Section: New Results

Bioinformatics Analysis

Genomics of Brassicaceae and agro-ecosystems insects

Participant : Fabrice Legeai.

Through its long term collaboration with INRA IGEPP, and its support to the BioInformatics of Agroecosystems Arthropods platform (http://bipaa.genouest.org), GenScale is involved in various genomic projects in the field of agricultural research. First, on plant genomics, we helped to identify duplicated copies of genes and repeated elements in the Brassica genomes [14]. Then, on major agricultural pests or their natural ennemies such as parasitoids, we conducted large scale analyses on the expression of effector genes involved in the adaptation of pea aphids to their host-plants [13]. Finally, we explored the expression of genes related to the virus machinery of bathyplectes parasitoids wasp of the alfalfa weevil [18].

Structural genome analysis of S. pyogenes strains

Participants : Emeline Roux, Dominique Lavenier.

The S. pyogenes bacteria is responsible for many human infections. With the increase in the prevalence of infections (750 million infections per year worldwide and 4th in terms of mortality from bacterial infection), a better understanding of adaptive and evolutionary mechanisms at play in this bacteria is essential. The molecular characterization of the different strains is done by the emm gene. A statistical analysis of the different types of emm on the Brittany population shows 3 main dynamics: sporadic types, endemic types or epidemic types. The last case was observed in Brittany for the type emm75 between 2009 and 2017. Two hypotheses can be considered: (1) the emergence of a new subtype or winning clone in an unimmunized population; (2) increased pathogenicity through genetic evolution of the strains, including the acquisition of new virulence factors. In collaboration with the microbiology department of the Rennes Hospital, we sequenced more than 30 S. pyogenes emm75 strains (Oxford Nanopore MinION sequencing) in order to study the dynamic of the epidemic thought their structural genomic variation.

Linking allele-specific expression and natural selection in wild populations

Participants : Mohammed Amin Madoui, Pierre Peterlongo.

Allele-specific expression (ASE) is now a widely studied mechanism at cell, tissue and organism levels. However, population-level ASE and its evolutionary impacts have still never been investigated. Here, we hypothesized a potential link between ASE and natural selection on the cosmopolitan copepod Oithona similis. We combined metagenomic and metatranscriptomic data from seven wild populations of the marine copepod O. similis sampled during the Tara Oceans expedition. We detected 587 single nucleotide variants (SNVs) under ASE and found a significant amount of 152 SNVs under ASE in at least one population and under selection across all the populations. This constitutes a first evidence that selection and ASE target more common loci than expected by chance, raising new questions about the nature of the evolutionary links between the two mechanisms [33].