de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-AGROCAMPUS OUEST, Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Inria Rennes – Bretagne Atlantique, and University of California
Subjects: [INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], Computer science, Sequence assembly, GENOMES, Health Informatics, Computational biology, Assessment, COMPASS, Genome, 03 medical and health sciences, 0302 clinical medicine, biology.animal, Quantitative Biology - Genomics, Gene, 030304 developmental biology, Sequence (medicine), Scaffolds, Genomics (q-bio.GN), Whole genome sequencing, 0303 health sciences, Genome assembly, Heterozygosity, biology, N50, Research, Vertebrate, De novo Assembly, Computer Science Applications, Fosmid, FOS: Biological sciences, Scalability, 030217 neurology & neurosurgery
Abstract: Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., Comment: Additional files available at http://korflab.ucdavis.edu/Datasets/Assemblathon/Assemblathon2/Additional_files/ Major changes 1. Accessions for the 3 read data sets have now been included 2. New file: spreadsheet containing details of all Study, Sample, Run, & Experiment identifiers 3. Made miscellaneous changes to address reviewers comments. DOIs added to GigaDB datasets
Published: 2013
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33. Assemblathon 1: A competitive assessment of de novo short read assembly methods

Author: Inanc Birol, Peter Skewes-Cox, Dariusz Przybylski, Paul J. Kersey, Guillaume Chapuis, Matthias Haimel, Sante Gnerre, Mark Diekhans, Petr Kosarev, Richard E. Green, Igor Seledtsov, Richard Durbin, Daniel S. Rokhsar, Miguel Betegon, Ngan Nguyen, Isaac Ho, J. Graham Ruby, Michelle Dimon, Aaron E. Darling, Ricardo H. Ramirez-Gonzalez, Daniel R. Zerbino, David R. Kelley, Ruibang Luo, Ian F Korf, Richard M. Leggett, Timothy I. Shaw, Keith Bradnam, Benedict Paten, Yingrui Li, Giles Hall, Vince Buffalo, Yinlong Xie, Shuangye Yin, Xiaoqiu Huang, Shaun D. Jackman, Victor V. Solovyev, Denis Vorobyev, Binghang Liu, T. Roderick Docking, Joseph L. DeRisi, Delphine Naquin, Ted Sharpe, Adam M. Phillippy, Mario Caccamo, Zemin Ning, Wing-Kin Sung, Jarrod Chapman, David B. Jaffe, John St. John, Pramila N. Ariyaratne, David Haussler, Fangfang Xia, Wen-Chi Chou, Sergey Koren, Dan MacLean, Joseph Fass, Rayan Chikhi, Iain MacCallum, Nicolas Maillet, Hung On Ken Yu, Nuno A. Fonseca, Dominique Lavenier, Michael C. Schatz, Dent Earl, Anuj Srivastava, Dawei Lin, Zhenyu Li, Wei Wu, Filipe J. Ribeiro, Shiaw-Pyng Yang, Jared T. Simpson, Center for Biomolecular Science and Engineering, University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Biomolecular Engineering Department, Genome Center [UC Davis], University of California [Davis] (UC Davis), Bioinformatics Core [University California Davis] (UC Davis), Computational and Mathematical Biology, Genome Institute of Singapore (GIS), School of computing [Singapore] (NUS), National University of Singapore (NUS), The Wellcome Trust Sanger Institute [Cambridge], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Center for Research in Advanced Computing Systems (CRACS INESC), Faculdade de Ciências da Universidade do Porto (FCUP), Universidade do Porto = University of Porto-Universidade do Porto = University of Porto, Genome Sciences Centre [Vancouver] (GSC), British Columbia Cancer Agency, DOE Joint Genome Institute [Walnut Creek], Department of Molecular & Cell Biology [Berkeley], University of California [Berkeley] (UC Berkeley), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Simons Center for Quantitative Biology [Cold Spring Harbor], Cold Spring Harbor Laboratory, Center for Bioinformatics and Computational Biology [Maryland] (CBCB), University of Maryland [College Park], University of Maryland System-University of Maryland System, National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, Monsanto Company, Institute of Bioinformatics [Georgia] (IOB), University of Georgia [USA], Howard Hughes Medical Institute [Chevy Chase] (HHMI), Howard Hughes Medical Institute (HHMI), Department of Biochemistry and Biophysics [San Francisco], University of California (UC), Biological and Medical Informatics [San Francisco] (BMI), University of California [San Francisco] (UC San Francisco), Department of Computer Science [Royal Holloway], Royal Holloway [University of London] (RHUL), Softberry Inc, Softberry, The Genome Analysis Centre (TGAC), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Computation Institute [Chicago], University of Chicago, Beijing Genomics Institute [Shenzhen] (BGI), Broad Institute [Cambridge], Harvard University-Massachusetts Institute of Technology (MIT), Department of Computer Science [Ames], Iowa State University (ISU), University of California [Santa Cruz] (UCSC), University of California-University of California, Bioinformatics Core [UC Davis], Universidade do Porto-Universidade do Porto, University of California [Berkeley], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, University of California, University of California [San Francisco] (UCSF), and Massachusetts Institute of Technology (MIT)-Harvard University [Cambridge]
Subjects: Genetics, Resource, 0303 health sciences, Genome, Bioinformatics, Sequence assembly, Genomics, Computational biology, Sequence Analysis, DNA, Biology, Short read, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 03 medical and health sciences, 0302 clinical medicine, Code (cryptography), Benchmark (computing), Data set (IBM mainframe), Base calling, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery, Genetics (clinical), 030304 developmental biology
Abstract: Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.
Published: 2011
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34. Utilisation d'une Grille de Calcul (GRISBI) pour le Traitement de Données NGS (New Generation Sequencing)

Author: Florence Maurier, Alexis Groppi, Aurélien Barré, Delphine Naquin, Aurélien Roult, Clément Gauthey, Christophe Blanchet, Tiphaine Martin, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), and Sciencesconf.org, CCSD
Subjects: Grille de calcul, Assemblage de novo, NGS, [INFO.INFO-DC] Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Gestionnaire de workflow, Calcul intensif
Abstract: International audience; Utilisation d'une Grille de Calcul (GRISBI) pour le Traitement de Données NGS (New Generation Sequencing)
Published: 2011

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34 results on '"Delphine, Naquin"'

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7. Genomics in the long-read sequencing era

8. Impact of the severity of negative energy balance on gene expression in the subcutaneous adipose tissue of periparturient primiparous Holstein dairy cows: Identification of potential novel metabolic signals for the reproductive system.

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10. Construction of a Transposon Mutant Library in the Pathogen Agrobacterium tumefaciens C58 and Identification of Genes Involved in Gall Niche Exploitation and Colonization

11. Construction of a Transposon Mutant Library in the Pathogen Agrobacterium tumefaciens C58 and Identification of Genes Involved in Gall Niche Exploitation and Colonization

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15. Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

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18. Genome Sequences of 11 Conspecific

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20. The biotroph Agrobacterium tumefaciens thrives in tumors by exploiting a wide spectrum of plant host metabolites

21. CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data.

22. Impact of the severity of negative energy balance on gene expression in the subcutaneous adipose tissue of periparturient primiparous Holstein dairy cows: Identification of potential novel metabolic signals for the reproductive system

23. Lifestyle of the biotroph Agrobacterium tumefaciens in the ecological niche constructed on its host plant

24. The Third Revolution in Sequencing Technology

25. The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family

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31. Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

32. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

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34. Utilisation d'une Grille de Calcul (GRISBI) pour le Traitement de Données NGS (New Generation Sequencing)

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34 results on '"Delphine, Naquin"'

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