Annotation of genomic sequences in plant species on the AUVE

In the context of the programmes on the genomics of soft wheat developed at regional (INRA Structure team, Function & Evolution of Wheat Genomes), national (projet EXEGESE-BLE), European (ETGI – European Triticeae Genomics Initiative) and International ( IWGSC – International Wheat Genomic Sequencing Consortium), and with the prospect of massive production of BAC* sequences^* over the next ten years, the INRA-UBP Mixed Research Unit (UMR) Improvement & Health of Plants in Clermont-Ferrand, in close collaboration with URGI INRA in Evry (Genomic-Info Research Unit, Fabrice Legeai), are developing an automatic annotation pipeline^* for this type of sequence, which comes essentially from species belonging to the Poaceae family: TriAnnotPipeline.

The innovative concept behind the project, which is certainly the only one of its kind, at least as far as Poaceae are concerned, is to associate one aspect of bioinformatics – automatic annotation of genomic sequences – with grid technology in order to obtain maximum computing power, which will eventually become a major limiting factor. The soft wheat genome (17000 Mb) is around 45 times larger than the rice genome and 140 times larger than that of Arabidopsis thaliana (two genomes which have undergone full sequencing).

With creation of the IWGSC, the international community has the long-term ambition of fully sequencing the soft wheat genome’s gene space, requiring annotation, re-annotation, and expert assessment of a very considerable number of BAC sequences in the decades to come. Furthermore, the possibility of carrying out rapid and reliable annotations on wheat will also enable large-scale comparative genomic analyses to be carried out, with the complete sequence of the rice genome now available, along with those of maize and sorghum (two graminae of major economic importance), whose respective sequencing is currently underway. In this context, the availability of a powerful tool has become essential, and LifeGrid can fulfil requirements.



Example of annotation of a BAC sequence for barley belonging to the Triticeaefamily.  

The project, which has led to our recruiting two engineers in computer science and bioinformatics, relies on close collaboration among three laboratories specialising in computer science, bioinformatics, and bioanalysis, a highly complementary collaboration perfectly geared to the project’s objectives. Moreover, the project will strengthen the Clermont-Ferrand site’s position as head of the national network and international leader in wheat genomics, as well as further our close collaboration with URGI, INRA’s bioinformatics platform, and IN2P3, expert in grid technology and AUVERGRID coordinator.Finally, it will also enable us to enter into collaboration with Japan’s NIAS (National Institute of Agrobiological Sciences, Dr. Takeshi Itoh) whose expertise in annotation of the complete genome, such as that of rice, is recognised worldwide.

PL

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