<em>NODULE ROOT</em> and <em>COCHLEATA</em> Maintain Nodule Development and Are Legume Orthologs of Arabidopsis <em>BLADE-ON-PETIOLE</em> Genes

During their symbiotic interaction with rhizobia, legume plants develop symbiosis-specific organs on their roots, called nodules, that house nitrogen-fixing bacteria. The molecular mechanisms governing the identity and maintenance of these organs are unknown. Using Medicago truncatula nodule root (noot) mutants and pea (Pisum sativum) cochleata (coch) mutants, which are characterized by the abnormal development of roots from the nodule, we identified the NOOT and COCH genes as being necessary for the robust maintenance of nodule identity throughout the nodule developmental program. NOOT and COCH are Arabidopsis thaliana BLADE-ON-PETIOLE orthologs, and we have shown that their functions in leaf and flower development are conserved in M. truncatula and pea. The identification of these two genes defines a clade in the BTB/POZ-ankyrin domain proteins that shares conserved functions in eudicot organ development and suggests that NOOT and COCH were recruited to repress root identity in the legume symbiotic organ

Etude de mutants d'insertion chez l'espèce modèle Medicago truncatula

Ce travail prend place dans le cadre de l'étude de la symbiose fixatrice d'azote, qui implique les légumineuses et les Rhizobia, bactéries du sol. Ces bactéries permettent la fixation de l'azote atmosphérique au sein de la nodosité racinaire. Le mécanisme moléculaire à l'origine de cet organe est peu connu et peu de gènes ont été caractérisés. Afin d'obtenir des mutations facilement caractérisables, des stratégies de mutagenèse insertionelle ont été testées au laboratoire chez Medicago truncatula. Mon travail a consisté à valider l'approche ADN-T chez M. truncatula. Nous avons tout d'abord testé le comportement de différents ADN-T. Deux lignées transgéniques ont ensuite été analysées plus précisément. Chez la lignée Sy4, L'ADN-T est inséré à proximité d'un gène codant une MAPKKK. Il ne semble pas y avoir d'homologues chez A. thaliana, et l'analyse phylogénétique suggère qu'il représente une nouvelle famille de kinase. Chez la lignée A7-1, l'ADN-T est inséré dans le gène GOLLUM et altère son expression, rendant la plante naine. Nous sommes en présence du premier mutant étiqueté chez M. truncatula. L'étude du gène GOLLUM a permis de déterminer que ce gène, homologue des hydrogénées bactériennes, est impliqué dans la morphogenèse en fonction de la pression partielle en 02. L'existence possible d'une interaction directe avec l'oxygène suggère un rôle comme senseur de l'oxygène. En conclusion, Ces travaux ont montré que la mutagenèse par l'ADN-T est faisable, en permettant d'obtenir le premier mutant étiqueté chez cette espèce. Cette technique sera étendue à l'étude de la symbiose fixatrice d'azote.This work takes place in the frame of the study of the interaction between legumes and rhizobia. These bacteria are able to fix the atmospheric nitrogen in the root nodule. The molecular mechanism responsible of the formation of this organ is not well known and only few genes have been characterized. The simple way to isolate mutations is to use known sequences as tag, like T-DNA or mobile elements that insert randomly in DNA. The aim of this work was to validate the T-DNA approach in the model legume Medicago truncatula. Firstly, we tested the behaviour of different T-DNAs in M. truncatula, and validated the T-DNA approach in this species. Two T-DNA lines have been analyzed in more details. In the Sy4 line, the T-DNA is inserted close to a gene coding a MAPKKK kinase. No homologue was found in Arabidopsis thaliana and phylogenetical analysis suggested that it belongs to a new family of kinases. In the A7-line, The T-DNA is inserted in a gene named GOLLUM, leading to a dwarf phenotype. This work represents the first characterization of a T-DNA mutant in M. truncatula. The GOLLUM gene is homologous to the prokaryotic Fe-hydrogenases and is implicated in the morphogenesis as a function of the O2 level. A possible interaction between the protein and the O2 suggests a role as oxygen sensor. In conclusion, this work demonstrated the feasibility of the T-DNA mutagenesis in M. truncatula, and we described the first T-DNA tagged mutant in this species. The work on the symbiosis will take advantage of this technical approach.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Données de séquençage numérique - L’exemple des données « sols »

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Groupe de travail sur les Métiers de la Bioinformatique (MetBIF)

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Le RMQS, une approche transposable à la caractérisation des sédiments ?

Le RMQS, une approche transposable à la caractérisation des sédiments ?. Workshop Franco-Suisse SédiCommuTOX : comment améliorer la qualité écotoxicologique des sédiments dans les milieux aquatiques continentaux par l’étude des communautés benthiques

Massively Parallel Boundary Integral Element Method Modeling of Particles in a Low Reynolds Number Mewtonian Fluid Flow

The analysis of many complex multiphase fluid flow systems is based on a scale decoupling procedure. At the macroscale continuum models are used to perform large-scale simulations. At the mesoscale statistical homogenization theory is used to derive continuum models based on representative volume elements (RVEs). At the microscale small-scale features, such as interfacial properties, are analyzed to be incorporated into mesoscale simulations. In this research mesoscopic simulations of hard particles suspended in a Newtonian fluid undergoing nonlinear shear flow are performed using a boundary element method. To obtain an RVE at higher concentrations, several hundred particles are included in the simulations, putting considerable demands on the computational resources both in terms of CPU and memory. Parallel computing provides a viable platform to study these large multiphase systems. The implementation of a portable, parallel computer code based on the boundary element method using a block-block data distribution is discussed in this paper. The code employs updated direct-solver technologies that make use of dual-processor compute nodes

Genome Sequence of the Potato Plant Pathogen Dickeya dianthicola Strain RNS04.9.

International audienceDickeya dianthicola is one of the causative agents of soft rot and blackleg diseases, which are currently identified in European countries in a wide range of crops. Here, we report the draft genome sequence of D. dianthicola strain RNS04.9, which was isolated from a potato plant with blackleg symptoms in 2004

Les plateformes analytiques d’AnaEE-France : des outils au service de la connaissance de la biodiversité

Les plateformes analytiques d’AnaEE-France : des outils au service de la connaissance de la biodiversité. Séminaire Ecoscope : Données et évaluation de la biodiversité. Quels enjeux, quels défis

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.European Research CouncilCNRSEuropean Molecular Biology LaboratoryGenoscope/CEAFrench GovernementFund for Scientific Research—Flanders, VIB, Stazione Zoologica Anton DohrnVIBStazione Zoologica Anton DohrnUNIMI

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.European Research CouncilCNRSEuropean Molecular Biology LaboratoryGenoscope/CEAFrench GovernementFund for Scientific Research—Flanders, VIB, Stazione Zoologica Anton DohrnVIBStazione Zoologica Anton DohrnUNIMIBANRVeolia Environment FoundationRegion BretagneWorld CourierIlluminaCap L’OrientEDF Foundation EDF DiversiterreFRBPrince Albert II de Monaco Foundatio