2012
Journée Jean Chevaugeon, 9ème rencontres de phytopathologie-Mycologie, Aussois 16-20 janvier 2012
19 Jan 2012 Fungal species resources: an integrated system for structural and functional genome annotation
Nicolas Lapalu, Joelle Amselem, Baptiste Brault, Laetitia Brigitte, Jonathan Kreplak, Françoise Alfama, Aminah Keliet, Erik Kimmel, Isabelle Luyten, Sébastien Reboux, Delphine Steinbach, Marc-Henri Lebrun and Hadi Quesneville
With the recent development of new generation sequencing technologies, a large number of genomes are sequenced leading to an increase in derived genomic data (RNAseq, ChIPseq). This increasing amount of data has to be stored, analyzed and searched (gene families, SNPs …). To face this challenge, the URGI platform ( http://urgi.versailles.inra.fr ) provides tools to store and annotate entirely sequenced genome such as annotation pipelines, databases and user-friendly interfaces to browse and query the data. Bioinformatics resources developed at URGI to provide structural and functional annotations to the scientific community working on fungal genomes are the following:
- Genomic large scale analysis:
- Transposable element detection and annotation package called REPET [1] with two pipelines: TEdenovo and TEannot.
- Gene prediction based on ab initio, EST and protein similarity-based finding software integrated in EuGene [2].
- Functional annotation pipeline of proteins based on (i) pattern matching and motif recognition, (ii) intracellular targeting prediction methods, and (iii) comparative genomics tools with other fungal genomes.
- Genome browser to explore genome annotations (Gbrowse) and synteny relationships (Synteny browser) between related genomes.
- A manual annotation system for gene structural curation (GMOD databases and interfaces Chado/Apollo). Curated data are shared by a consortium on line.
- Genome Report System (GRS) allows queries of structural and functional data stored in a Chado database, including cross references, and Gene Ontology. An editing module (GRS edition) allows manual functional annotation.
- Quick and advanced search are proposed, respectively through GnpIS QuickSearch and BioMart (complex search criteria on Datamart, GMOD Tool). BioMart results could be exported to a Galaxy server for further bioinformatic analysis.
We will present this integrated genome annotation system successfully used for fungal genomes such as Botrytis cinerea T4 [3] and Leptosphaeria maculans [4] in the frame of their genome sequencing project. Portals for the different species are available at here .
Keywords: annotation fungi genome
[Download pdf: 2.88 MB]
Creation date: 26 Jan 2012
eZ PublishPublication supervisor: A-F. Adam-Blondon
Read Credits & General Terms of Use
Read How to cite