Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid
Résumé
Phenotypic plasticity is an adaptive process widespread in Insects. This involves the capacity of embryos to sense external local environmental cues during their development with alternative routes providing a final phenotype adapted to those new cues. In our lab, we describe and analyse the gene expression regulation rules during the establishment of the phenotypic plasticity of the reproductive mode in aphids due to the change of the photoperiod in the fall. The development of sexual and asexual embryos that differ mainly by their production of haploid meiotic gametes or diploid non-recombinant gametes is thus compared. We developed an integrative genomics approach that aims to define all the functional DNA elements in the formation of alternative morphs. We thus combine genomics (nucleic acid sequencing), bioinformatics and mathematic modelling to construct gene networks describing and modelling the molecular processes acting in the phenotypic plasticity of the reproductive mode. We annotated functional DNA elements (open chromatin, long non-coding RNAs, microRNAs, mRNAs), predicted their putative interactions and modelled their network functioning. We identified two major biological processes as important signatures of these networks: “oogenesis” and “central nervous system”. We analysed more deeply some of the candidates to fill the gap between prediction, hypotheses and biological observations.