Author: "Delphine Charif" / Language: english - Searchworks@Jio Institute Digital Library Search Results

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1. Rapid meiotic prophase chromosome movements in Arabidopsis thaliana are linked to essential reorganization at the nuclear envelope

Author: Laurence Cromer, Mariana Tiscareno-Andrade, Sandrine Lefranc, Aurélie Chambon, Aurélie Hurel, Manon Brogniez, Julie Guérin, Ivan Le Masson, Gabriele Adam, Delphine Charif, Philippe Andrey, and Mathilde Grelon
Subjects: Science
Abstract: Abstract Meiotic rapid prophase chromosome movements (RPMs) require connections between the chromosomes and the cytoskeleton, involving SUN (Sad1/UNC-84)-domain-containing proteins at the inner nuclear envelope (NE). RPMs remain significantly understudied in plants, with respect to their importance in the regulation of meiosis. Here, we demonstrate that Arabidopsis thaliana meiotic centromeres undergo rapid (up to 500 nm/s) and uncoordinated movements during the zygotene and pachytene stages. These centromere movements are not affected by altered chromosome organization and recombination but are abolished in the double mutant sun1 sun2. We also document the changes in chromosome dynamics and nucleus organization during the transition from leptotene to zygotene, including telomere attachment to SUN-enriched NE domains, bouquet formation, and nucleolus displacement, all of which were defective in sun1 sun2. These results establish A. thaliana as a model species for studying the functional implications of meiotic RPMs and demonstrate the mechanistic conservation of telomere-led RPMs in plants.
Published: 2024
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2. A transcriptomic dataset for investigating the Arabidopsis Unfolded Protein Response under chronic, proteotoxic endoplasmic reticulum stress

Author: Amélie Ducloy, Marianne Azzopardi, Caroline Ivsic, Gwendal Cueff, Delphine Sourdeval, Delphine Charif, and Jean-Luc Cacas
Subjects: Protein homeostasis, Asparagine-linked glycosylation, Inositol-requiring enzyme-1, Tunicamycin, Plant, Shoots, Computer applications to medicine. Medical informatics, R858-859.7, Science (General), Q1-390
Abstract: The Unfolded Protein Response (UPR) is a retrograde, ER-to-nucleus, signalling pathway which is conserved across kingdoms. In plants, it contributes to development, reproduction, immunity and tolerance to abiotic stress. This RNA sequencing (RNA-seq) dataset was produced from 14-day-old Arabidopsis thaliana seedlings challenged by tunicamycin (Tm), an antibiotic inhibiting Asn-linked glycosylation in the endoplasmic reticulum (ER), causing an ER stress and eventually activating the UPR. Wild-type (WT) and a double mutant deficient for two main actors of the UPR (INOSITOL-REQUIRING ENZYME 1A and INOSITOL-REQUIRING ENZYME 1B) were used as genetic backgrounds in our experimental setup, allowing to distinguish among differentially-expressed genes (DEGs) which ones are dependent on or independent on IRE1s. Also, shoots and roots were harvested separately to determine organ-specific transcriptomic responses to Tm. Library and sequencing were performed using DNBseq™ technology by the Beijing Genomics Institute. Reads were mapped and quantified against the Arabidopsis genome. Differentially-expressed genes were identified using Rflomics upon filtering and normalization by the Trimmed Mean of M-value (TMM) method. While the genotype effect was weak under mock conditions (with a total of 182 DEGs in shoots and 195 DEGs in roots), the tunicamycin effect on each genotype was characterized by several hundred of DEGs in both shoots and roots. Among these genes, 872 and 563 genes were statistically up- and down-regulated in the shoot tissues of the double mutant when compared to those of WT, respectively. In roots of Tm-challenged seedlings, 425 and 439 genes were significantly up- and down-regulated in mutants with respect to WT. We believe that our dataset could be reused for investigating any biological questions linked to ER homeostasis and its role in plant physiology.
Published: 2024
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3. Genome-wide specificity of plant genome editing by both CRISPR–Cas9 and TALEN

Author: Nadia Bessoltane, Florence Charlot, Anouchka Guyon-Debast, Delphine Charif, Kostlend Mara, Cécile Collonnier, Pierre-François Perroud, Mark Tepfer, and Fabien Nogué
Subjects: Medicine, Science
Abstract: Abstract CRISPR and TALENs are efficient systems for gene editing in many organisms including plants. In many cases the CRISPR–Cas or TALEN modules are expressed in the plant cell only transiently. Theoretically, transient expression of the editing modules should limit unexpected effects compared to stable transformation. However, very few studies have measured the off-target and unpredicted effects of editing strategies on the plant genome, and none of them have compared these two major editing systems. We conducted, in Physcomitrium patens, a comprehensive genome-wide investigation of off-target mutations using either a CRISPR–Cas9 or a TALEN strategy. We observed a similar number of differences for the two editing strategies compared to control non-transfected plants, with an average of 8.25 SNVs and 19.5 InDels for the CRISPR-edited plants, and an average of 17.5 SNVs and 32 InDels for the TALEN-edited plants. Interestingly, a comparable number of SNVs and InDels could be detected in the PEG-treated control plants. This shows that except for the on-target modifications, the gene editing tools used in this study did not show a significant off-target activity nor unpredicted effects on the genome, and did not lead to transgene integration. The PEG treatment, a well-established biotechnological method, in itself, was the main source of mutations found in the edited plants.
Published: 2022
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4. Datasets of seed mucilage traits for Arabidopsis thaliana natural accessions with atypical outer mucilage

Author: Mireille Cambert, Adeline Berger, Christine Sallé, Stéphanie Esling, Delphine Charif, Tudel Cadoret, Marie-Christine Ralet, Helen M. North, and Corinne Rondeau-Mouro
Subjects: Science
Abstract: Measurement(s) intrinsic viscosity • galacturonic acid • seed and inner mucilage layer width • Transverse Spin Relaxation Time • Transverse Spin Relaxation intensity • mucilage • neutral sugar content • mass per seed • sample mass Technology Type(s) size-exclusion chromatography • colorimetry • immunolabeling method • confocal microscopy • nuclear magnetic resonance spectroscopy • Time-domain NMR • biochemical, histological and Time-Domain NMR analyses • biochemical method using orcinol • microbalance Sample Characteristic - Organism Arabidopsis thaliana Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.13320593
Published: 2021
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5. Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction

Author: Stefania Del Prete, Anne Molitor, Delphine Charif, Nadia Bessoltane, Ludivine Soubigou-Taconnat, Cécile Guichard, Véronique Brunaud, Fabienne Granier, Paul Fransz, and Valérie Gaudin
Subjects: Floral transition, Leaf, Arabidopsis, Transcription, Non-coding RNA, Transcription factors, Botany, QK1-989
Abstract: Abstract Background The floral transition is a complex developmental event, fine-tuned by various environmental and endogenous cues to ensure the success of offspring production. Leaves are key organs in sensing floral inductive signals, such as a change in light regime, and in the production of the mobile florigen. CONSTANS and FLOWERING LOCUS T are major players in leaves in response to photoperiod. Morphological and molecular events during the floral transition have been intensively studied in the shoot apical meristem. To better understand the concomitant processes in leaves, which are less described, we investigated the nuclear changes in fully developed leaves during the time course of the floral transition. Results We highlighted new putative regulatory candidates of flowering in leaves. We observed differential expression profiles of genes related to cellular, hormonal and metabolic actions, but also of genes encoding long non-coding RNAs and new natural antisense transcripts. In addition, we detected a significant increase in ploidy level during the floral transition, indicating endoreduplication. Conclusions Our data indicate that differentiated mature leaves, possess physiological plasticity and undergo extensive nuclear reprogramming during the floral transition. The dynamic events point at functionally related networks of transcription factors and novel regulatory motifs, but also complex hormonal and metabolic changes.
Published: 2019
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6. Corrigendum: FANCM Limits Meiotic Crossovers in Brassica Crops

Author: Aurélien Blary, Adrián Gonzalo, Frédérique Eber, Aurélie Bérard, Hélène Bergès, Nadia Bessoltane, Delphine Charif, Catherine Charpentier, Laurence Cromer, Joelle Fourment, Camille Genevriez, Marie-Christine Le Paslier, Maryse Lodé, Marie-Odile Lucas, Nathalie Nesi, Andrew Lloyd, Anne-Marie Chèvre, and Eric Jenczewski
Subjects: FANCM, Translational biology, Brassica, meiotic crossover, TILLING, plant breeding, Plant culture, SB1-1110
Published: 2020
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7. FANCM Limits Meiotic Crossovers in Brassica Crops

Author: Aurélien Blary, Adrián Gonzalo, Frédérique Eber, Aurélie Bérard, Hélène Bergès, Nadia Bessoltane, Delphine Charif, Catherine Charpentier, Laurence Cromer, Joelle Fourment, Camille Genevriez, Marie-Christine Le Paslier, Maryse Lodé, Marie-Odile Lucas, Nathalie Nesi, Andrew Lloyd, Anne-Marie Chèvre, and Eric Jenczewski
Subjects: FANCM, Translational biology, Brassica, meiotic crossover, TILLING, plant breeding, Plant culture, SB1-1110
Abstract: Meiotic crossovers (COs) are essential for proper chromosome segregation and the reshuffling of alleles during meiosis. In WT plants, the number of COs is usually small, which limits the genetic variation that can be captured by plant breeding programs. Part of this limitation is imposed by proteins like FANCM, the inactivation of which results in a 3-fold increase in COs in Arabidopsis thaliana. Whether the same holds true in crops needed to be established. In this study, we identified EMS induced mutations in FANCM in two species of economic relevance within the genus Brassica. We showed that CO frequencies were increased in fancm mutants in both diploid and tetraploid Brassicas, Brassica rapa and Brassica napus respectively. In B. rapa, we observed a 3-fold increase in the number of COs, equal to the increase observed previously in Arabidopsis. In B. napus we observed a lesser but consistent increase (1.3-fold) in both euploid (AACC) and allohaploid (AC) plants. Complementation tests in A. thaliana suggest that the smaller increase in crossover frequency observed in B. napus reflects residual activity of the mutant C copy of FANCM. Altogether our results indicate that the anti-CO activity of FANCM is conserved across the Brassica, opening new avenues to make a wider range of genetic diversity accessible to crop improvement.
Published: 2018
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8. A cryptic cytoplasmic male sterility unveils a possible gynodioecious past for Arabidopsis thaliana.

Author: Nicolas Gobron, Cezary Waszczak, Matthieu Simon, Sophie Hiard, Stéphane Boivin, Delphine Charif, Aloïse Ducamp, Estelle Wenes, and Françoise Budar
Subjects: Medicine, Science
Abstract: Gynodioecy, the coexistence of hermaphrodites and females (i.e. male-sterile plants) in natural plant populations, most often results from polymorphism at genetic loci involved in a particular interaction between the nuclear and cytoplasmic genetic compartments (cytonuclear epistasis): cytoplasmic male sterility (CMS). Although CMS clearly contributes to the coevolution of involved nuclear loci and cytoplasmic genomes in gynodioecious species, the occurrence of CMS genetic factors in the absence of sexual polymorphism (cryptic CMS) is not easily detected and rarely taken in consideration. We found cryptic CMS in the model plant Arabidopsis thaliana after crossing distantly related accessions, Sha and Mr-0. Male sterility resulted from an interaction between the Sha cytoplasm and two Mr-0 genomic regions located on chromosome 1 and chromosome 3. Additional accessions with either nuclear sterility maintainers or sterilizing cytoplasms were identified from crosses with either Sha or Mr-0. By comparing two very closely related cytoplasms with different male-sterility inducing abilities, we identified a novel mitochondrial ORF, named orf117Sha, that is most likely the sterilizing factor of the Sha cytoplasm. The presence of orf117Sha was investigated in worldwide natural accessions. It was found mainly associated with a single chlorotype in accessions belonging to a clade predominantly originating from Central Asia. More than one-third of accessions from this clade carried orf117Sha, indicating that the sterilizing-inducing cytoplasm had spread in this lineage. We also report the coexistence of the sterilizing cytoplasm with a non-sterilizing cytoplasm at a small, local scale in a natural population; in addition a correlation between cytotype and nuclear haplotype was detected in this population. Our results suggest that this CMS system induced sexual polymorphism in A. thaliana populations, at the time when the species was mainly outcrossing.
Published: 2013
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9. Wolbachia interferes with ferritin expression and iron metabolism in insects.

Author: Natacha Kremer, Denis Voronin, Delphine Charif, Patrick Mavingui, Bertrand Mollereau, and Fabrice Vavre
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: Wolbachia is an intracellular bacterium generally described as being a facultative reproductive parasite. However, Wolbachia is necessary for oogenesis completion in the wasp Asobara tabida. This dependence has evolved recently as a result of interference with apoptosis during oogenesis. Through comparative transcriptomics between symbiotic and aposymbiotic individuals, we observed a differential expression of ferritin, which forms a complex involved in iron storage. Iron is an essential element that is in limited supply in the cell. However, it is also a highly toxic precursor of Reactive Oxygen Species (ROS). Ferritin has also been shown to play a key role in host-pathogen interactions. Measuring ferritin by quantitative RT-PCR, we confirmed that ferritin was upregulated in aposymbiotic compared to symbiotic individuals. Manipulating the iron content in the diet, we showed that iron overload markedly affected wasp development and induced apoptotic processes during oogenesis in A. tabida, suggesting that the regulation of iron homeostasis may also be related to the obligate dependence of the wasp. Finally, we demonstrated that iron metabolism is influenced by the presence of Wolbachia not only in the obligate mutualism with A. tabida, but also in facultative parasitism involving Drosophila simulans and in Aedes aegypti cells. In these latter cases, the expression of Wolbachia bacterioferritin was also increased in the presence of iron, showing that Wolbachia responds to the concentration of iron. Our results indicate that Wolbachia may generally interfere with iron metabolism. The high affinity of Wolbachia for iron might be due to physiological requirement of the bacterium, but it could also be what allows the symbiont to persist in the organism by reducing the labile iron concentration, thus protecting the cell from oxidative stress and apoptosis. These findings also reinforce the idea that pathogenic, parasitic and mutualistic intracellular bacteria all use the same molecular mechanisms to survive and replicate within host cells. By impacting the general physiology of the host, the presence of a symbiont may select for host compensatory mechanisms, which extends the possible consequences of persistent endosymbiont on the evolution of their hosts.
Published: 2009
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10. Corrigendum: FANCM Limits Meiotic Crossovers in Brassica Crops

Author: Maryse Lodé, Aurélie Bérard, Joëlle Fourment, Anne-Marie Chèvre, Delphine Charif, Camille Genevriez, Adrián Gonzalo, Hélène Bergès, Nathalie Nesi, Eric Jenczewski, Marie-Odile Lucas, Aurélien Blary, Laurence Cromer, Marie-Christine Le Paslier, Catherine Charpentier, Frédérique Eber, Nadia Bessoltane, Andrew H. Lloyd, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de Ressources Génomiques Végétales (CNRGV), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: TILLING, Genetics, biology, Brassica, Translational biology, Plant Science, lcsh:Plant culture, biology.organism_classification, meiotic crossover, Meiosis, FANCM, plant breeding, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Plant breeding, ComputingMilieux_MISCELLANEOUS, polyploidy
Abstract: International audience
Published: 2020
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11. Identifying and isolating meiotic mutants in a polyploid brassica crop

Author: Marie-Christine Le Paslier, Adrián Gonzalo, Emilie Montes, Nadia Bessoltane, Delphine Charif, Nathalie Nesi, Lydia Jaffrelo, Aurélie Bérard, Nicolas Christophorou, Marina Pfalz, Eric Jenczewski, Aurélien Blary, Charles Poncet, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRA BAP division (Appel a Manifestation d'interet 2012, HyperRec), 'Young Scientist Contracts' (CJS) from INRA, Mónica Pradillo, Stefan Heckmann, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-14-CE19-0004,CROC,Contrôle de la fréquence de recombinaison méiotique pour accélérer l'innovation variétales chez les espèces cultivées polyploïdes(2014), European Project: 606956,EC:FP7:PEOPLE,FP7-PEOPLE-2013-ITN,COMREC(2013), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, TILLING, Computational biology, Biology, Gene editing, 01 natural sciences, Polyploidy, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Genome editing, Meiosis, Polyploid, Guide RNA, Microfluidic PCR, Gene, 2. Zero hunger, Meiotic recombination, fungi, Brassica napus, food and beverages, Reverse genetics, 030104 developmental biology, Targeting induced local lesions in genomes, Homologous recombination, 010606 plant biology & botany
Abstract: International audience; This chapter provides a detailed description of TILLING and CRISPR-Cas9 approaches for the purpose of studying genes/factors involved in meiotic recombination in the polyploid species B. napus. The TILLING approach involves the screening and identification of EMS-mutagenized M2 B. napus plants. The strategy for high-throughput plant pooling, the set up for microfluidic PCR and sequencing is provided and the parameters for the analysis of sequence results and the detection of mutants are explained. The CRISPR-Cas system relies on the optimal design of guide RNAs and their efficient expression. The procedure for the generation and detection of knockout mutants is described with the aims to simultaneously target homologous genes.
Published: 2020
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12. Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop

Author: Guillem Rigaill, Eric Jenczewski, Catherine Charpentier, Sandrine Balzergue, Delphine Charif, Andrew H. Lloyd, Aurélien Blary, Etienne Delannoy, Joseph Tran, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité (COMUE) (USPC), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA), ANR project ANR-2010- BLANC-628 SVSE7- DUPLIC and a grant from the Biology and Plant Breeding division of INRA (AAP-GAP-2012- VARCO), LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0301 basic medicine, Genome evolution, Physiology, Gene Dosage, Plant Science, Biology, Gene dosage, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Structural variation, Polyploidy, 03 medical and health sciences, homoeologous exchanges, Gene duplication, Gene expression, Genetic variation, Copy-number variation, Gene, Genetics, Recombination, Genetic, meiotic recombination, Brassica napus (Rapeseed), Sequence Analysis, RNA, Brassica napus, polyploid, copy number variation, Genetic Variation, 030104 developmental biology, Organ Specificity, gene expression, Genome, Plant
Abstract: International audience; Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined. Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges (HE) on gene expression in Brassica napus, a representative allotetraploid crop. We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs. Thus, when homoeologous gene pairs have unbalanced transcriptional contributions before the HE, duplication of one copy does not accurately compensate for loss of the other and combined homoeologue expression also changes. These effects are, however, mitigated over time. This study sheds light on the origins, timing and functional consequences of homeologous exchanges in allopolyploids. It demonstrates that the interplay between new structural variation and the resulting impacts on gene expression, influences allopolyploid genome evolution.
Published: 2018
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13. Xyloglucan Metabolism Differentially Impacts the Cell Wall Characteristics of the Endosperm and Embryo during Arabidopsis Seed Germination

Author: Delphine Effroy-Cuzzi, Julien Sechet, Anne Frey, Delphine Charif, Grégory Mouille, François Perreau, Adeline Berger, Helen M. North, Loïc Rajjou, Gwendal Cueff, Annie Marion-Poll, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and National Research Agency [ANR-2010-BLAN-1233-01, ANR-11-BSV5-0007]
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Plant Science, 01 natural sciences, Hypocotyl, Endosperm, Cell Wall, Gene Expression Regulation, Plant, Radicle, Developmental, Glucans, Arabidopsis Proteins/genetics/metabolism, Triazoles/pharmacology, biology, Gene Expression Regulation, Developmental, food and beverages, Seeds/growth & development/metabolism, Articles, Plants, Plants, Genetically Modified, Xylosidases, Biochemistry, Germination, Seeds, Glucans/*metabolism, Xylans, Xylosidases/genetics/metabolism, Genetically Modified, Genes, Plant, Arabidopsis/genetics/*growth & development/*metabolism, Cell wall, 03 medical and health sciences, Genetics, Cell Wall/metabolism, Protein Processing, Xylans/*metabolism, Arabidopsis Proteins, fungi, Endosperm/growth & development/metabolism, Post-Translational, Plant, Triazoles, biology.organism_classification, 030104 developmental biology, Genes, Gene Expression Regulation, Germination/drug effects/genetics/physiology, Mutation, Dormancy, abscisic-acid, monoclonal-antibodies, aba accumulation, gene-expression, growth defects, thaliana seeds, messenger-rna, dormancy, mutant, deficient, Protein Processing, Post-Translational, 010606 plant biology & botany
Abstract: International audience; Cell wall remodeling is an essential mechanism for the regulation of plant growth and architecture, and xyloglucans (XyGs), the major hemicellulose, are often considered as spacers of cellulose microfibrils during growth. In the seed, the activity of cell wall enzymes plays a critical role in germination by enabling embryo cell expansion leading to radicle protrusion, as well as endosperm weakening prior to its rupture. A screen for Arabidopsis (Arabidopsis thaliana) mutants affected in the hormonal control of germination identified a mutant, xyl1, able to germinate on paclobutrazol, an inhibitor of gibberellin biosynthesis. This mutant also exhibited reduced dormancy and increased resistance to high temperature. The XYL1 locus encodes an alpha-xylosidase required for XyG maturation through the trimming of Xyl. The xyl1 mutant phenotypes were associated with modifications to endosperm cell wall composition that likely impact on its resistance, as further demonstrated by the restoration of normal germination characteristics by endosperm-specific XYL1 expression. The absence of phenotypes in mutants defective for other glycosidases, which trim Gal or Fuc, suggests that XYL1 plays the major role in this process. Finally, the decreased XyG abundance in hypocotyl longitudinal cell walls of germinating embryos indicates a potential role in cell wall loosening and anisotropic growth together with pectin de-methylesterification.
Published: 2016
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14. Meiotic Gene Evolution: Can You Teach a New Dog New Tricks?

Author: Eric Jenczewski, Catherine Feuillet, Harry Belcram, Arnaud Remay, Frédéric Choulet, Marion Ranoux, Delphine Charif, Catherine Marquis, Boulos Chalhoub, Lise Pingault, Natasha Glover, Sonia Vautrin, Fabienne Granier, Joëlle Fourment, Gilles Lassalle, William Marande, Hélène Bergès, Joseph Tran, Pierre Sourdille, Andrew H. Lloyd, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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), BioGEVES, Institut National de la Recherche Agronomique (INRA)-Ministère en charge de l'Agriculture-Groupement National Interprofessionnel des Semences, Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Whole genome duplication, Biology, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Magnoliopsida, Polyploid, Meiosis, Gene Duplication, Gene duplication, evolution, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Genetics, meiosis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Homologous Recombination, Molecular Biology, Gene, genome, Ecology, Evolution, Behavior and Systematics, polyploidy, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, fungi, Meiotic drive, duplication, [SDE]Environmental Sciences, Homologous recombination, whole genome duplication, Genome, Plant, 010606 plant biology & botany
Abstract: International audience; Meiosis, the basis of sex, evolved through iterative gene duplications. To understand whether subsequent duplications have further enriched the core meiotic "tool-kit," we investigated the fate of meiotic gene duplicates following whole genome duplication (WGD), a common occurrence in eukaryotes. We show that meiotic genes return to a single copy more rapidly than genome-wide average in angiosperms, one of the lineages in which WGD is most vividly exemplified. The rate at which duplicates are lost decreases through time, a tendency that is also observed genome-wide and may thus prove to be a general trend post-WGD. The sharpest decline is observed for the subset of genes mediating meiotic recombination; however, we found no evidence that the presence of these duplicates is counterselected in two recent polyploid crops selected for fertility. We therefore propose that their loss is passive, highlighting how quickly WGDs are resolved in the absence of selective duplicate retention.
Published: 2014
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15. A Cryptic Cytoplasmic Male Sterility Unveils a Possible Gynodioecious Past for Arabidopsis thaliana

Author: Cezary Waszczak, Estelle Wenes, Stéphane Boivin, Delphine Charif, Matthieu Simon, Sophie Hiard, Aloïse Ducamp, Nicolas Gobron, Françoise Budar, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, French Ministry in charge of Research, and VERT Marie Curie Early Training Site
Subjects: 0106 biological sciences, Evolutionary Genetics, Cytoplasm, [SDV]Life Sciences [q-bio], Arabidopsis, Gynodioecy, Plant Science, Plant Genetics, 01 natural sciences, MITOCHONDRIAL GENOMES, Phylogeny, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, Cytoplasmic male sterility, Biological Evolution, Mitochondria, POPULATIONS, Medicine, Research Article, EXPRESSION, INCOMPATIBILITY, Plant Infertility, Sterility, Science, Arabidopsis Thaliana, Population, Outcrossing, NUCLEAR, Biology, RAPHANUS-RAPHANISTRUM, Chromosomes, Plant, Mitochondrial Proteins, 03 medical and health sciences, Open Reading Frames, Model Organisms, Plant and Algal Models, FERTILITY, education, Crosses, Genetic, 030304 developmental biology, Cell Nucleus, Evolutionary Biology, Population Biology, Haplotype, Chromosome, Biology and Life Sciences, DNA, EVOLUTION, Genetic Loci, Genetic Polymorphism, Epistasis, SELF-COMPATIBILITY, Population Genetics, 010606 plant biology & botany
Abstract: Gynodioecy, the coexistence of hermaphrodites and females (i.e. male-sterile plants) in natural plant populations, most often results from polymorphism at genetic loci involved in a particular interaction between the nuclear and cytoplasmic genetic compartments (cytonuclear epistasis): cytoplasmic male sterility (CMS). Although CMS clearly contributes to the coevolution of involved nuclear loci and cytoplasmic genomes in gynodioecious species, the occurrence of CMS genetic factors in the absence of sexual polymorphism (cryptic CMS) is not easily detected and rarely taken in consideration. We found cryptic CMS in the model plant Arabidopsis thaliana after crossing distantly related accessions, Sha and Mr-0. Male sterility resulted from an interaction between the Sha cytoplasm and two Mr-0 genomic regions located on chromosome 1 and chromosome 3. Additional accessions with either nuclear sterility maintainers or sterilizing cytoplasms were identified from crosses with either Sha or Mr-0. By comparing two very closely related cytoplasms with different male-sterility inducing abilities, we identified a novel mitochondrial ORF, named orf117Sha, that is most likely the sterilizing factor of the Sha cytoplasm. The presence of orf117Sha was investigated in worldwide natural accessions. It was found mainly associated with a single chlorotype in accessions belonging to a clade predominantly originating from Central Asia. More than one-third of accessions from this clade carried orf117Sha, indicating that the sterilizing-inducing cytoplasm had spread in this lineage. We also report the coexistence of the sterilizing cytoplasm with a non-sterilizing cytoplasm at a small, local scale in a natural population; in addition a correlation between cytotype and nuclear haplotype was detected in this population. Our results suggest that this CMS system induced sexual polymorphism in A. thaliana populations, at the time when the species was mainly outcrossing.
Published: 2013
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16. Influence of Wolbachia on host gene expression in an obligatory symbiosis

Author: Patrick Mavingui, Patrick Wincker, Hélène Henri, Delphine Charif, Natacha Kremer, Fabrice Vavre, Frédérick Gavory, Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Physiologie de l'Insecte : Signalisation et Communication (PISC), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), ANR-06-BLAN-0316,ENDOSYMBART,ENDO SYMBiosis in ARThropods(2006), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), UMR CNRS 5558, IFR 41, GDR 2153, Agence Nationale de la Recherche (ANR-06-BLANC-0316), Fondation Innovations en Infectiologie (FINOVI 005), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), An algorithmic view on genomes, cells, and environments ( BAMBOO ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Physiologie de l'Insecte : Signalisation et Communication ( PISC ), Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -AgroParisTech, Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), and ANR-06-BLAN-0316,ENDOSYMBART,ENDO SYMBiosis in ARThropods ( 2006 )
Subjects: Male, Microbiology (medical), Wasps, lcsh:QR1-502, Genes, Insect, Microbiology, lcsh:Microbiology, Parasitoid wasp, reproduction, 03 medical and health sciences, Aposymbiotic, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Animals, arthropode, Symbiosis, Gene, 030304 developmental biology, Genetics, Regulation of gene expression, Parasitoid Wasp, 0303 health sciences, wolbachia, biology, 030306 microbiology, Ecology, Intracellular parasite, Gene Expression Profiling, Research, Ovary, Microbiology and Parasitology, Suppression Subtractive Hybridization, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Microbiologie et Parasitologie, Gene expression profiling, Gene Ontology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Gene Expression Regulation, Cytoplasmic Incompatibility, Host-Pathogen Interactions, bacteria, Wolbachia, Female, bactérie intracellulaire, Wolbachia Infection, symbiose, Cytoplasmic incompatibility, expression des gènes
Abstract: Background Wolbachia are intracellular bacteria known to be facultative reproductive parasites of numerous arthropod hosts. Apart from these reproductive manipulations, recent findings indicate that Wolbachia may also modify the host’s physiology, notably its immune function. In the parasitoid wasp, Asobara tabida, Wolbachia is necessary for oogenesis completion, and aposymbiotic females are unable to produce viable offspring. The absence of egg production is also associated with an increase in programmed cell death in the ovaries of aposymbiotic females, suggesting that a mechanism that ensures the maintenance of Wolbachia in the wasp could also be responsible for this dependence. In order to decipher the general mechanisms underlying host-Wolbachia interactions and the origin of the dependence, we developed transcriptomic approaches to compare gene expression in symbiotic and aposymbiotic individuals. Results As no genetic data were available on A. tabida, we constructed several Expressed Sequence Tags (EST) libraries, and obtained 12,551 unigenes from this species. Gene expression was compared between symbiotic and aposymbiotic ovaries through in silico analysis and in vitro subtraction (SSH). As pleiotropic functions involved in immunity and development could play a major role in the establishment of dependence, the expression of genes involved in oogenesis, programmed cell death (PCD) and immunity (broad sense) was analyzed by quantitative RT-PCR. We showed that Wolbachia might interfere with these numerous biological processes, in particular some related to oxidative stress regulation. We also showed that Wolbachia may interact with immune gene expression to ensure its persistence within the host. Conclusions This study allowed us to constitute the first major dataset of the transcriptome of A. tabida, a species that is a model system for both host/Wolbachia and host/parasitoid interactions. More specifically, our results highlighted that symbiont infection may interfere with numerous pivotal processes at the individual level, suggesting that the impact of Wolbachia should also be investigated beyond reproductive manipulations.
Published: 2012
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17. Feminizing Wolbachia: a transcriptomics approach with insights on the immune response genes in Armadillidium vulgare

Author: Delphine Charif, Frédéric Gavory, Frédéric D. Chevalier, Pierre Grève, Juline Herbinière-Gaboreau, Christine Braquart-Varnier, Guillaume Mitta, Didier Bouchon, Patrick Wincker, Ecologie, Evolution, Symbiose (EES), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecologie et évolution des interactions [2011-2014] (2EI), Université de Perpignan Via Domitia (UPVD)-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), Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Microbiology (medical), Male, Feminization (biology), lcsh:QR1-502, medicine.disease_cause, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Immune system, Hemolymph, Botany, medicine, Animals, Symbiosis, 030304 developmental biology, Armadillidium vulgare, Genetics, Expressed Sequence Tags, 0303 health sciences, biology, 030306 microbiology, Host (biology), Research, Gene Expression Profiling, Ovary, Pathogenic bacteria, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 3. Good health, Gene Expression Regulation, bacteria, Wolbachia, Female, Immunocompetence, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Isopoda
Abstract: Background Wolbachia are vertically transmitted bacteria known to be the most widespread endosymbiont in arthropods. They induce various alterations of the reproduction of their host, including feminization of genetic males in isopod crustaceans. In the pill bug Armadillidium vulgare, the presence of Wolbachia is also associated with detrimental effects on host fertility and lifespan. Deleterious effects have been demonstrated on hemocyte density, phenoloxidase activity, and natural hemolymph septicemia, suggesting that infected individuals could have defective immune capacities. Since nothing is known about the molecular mechanisms involved in Wolbachia-A. vulgare interactions and its secondary immunocompetence modulation, we developed a transcriptomics strategy and compared A. vulgare gene expression between Wolbachia-infected animals (i.e., “symbiotic” animals) and uninfected ones (i.e., “asymbiotic” animals) as well as between animals challenged or not challenged by a pathogenic bacteria. Results Since very little genetic data is available on A. vulgare, we produced several EST libraries and generated a total of 28 606 ESTs. Analyses of these ESTs revealed that immune processes were over-represented in most experimental conditions (responses to a symbiont and to a pathogen). Considering canonical crustacean immune pathways, these genes encode antimicrobial peptides or are involved in pathogen recognition, detoxification, and autophagy. By RT-qPCR, we demonstrated a general trend towards gene under-expression in symbiotic whole animals and ovaries whereas the same gene set tends to be over-expressed in symbiotic immune tissues. Conclusion This study allowed us to generate the first reference transcriptome ever obtained in the Isopoda group and to identify genes involved in the major known crustacean immune pathways encompassing cellular and humoral responses. Expression of immune-related genes revealed a modulation of host immunity when females are infected by Wolbachia, including in ovaries, the crucial tissue for the Wolbachia route of transmission.
Published: 2012
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18. Host gene response to endosymbiont and pathogen in the cereal weevil \textitSitophilus oryzae

Author: Carole Vincent-Monégat, Patrick Wincker, Abdelaziz Heddi, Agnès Vallier, Delphine Charif, Frédérick Gavory, Aurélien Vigneron, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), INRA, INSA de Lyon, French Agence Nationale de la Recherche [ANR-06-BLANC-0316, ANR-2010-BLAN170101], and COST action [FA0701]
Subjects: [SDV]Life Sciences [q-bio], lcsh:QR1-502, Nitrogen compound metabolic process, lcsh:Microbiology, 0302 clinical medicine, PEPTIDOGLYCAN RECOGNITION PROTEIN, NEGATIVE BACTERIAL-INFECTION, DUPLEX-SPECIFIC NUCLEASE, INNATE IMMUNE-RESPONSE, B FACTOR RELISH, CELL-DEATH, MUTUALIST WIGGLESWORTHIA, DROSOPHILA-MELANOGASTER, GENOME SEQUENCE, DEFICIENCY IMD, 2. Zero hunger, 0303 health sciences, Sitophilus, Microbiota, Genomics, Larva, Host-Pathogen Interactions, Insect Proteins, Gammaproteobacteria, Symbiotic bacteria, Microbiology (medical), Molecular Sequence Data, Biology, Microbiology, Host Specificity, 03 medical and health sciences, Aposymbiotic, Immune system, Bacterial Proteins, Animals, Symbiosis, 030304 developmental biology, Gene Library, Host (biology), Bacteriocyte, Research, fungi, Bacteriome, Sequence Analysis, DNA, biology.organism_classification, Gene Expression Regulation, Weevils, 030217 neurology & neurosurgery
Abstract: Background Insects thriving on nutritionally poor habitats have integrated mutualistic intracellular symbiotic bacteria (endosymbionts) in a bacteria-bearing tissue (the bacteriome) that isolates the endosymbionts and protects them against a host systemic immune response. Whilst the metabolic and physiological features of long-term insect associations have been investigated in detail over the past decades, cellular and immune regulations that determine the host response to endosymbionts and pathogens have attracted interest more recently. Results To investigate bacteriome cellular specificities and weevil immune responses to bacteria, we have constructed and sequenced 7 cDNA libraries from Sitophilus oryzae whole larvae and bacteriomes. Bioinformatic analysis of 26,886 ESTs led to the generation of 8,941 weevil unigenes. Based on in silico analysis and on the examination of genes involved in the cellular pathways of potential interest to intracellular symbiosis (i.e. cell growth and apoptosis, autophagy, immunity), we have selected and analyzed 29 genes using qRT-PCR, taking into consideration bacteriome specificity and symbiosis impact on the host response to pathogens. We show that the bacteriome tissue accumulates transcripts from genes involved in cellular development and survival, such as the apoptotic inhibitors iap2 and iap3, and endosomal fusion and trafficking, such as Rab7, Hrs, and SNARE. As regards our investigation into immunity, we first strengthen the bacteriome immunomodulation previously reported in S. zeamais. We show that the sarcotoxin, the c-type lysozyme, and the wpgrp2 genes are downregulated in the S. oryzae bacteriome, when compared to aposymbiotic insects and insects challenged with E. coli. Secondly, transcript level comparison between symbiotic and aposymbiotic larvae provides evidence that the immune systemic response to pathogens is decreased in symbiotic insects, as shown by the relatively high expression of wpgrp2, wpgrp3, coleoptericin-B, diptericin, and sarcotoxin genes in aposymbiotic insects. Conclusions Library sequencing significantly increased the number of unigenes, allowing for improved functional and genetic investigations in the cereal weevil S. oryzae. Transcriptomic analyses support selective and local immune gene expression in the bacteriome tissue and uncover cellular pathways that are of potential interest to bacteriocyte survival and homeostasis. Bacterial challenge experiments have revealed that the systemic immune response would be less induced in a symbiotic insect, thus highlighting new perspectives on host immunity in long-term invertebrate co-evolutionary associations.
Published: 2012
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19. Wolbachia interferes with ferritin expression and iron metabolism in insects

Author: Fabrice Vavre, Natacha Kremer, Denis Voronin, Patrick Mavingui, Delphine Charif, Bertrand Mollereau, Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire de Biologie Moléculaire de la Cellule (LBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire de Biologie Moléculaire de la Cellule ( LBMC ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: Insecta, [SDV]Life Sciences [q-bio], Wasps, Evolutionary Biology/Developmental Evolution, Aedes, lcsh:QH301-705.5, 0303 health sciences, biology, Chromosome Mapping, Bacterioferritin, Cell biology, Evolutionary Biology/Microbial Evolution and Genomics, Drosophila, Female, Wolbachia, Drosophila melanogaster, Research Article, lcsh:Immunologic diseases. Allergy, Iron, Molecular Sequence Data, Immunology, Rickettsiaceae Infections, Parasitism, Evolutionary Biology/Evolutionary Ecology, Microbiology, Host-Parasite Interactions, 03 medical and health sciences, Aposymbiotic, Virology, Botany, Genetics, Animals, Symbiosis, Molecular Biology, 030304 developmental biology, [ SDV ] Life Sciences [q-bio], Evolutionary Biology/Evolutionary and Comparative Genetics, Base Sequence, Obligate, 030306 microbiology, Intracellular parasite, biology.organism_classification, Ferritin, lcsh:Biology (General), Gene Expression Regulation, Genetic Loci, Ferritins, biology.protein, Nucleic Acid Conformation, Parasitology, lcsh:RC581-607
Abstract: Wolbachia is an intracellular bacterium generally described as being a facultative reproductive parasite. However, Wolbachia is necessary for oogenesis completion in the wasp Asobara tabida. This dependence has evolved recently as a result of interference with apoptosis during oogenesis. Through comparative transcriptomics between symbiotic and aposymbiotic individuals, we observed a differential expression of ferritin, which forms a complex involved in iron storage. Iron is an essential element that is in limited supply in the cell. However, it is also a highly toxic precursor of Reactive Oxygen Species (ROS). Ferritin has also been shown to play a key role in host–pathogen interactions. Measuring ferritin by quantitative RT-PCR, we confirmed that ferritin was upregulated in aposymbiotic compared to symbiotic individuals. Manipulating the iron content in the diet, we showed that iron overload markedly affected wasp development and induced apoptotic processes during oogenesis in A. tabida, suggesting that the regulation of iron homeostasis may also be related to the obligate dependence of the wasp. Finally, we demonstrated that iron metabolism is influenced by the presence of Wolbachia not only in the obligate mutualism with A. tabida, but also in facultative parasitism involving Drosophila simulans and in Aedes aegypti cells. In these latter cases, the expression of Wolbachia bacterioferritin was also increased in the presence of iron, showing that Wolbachia responds to the concentration of iron. Our results indicate that Wolbachia may generally interfere with iron metabolism. The high affinity of Wolbachia for iron might be due to physiological requirement of the bacterium, but it could also be what allows the symbiont to persist in the organism by reducing the labile iron concentration, thus protecting the cell from oxidative stress and apoptosis. These findings also reinforce the idea that pathogenic, parasitic and mutualistic intracellular bacteria all use the same molecular mechanisms to survive and replicate within host cells. By impacting the general physiology of the host, the presence of a symbiont may select for host compensatory mechanisms, which extends the possible consequences of persistent endosymbiont on the evolution of their hosts., Author Summary Wolbachia are intracellular bacteria that infect numerous invertebrate species, where they are generally facultative for their host. Surprisingly, the wasp Asobara tabida is dependent on Wolbachia for egg production: in uninfected females, the cells necessary for egg maturation die prematurely as a result of apoptosis. When we analyzed the genetic basis of this dependence, we found that ferritin, a protein involved in the regulation of iron homeostasis, was over-expressed in uninfected individuals. We also found that Wolbachia interferes with iron metabolism and ferritin expression in other host–Wolbachia associations. Furthermore, Wolbachia itself responds to changes in iron concentration by changing the expression of bacterioferritin. Iron is in short supply within the cell, and is necessary for both host and symbiont; our findings highlight the key role of iron in host–symbiont interactions, as had previously been shown for host–pathogen interactions. Furthermore, iron homeostasis is involved in the regulation of oxidative stress, which in turn is involved in inducing cell death. Wolbachia could also interfere with iron in a way that limits oxidative stress and cell death, thus promoting its persistence within host cells. In A. tabida, we show that iron induced cell death in the ovaries, suggesting that iron metabolism could also be linked to the evolution of dependence.
Published: 2009
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20. A new case of Wolbachia dependence in the genus Asobara: evidence for parthenogenesis induction in Asobara japonica

Author: Natacha Kremer, Delphine Charif, Ken Kraaijeveld, Hélène Henri, G Prévost, M Bataille, Fabrice Vavre, Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], food.ingredient, Molecular Sequence Data, Parthenogenesis, Wasps, Zoology, Parasitoid, Sexual Behavior, Animal, food, Species Specificity, Human population genetics, parasitic diseases, Genetics, Animals, Mating, Symbiosis, Phylogeny, Genetics (clinical), reproductive and urinary physiology, Asobara, biology, Obligate, Ecology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Host-Pathogen Interactions, bacteria, Female, Wolbachia, Braconidae
Abstract: Wolbachia is a maternally inherited bacterium that is widely distributed among arthropods, in which it manipulates the reproduction of its hosts. Although generally facultative for its hosts, Wolbachia has recently become obligatory in Asobara tabida (Hymenoptera: Braconidae) in which it is required for the completion of oogenesis. Here, we describe a new Wolbachia strain (wAjap) that is associated with the genus Asobara and infects Asobara japonica. wAjap was detected in all female-biased populations of A. japonica found in the main islands of Japan, but not in the arrhenotokous populations from the southern islands. Using phylogenetic analyses based on multi-locus sequence typing (MLST), we show that this strain is closely related to wAtab3 (the strain required for oogenesis in A. tabida), even though they differ on Wolbachia surface protein (WSP) and WO phage sequences. Using antibiotic treatments, we show that cured thelytokous females are not dependent on Wolbachia for oogenesis. However, they produced only sons, showing that wAjap induces thelytokous parthenogenesis. Analyses of mating behavior and offspring production of individuals from Wolbachia-infected populations showed that while males were still sexually functional, females no longer attract males, making Wolbachia an obligate partner for daughter production in thelytokous populations. The fact that Wolbachia has become independently obligatory in two species of the same genus tends to show that dependence evolution can be common and swift, although no clear benefit for the parasitoid can be attributed to this dependence. Although dependence should lead to co-divergence between Wolbachia and its hosts, the very few cases of co-speciation observed in host-Wolbachia associations question the stability of these obligatory associations.
Published: 2009
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21. Interaction between host genotype and environmental conditions affects bacterial density in Wolbachia symbiosis

Author: Michel Boulétreau, Fabrice Vavre, Hélène Henri, Laurence Mouton, Delphine Charif, Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Genotype, Wasps, Bacterial population, Breeding, Population density, Symbiosis, parasitic diseases, Animals, Host genotype, reproductive and urinary physiology, Genetics, Population Density, Analysis of Variance, biology, Ecology, Host (biology), Temperature, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Host-Pathogen Interactions, Linear Models, bacteria, Wolbachia, Female, General Agricultural and Biological Sciences, Leptopilina heterotoma, Research Article
Abstract: Regulation of microbial population density is a necessity in stable symbiotic interactions. In Wolbachia symbiosis, both bacterial and host genotypes are involved in density regulation, but environmental factors may also affect bacterial population density. Here, we studied the interaction between three strains of Wolbachia in two divergent homozygous lines of the wasp Leptopilina heterotoma at two different temperatures. Wolbachia density varied between the two host genotypes at only one temperature. Moreover, at this temperature, reciprocal-cross F1 insects displayed identical Wolbachia densities, which were intermediate between the densities in the two parental lines. While these findings confirm that the host genotype plays an important role in Wolbachia density, they also highlight its interaction with environmental conditions, making possible the evolution of local adaptations for the regulation of Wolbachia density.
Published: 2007

22. A Survey of the Bacteriophage WO in the Endosymbiotic Bacteria Wolbachia

Author: Michel Boulétreau, Delphine Charif, Fabrice Vavre, Hélène Henri, Laurent Gavotte, Richard Stouthamer, Sylvain Charlat, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE)
Subjects: [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Insecta, Gene Transfer, Horizontal, Genes, Viral, Nematoda, viruses, Molecular Sequence Data, Polymerase Chain Reaction, Microbiology, Evolution, Molecular, Transduction (genetics), Phylogenetics, Genetics, Animals, Bacteriophages, Bacteriophage Typing, Molecular Biology, Gene, Phylogeny, Ecology, Evolution, Behavior and Systematics, biology, Intracellular parasite, biology.organism_classification, Lytic cycle, DNA, Viral, Horizontal gene transfer, Capsid Proteins, Wolbachia, Bacteria
Abstract: Bacteriophages are common viruses infecting prokaryotes. In addition to their deadly effect, phages are also involved in several evolutionary processes of bacteria, such as coding functional proteins potentially beneficial to them, or favoring horizontal gene transfer through transduction. The particular lifestyle of obligatory intracellular bacteria usually protects them from phage infection. However, Wolbachia, an intracellular alpha-proteobacterium, infecting diverse arthropod and nematode species and best known for the reproductive alterations it induces, harbors a phage named WO, which has recently been proven to be lytic. Here, phage infection was checked in 31 Wolbachia strains, which induce 5 different effects in their hosts and infect 25 insect species and 3 nematodes. Only the Wolbachia infecting nematodes and Trichogramma were found devoid of phage infection. All the 25 detected phages were characterized by the DNA sequence of a minor capsid protein gene. Based on all data currently available, phylogenetic analyses show a lack of congruency between Wolbachia or insect and phage WO phylogenies, indicating numerous horizontal transfers of phage among the different Wolbachia strains. The absence of relation between phage phylogeny and the effects induced by Wolbachia suggests that WO is not directly involved in these effects. Implications on phage WO evolution are discussed.
Published: 2007

23. Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

Author: Christine Oger-Desfeux, Alex Widmer, Delphine Charif, Nicolas Blavet, Gabriel A. B. Marais, Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Heterozygote, lcsh:QH426-470, [SDV]Life Sciences [q-bio], lcsh:Biotechnology, Ecological and Environmental Phenomena, SNP, Computational biology, cDNA library, Polymorphism, Single Nucleotide, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Genome Size, Dianthus, Sequence Homology, Nucleic Acid, lcsh:TP248.13-248.65, Databases, Genetic, Genetics, EST, Silene, Genome size, database, 030304 developmental biology, Expressed Sequence Tags, 2. Zero hunger, 0303 health sciences, Expressed sequence tag, Massive parallel sequencing, Contig, biology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Molecular Sequence Annotation, biology.organism_classification, 3. Good health, lcsh:Genetics, DNA microarray, Transcriptome, Research Article, 010606 plant biology & botany, Biotechnology
Abstract: Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a plant model system. The genes characterized will be useful for future research not only in the species included in the present study, but also in related species for which no genomic resources are yet available. Our results demonstrate the efficiency of massively parallel transcriptome sequencing in a comparative framework as an approach for developing genomic resources in diverse groups of non-model organisms.
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24. MareyMap: an R-based tool with graphical interface for estimating recombination rates.

Subjects: *DROSOPHILIDAE, *ARABIDOPSIS, *CAENORHABDITIS elegans, *INTERPOLATION
Abstract: Summary: Comparing genetic and physical maps (the so-called Marey map approach) is still the most widely used approach to estimate genome-wide recombination rates. Remarkably, there is no available bioinformatics tool specifically devoted to Marey map approach. Here, we developed such a tool called MareyMap based on GNU R and Tcl/Tk. MareyMap offers a user-friendly graphical interface and includes useful features, such as data cleaning process, sophisticated interpolation methods to estimate local rates, possibility of complex queries, various range of importâexport files. Moreover, MareyMap comes with ready-to-use maps for human, Drosophila, Caenorhabditis elegans and Arabidopsis. MareyMap has been made so that it can be easily upgraded with new data and interpolation methods. Availability: http://pbil.univ-lyon1.fr/software/mareymap/ Contact: marais@biomserv.univ-lyon1.fr [ABSTRACT FROM AUTHOR]
Published: 2007
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24 results on '"Delphine Charif"'

1. Rapid meiotic prophase chromosome movements in Arabidopsis thaliana are linked to essential reorganization at the nuclear envelope

2. A transcriptomic dataset for investigating the Arabidopsis Unfolded Protein Response under chronic, proteotoxic endoplasmic reticulum stress

3. Genome-wide specificity of plant genome editing by both CRISPR–Cas9 and TALEN

4. Datasets of seed mucilage traits for Arabidopsis thaliana natural accessions with atypical outer mucilage

5. Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction

6. Corrigendum: FANCM Limits Meiotic Crossovers in Brassica Crops

7. FANCM Limits Meiotic Crossovers in Brassica Crops

8. A cryptic cytoplasmic male sterility unveils a possible gynodioecious past for Arabidopsis thaliana.

9. Wolbachia interferes with ferritin expression and iron metabolism in insects.

10. Corrigendum: FANCM Limits Meiotic Crossovers in Brassica Crops

11. Identifying and isolating meiotic mutants in a polyploid brassica crop

12. Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop

13. Xyloglucan Metabolism Differentially Impacts the Cell Wall Characteristics of the Endosperm and Embryo during Arabidopsis Seed Germination

14. Meiotic Gene Evolution: Can You Teach a New Dog New Tricks?

15. A Cryptic Cytoplasmic Male Sterility Unveils a Possible Gynodioecious Past for Arabidopsis thaliana

16. Influence of Wolbachia on host gene expression in an obligatory symbiosis

17. Feminizing Wolbachia: a transcriptomics approach with insights on the immune response genes in Armadillidium vulgare

18. Host gene response to endosymbiont and pathogen in the cereal weevil \textitSitophilus oryzae

19. Wolbachia interferes with ferritin expression and iron metabolism in insects

20. A new case of Wolbachia dependence in the genus Asobara: evidence for parthenogenesis induction in Asobara japonica

21. Interaction between host genotype and environmental conditions affects bacterial density in Wolbachia symbiosis

22. A Survey of the Bacteriophage WO in the Endosymbiotic Bacteria Wolbachia

23. Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

24. MareyMap: an R-based tool with graphical interface for estimating recombination rates.

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24 results on '"Delphine Charif"'

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