Formulaire pour demande d' homologation cati

ISYIP: Plate-forme bio-informatique pour la génomiques sur les insectes

Centres (Sites) INRA Rennes, plateforme Genouest, INRIA/IRISA

Départements SPE
Responsable : F. Legeai
ISyIP (Information System for Insect Pests) is a central platform for sharing resources and standards critical to guarantee data integration and interoperability, and to improve the coherence of the protocols set up by its various partners engaged into the genomics and post-genomics analysis of agricultural relevant insects (pest and their parasitoids) genomics and postegenomics. . Apart from giving access to the data, the main utility of this to settle an environment to allow a larger community to elaborate complex genomics analyses, browsing, mixing or crossing heterogeneous data.

Since 5 years, ISyIP, is including LepidoDB http://www.inra.fr/lepidodb (386 visitors in 2011) and http://www.aphidabse.org (8514 visitors in 2011) and develops expertise and pipelines for NGS data management (e.g., cleaning, mapping, assembly, SNP discovery, differential expression analysis, smallRNA prediction and annotation). The team benefits from the housing of the Genouest platform, an IBISA platform, member of RENABI (French network of bioinformatics platforms).

The platform aims at developing particular treatments for heterogeneous genomics dataset embracing a large panel of “omics” (e.g. genomics, transcriptomics, epigenomics, methylomics or proteogenomics). These treatments are covering different skills and hence necessitates a strong collaboration with the INRIA GenScale team headed by D. Lavenier. For instance, it includes the mapping and assembly of a very large number of reads implying the development of advanced algorithms able to fit, within a reasonable time, with particular large scaled data (paired-ends or mate-pair, genome, mRNAs, short RNAs or short polypeptides issued from proteomics experiments). It also needs the development of new strategies to compare resequenced genomes in order to predict and study structural variants.
Finally, although exploring all these data separately remains already challenging, it is also focusing in elaborating strategies for comparing enhanced integrated genomes to emphasize the role of epigenetics states in the gene regulation, especially in the context of reproductive polyphenism of aphid or host-plant specialization of spodoptera frugiperda.
The IsyIP platform will be involved in an increasing number of project generating a large set of various data. For instance, it will host and analyses 4 reference genomes (Myzus persicae, spodoptera frugiperda, diabrotica virgifera, hyposother didymator), and the re-sequencing of 40 strains of pea aphid and the rice-variant of spodoptera frugiperda as well as tens of transcriptomics data. Furthermore, this platform takes part of the i5K project for the sequencing of 5000 insect genomes.
At INRA SPE, ISyIP is working has a strong partnership with the laboratories DGIMI in Montpellier, PISC in Versailles, ISA in Sophia Antipolis, BF2I in Lyon and IGEPP in Rennes.

Axe 2 : Génomique comparative et caractérisation de la biodiversité

ANATool : The Arabidopsis Natural Accession Tool

https://www.versailles.inra.fr/ijpb/crb/anatool

Matthieu Simon¹, Adeline Simon², Fréderic Martins³, Lucy Botran¹, Sébastien Tisné¹, Fabienne Granier¹, Olivier Loudet¹ and Christine Camilleri¹

¹Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78000 Versailles, France

²BIOGER, UR1290 INRA-AgroParisTech, 78850 Thiverval-Grignon, France

³Plateforme Génomique, Génopole Toulouse/Midi-Pyrénées, 31326 Castanet-Tolosan, France

Contact for biology: [e-mail]

Contact for bioinformatics: [e-mail]

Publication : Simon M, Simon A, Martins F, Botran L, Tisné S, Granier F, Loudet O, Camilleri C (2012). DNA fingerprinting and new tools for fine-scale discrimination of Arabidopsis thaliana accessions. Plant J. 2012 Mar;69(6):1094-101.
Summary: The Arabidopsis Natural Accession Tool web interface was developed for the Arabidopsis community to provide access to all fingerprinting data obtained on natural accessions managed at the Arabidopsis thaliana Resource Centre for Genomics at INRA Versailles, France.

The genotyping assay was performed at the Genomics facility at INRA Toulouse, France using a GoldenGate assay which interrogates all 384 SNPs simultaneously and VeraCode technology was used for reading. The final data matrix of 341 informative markers for 591 accessions is available through the ANATool interface

The smallest number of markers that uniquely defines each haplotype was defined. This pattern is called a fingerprint and is composed of a combination of different SNPs for each haplotype.

From the ANATool interface, four types of queries can be submitted to (1) find the fingerprint of a given accession; (2) find genotypes from a selection of accessions and markers; (3) find accessions from a selection of markers and genotypes; and (4) find the minimal marker set required to distinguish among a set of given accessions. Optimized SNP sets are also available to quickly fingerprint natural accessions of Arabidopsis. Thus, ANATool is a simple, readily accessible and fast (only DNA fragments need to be sequenced) tool for confirming the identity of accessions at any laboratory working on Arabidopsis.

The development of ANATool was funded by INRA and by the French national biomedical, biological and agricultural research infrastructures network GIS-IBiSA.