Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots

Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species

Trois zones de coconstruction de savoirs professionnels issues des médiations de débats en groupe

Cette contribution présente un cadre d’analyse des pratiques professionnelles structuré autour de trois zones de coconstruction de savoirs, dégagé des conversations entre des enseignantes ayant participé à une rechercheformation. L’analyse de leurs négociations conversationnelles autour des cas de pratique a permis de mettre en lumière les « zones partagées » de savoirs, « admises » ou encore « contestées » qui sous-tendent leur territoire de pratique. Nous montrons l’intérêt de ce cadre d’analyse pour la production de connaissances scientifiques à propos d’une activité professionnelle et pour une démarche de développement professionnel de praticiens en exercice. Enin, nous examinons les conditions de réalisation d’une intervention supportant ces deux visées, nous attardant en particulier sur les médiations à mobiliser pour nous donner accès aux savoirs d’une pratique professionnelle à partir de la rélexivité des praticiens, et nous soulignons les contributions pour les communautés scientifique, notamment pour le domaine de la communication, et professionnelle de ce cadre d’analyse.This paper presents an analytical framework of teacher professional knowledge, developed from the analysis of teacher’s conversations during a research-training project. Based on the analysis of their conversational negotiations around practical cases, this framework enlightens the professional group activity by identifying three areas of knowledge, “shared”, “accepted” and “contested”, which frames the territory of their practice. We expose this framework’s value for scientiic production of knowledge on a professional activity and for the professional development of practitioners. Finally, we examine the conditions of implementing a kind of intervention that supports those two aims, focusing in particular on the mediations to be mobilized in order to gain access to the knowledge of a professional practice based on the relexivity of the practitioners, and we highlight the contribution of this framework for scientiic communities – especially the communication domain – and the professional ones

GNPAnnot community annotation system applied to sugarcane bac clone sequences (W572)

A large amount of data is being produced by current genome sequencing projects. Sequence annotations and analyses need to be organized into databases and widely accessible. Like other species, sugarcane would benefit from centralized and innovative systems to study its genome. The GNPAnnot community annotation system (CAS) could be particularly relevant to the SUGESI sequencing project. It consists in a system for structural and functional annotations supported by comparative genomics allowing both automatic predictions and manual curations of genes and transposable elements. The core of the GNPAnnot CAS dedicated to tropical plants is made of GMOD components.The Chado database can be browsed using the Generic Genome Browser (GBrowse) which provides links to genome editors (ie. Artemis and Apollo). We developed the Chado controller in order to manage public and private annotation projects. It also provides an annotation history page for each gene or transposable element and an annotation inspector that automates several tasks and reports annotation mistakes. GNPAnnot CAS has already been used to annotate sugarcane BAC clones sequences and could be useful to facilitate the annotation of novel sugarcane sequences. (Résumé d'auteur

GNPAnnot: a community annotation system applied to sugarcane sequences : W745

A large amount of data is being produced by current genome sequencing projects. Sequence annotations need to be organized into databases and widely accessible. Like other species, sugarcane would benefit from centralized and innovative systems to study its genome. GNPAnnot is a community system performing structural and functional annotations of genes and allowing both automatic predictions and manual curations of genes and transposable elements (TEs). The system is currently being used for various plants, insect and fungus species. The GNPAnnot pipeline is made of a collection of programs that are connected together to automate genomic sequence annotations. Sequences and results are stored into the Chado GMOD database and can be visualized through a genome browser accessible from the Web portal of the SouthGreen bioinformatic platform (http://southgreen.cirad.fr/). Annotations can be manually edited using the Artemis genome editor. A database controller has been developed (Chado controller) in order to manage public and private annotation projects. It also provides an annotation history page for each gene or TE, and an annotation inspector that reports manual annotation mistakes. The GNPAnnot system is currently being used to annotate sugarcane BAC sequences in the framework of the SUGESI (Sugarcane Genome Sequencing Initiative) that aims at sequencing around 5,000 BACs, from cultivar R570, corresponding to the gene rich part of a monoploid genome of sugarcane. The GNPAnnot system has been developed by partners of CIRAD, INRA and Bioversity and has been supported by the French National Research Agency and the Genoplante joint program. (Résumé d'auteur

La mobilisation d’une perspective interactionniste pour éclairer la négociation du territoire de pratique des coachs en gestion

Le point de vue adopté pour étudier le coaching en gestion est généralement prescriptif vis-à-vis de la pratique, posant des modèles théoriques comme référents, privilégiant une approche déductive et des méthodologies quantitatives pour mesurer ses impacts en termes de retour sur investissement, de niveau de satisfaction client. Sans nier l’importance de s’interroger sur le service rendu, il peut être réducteur d’envisager la pratique à travers des indicateurs de performance décontextualisés. Y a-t-il un intérêt à renouveler le regard posé sur l’objet pour une autre compréhension de la pratique et de ses enjeux? Cette contribution s’appuie sur une recherche doctorale (2012) qui interroge le développement du coaching dans la mosaïque des professions d’accompagnement au développement professionnel de gestionnaires. Menée selon une perspective interactionniste, elle s’est attachée à recontextualiser l’émergence de cette pratique, mettant au cœur de l’interprétation les interactions qui la coconstruisent

A community annotation system for Musa genomes

Poster presented at ISHS/ProMusa Banana Symposium Global Perspectives on Asian Challenges. Guangzhou (China), 14-18 Sep 200

Quand les acteurs mettent en mots leur expérience

Cet article offre une réflexion sur la place des acteurs dans la recherche en s’appuyant sur une investigation qui a porté sur des interventions de coaching en entreprise. Il a pour but de montrer comment les choix qui ont présidé à cette recherche témoignent d’une conception d’acteur compétent, c'est-à-dire capable de réfléchir à ses pratiques et capable d’en parler. Ainsi sont présentées les propositions théoriques qui ont permis d’éclairer l’agir professionnel des coachs, la méthode d’enquête qui a conduit à la construction de récits de pratique ancrés dans leur expérience, de même que la méthode d’analyse inductive qui a facilité la mise en relief des savoirs pratiques mobilisés par des coachs lors d’une intervention. Finalement, une réflexion critique sur ces différentes étapes, en relation avec le statut des données et les places respectives de l’acteur et du chercheur sera posée

Crop ontology in support of conservation and use of banana genetic resources

Poster presented at Workshop on Crop Ontology and Phenotyping Data Interoperability. Montpellier (France), 31 Mar-4 Apr 201

Function prediction in plant genomes from large scale phylogenomics analyses : P0932

With the increasing number of plant genomes being sequenced, a major challenge is to accurately transfer annotations from well characterized genomes to newly obtained sequences. GreenPhylDB is a database designed for comparative and functional genomics based on complete genome-derived gene sequences. The database currently includes gene families of protein sequences from 22 plant species, including socio-economically important crops like rice, sorghum, maize, cassava and banana. Genes from all these species are organized in clusters based on sequence similarity. The clusters are manually annotated (i.e. properly named and classified) and sequences included in each cluster are characterized by phylogenetic analysis in order to elucidate evolutionary relationships (e.g. orthologs, super-orthologs, in/out-paralogs) among genes. GreenPhyl provides a reliable and stable catalog of gene families useful for annotation on new genome sequences in plants. With its improved user interface, the new release of GreenPhyl keeps the previous gene clustering quality and introduces additional features such as specific search engines (quick search, deep search, InterPro domain combination and GO family browser). The GreenPhyl's pipeline relies on RapGreen, a new version of the RAP reconciliation tool (Dufayard et al, 2005) that allows us to root gene trees and infer orthology relationships between sequences of a family. GreenPhyl version 3 is available at http://www.greenphyl.org and is a collaborative resource of SouthGreen (southgreen.cirad.fr), a bioinformatics platform applied to the genetic and genomic resources analyses of the South and Mediterranean plants. (Résumé d'auteur