Section: New Results

Applications

CAMI: Critical Assessment of Metagenomic Interpretation

Participants: C. Deltel, D. Lavenier, C. Lemaitre, P. Peterlongo, G. Rizk

The interpretation of metagenomes relies on sophisticated computational approaches such as short read assembly, binning and taxonomic classification. All subsequent analyses can only be as meaningful as the outcome of these initial data processing methods (http://www.cami-challenge.org/ ). The CAMI initiative aims to evaluate these methods independently, comprehensively and without bias. The goal is to supply users with exhaustive quantitative data about the performance of methods in many relevant scenarios. In 2015, we participate to CAMI within the "assembly" category using the Minia assembly pipeline. Results are provided here: https://data.cami-challenge.org/ . For the medium challenge datasets, our assemblies are refered under the identifiers goofy-wilson and fervent-blackwell.

Assembly and Annotation of Arthropods Genomes

Participants: A. Gouin, F. Legeai, C. Lemaitre

Within a large international network of biologists, GenScale has contributed to various projects for identifying important components such as protein coding or non coding genes involved in the adaptation of major agricultural pests to their environment. We provided the assembly and the annotation of 4 new aphids, 3 parasitic wasps, and improved the assembly of 2 variants of fall army worm by removing unwanted sequences due to heterozygosity [41] , [42] . Following specific agreement or policy, these new genomes and annotations are available for a restricted consortium or a large community through the BioInformatics platform for Agro-ecosystems Arthropods (http://bipaa.genouest.org/is ). These results, and further analyses led to a better understanding of the biology, evolution and life history traits of Spodoptera frugiperda [19] , the identiifcation and characterization of new genome of pea aphid symbionts [22] and the identification of differentially expressed genes in the sensory system of Sesamia nonagrioides [21] .

Study of the rapeseed genome structure

Participants: D. Lavenier, C. Lemaitre, S. Letort, P. Peterlongo

In collaboration with IGEPP (Institut de Génétique, Environnement et Protection des Plantes), INRA, and through two national projects, PIA Rapsodyn and France-Génomique Polysuccess, we are involved in the genome analysis of several rapeseed varieties. The Rapsodyn project has the ambition to insure long-term competitiveness of the rapeseed production through improvement of the oil yield and reduction of nitrogen inputs during the crop cycle. Rapeseed varieties must thus be selected from genotypes that favor low nitrogen input. DiscoSNP++ is here used to locate new variants among the large panel of rapeseed varieties which have been sequenced during the project. The PolySuccess project aims to answer the following question: how a polyploid, such as the oilseed rape plant, becomes a new species? Oilseed rape (Brassica napus) beeing a natural hybrid between B.rapa and B.oleracea, different genomes of these three species have been sequenced to study their structures. The Minia assembly pipeline provides a fast way to generate contigs that are used for studying gene specificities.