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Publications

URGI members are underlined in authors list. In the talks sections, names in bold are the speakers.

There are different types of publications, Papers with reading comittee (ACL), Papers in books (ACT), Invited talks (INV), Talks (COM), Posters (COM), Specialised Media and Press (SMP) and Thesis.

Other
COM (communication)
 02 Nov 2023 [hal-04267953] SNP discovery by exome capture and resequencing in a pea genetic resource collection
Pea is a major pulse crop in temperate regions and a model plant in genetics. Large genetic marker resources are needed to assess the genetic diversity in the species genepool and to provide selection tools for breeders. In this study, we used second-generation sequencing to perform an exome-capture protocol using a diverse pea germplasm collection, and produced a resource of over 2 million Single Nucleotide Polymorphisms. This dataset was then used to characterize the genetic diversity present in the panel and compute phylogenetic and structure analyses. The development of this resource paves the way for Genome-wide association studies and the development of powerful genotyping tool
et al.
In ProdINRA
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COM (communication)
 11 Oct 2023 [hal-04237621] Linking heterogeneous data from model plant species in a graph database
More and more data are available nowadays due to emerging technology and tools to analyze genomes. In this situation, it is necessary to identify or develop tools to connect all these data together. In this context, graph database seems to be an appealing method to connect data as nodes and relation between them as edges or links. Graph NEO4J TE contains genomic data on two model plant species, one dicot and one monocot A.thaliana and B.distachyon. It puts into interaction genomic coordinates between entities like structural gene annotation, transposable elements, transcription factor binding site and other allowing to search possible positional relation between these entities. We enrich these information with functional annotation, phenotyping characterization data and localization data linked with our genomic data using pivotal node like accession or gene. Neo4J allows RDF importation into the database. We have been able to successfully import gene ontology into our database and to import AgroLD rice gene data from turtle files (zenodo repository) and bind these information with our own database with a simple query. Finally we can export our own dataset in RDF format. That RDF can be imported into other instance of neo4j database. The database has been developed in « Graph » working group of CATI GREP. In this group 3 project are in development on different species and thematic. We have commonly defined the modelisation of nodes and relationship to allow connections between graphs.
et al.
In ProdINRA
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COM (communication)
 15 Sep 2023 [hal-04208925] Insertion et exploitation de données hétérogènes dans un graphe de connaissance
Une base de données orientée graphe a été construite au sein de l’URGI sur 2 espèces modèles de plante : une monocotylédone (Brachypodium distachyon) et une dicotylédone (Arabidopsis thaliana). Elle intègre de nombreuses données hétérogènes: annotations de génome (annotations structurale et fonctionnelles de gènes, éléments transposables (ET), séquences non codantes conservées (CNS), site de fixation de facteur de transcription (TFBS), relations d’homologie et d’orthologie. De nombreuses études montrent que les éléments transposables (ET) sont cooptés dans des séquences cis-régulatrices. Les ET peuvent donc affecter la transcription des gènes adjacents en recrutant des facteurs de transcription supplémentaires par exemple. Certaines famille d’ET qui portent des TFBS sont notamment connus pour être activée en réponse à certains stress abiotique comme ONSEN/ATCOPIA78 qui est activée par un stress thermique chez Arabidopsis thaliana. La base graphe permet d’identifier quelles sont les familles d’ET spécifiquement liées à des TFBS. Une analyse approfondie sur ces familles d’ET et leurs relations avec les gènes et réseaux de gènes impliqués dans des traits d’adaptation permettra d’améliorer la prédiction de leur impact fonctionnel chez leur hôte. Ce travail s’intéresse aux questions d’exploitation et d’interrogation des relations existantes entre les données par le biais de l’outil base de données orientées graphe. Il permet de développer des questions complexes faisant interagir plusieurs sources de données.
et al.
In ProdINRA
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COM (communication)
 04 Sep 2023 [hal-04195707] PlantBioinfoPF (URGI) et son offre de service d'annotation des éléments transposables dans les génomes
Les outils d'annotation des éléments transposables (ET) sont de plus en plus accessibles au grand public mais peuvent rester complexes dans le traitement de génomes de grandes tailles ou en trop grand nombre pour des non initiés. La plateforme PlantBioinfoPF hebergée par l'URGI propose l'accès à des ressources de calculs adaptées et un service d'annotation des ET dans les génomes. Illustration au travers de 2 projets et présentation de l'offre de service.
et al.
In ProdINRA
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COM (communication)
 30 Aug 2023 [hal-04191716] Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes
While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for di erent traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities o ered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.
et al.
In ProdINRA
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COM (communication)
 25 Jul 2023 [hal-04169996] REPET evolutions: faster and easier
The detection and annotation of transposable elements (TEs) are now considered mandatory to any genome sequencing project. To this aim, the REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyse TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them according to TE features and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations. The REPET package is in continuous improvement. Several implementations and algorithms to reduce the time required for analysing large genome have been tested. With our new speed improvements and tuned annotation strategies, REPET is now able to annotate and analyse easily large genomes up to 3 Gb. Now, we chain all required steps through a process called "Repet-Factory". This process uses parameters optimized for specificity and computing time. It is capable of successively annotate several genomes in batches with all the traceability required for reproducibility. We also simplified the distribution of REPET by developing a Docker image of REPET
et al.
In ProdINRA
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Update: 19 Nov 2010
Creation date: 01 Dec 2009