gene networks of RNAs for deciphering the plasticity of the reproductive mode in aphids

This projects aims at developing a system biology approach applied to large sets of data in genomics. It aims at constructing gene networks in order to identify functions and functional elements involved in the phenotypic plasticity of the reproductive mode in aphids. This life trait is responsible for the capacity of these pests to infest plants and culture, creating large damage affecting the yields. This project is centered on data already obtained on different types of interacting RNAs such as mRNAs, microRNAs, lncRNAs, piRNAs) in aphid embryos (more precisely in pea aphid Acyrthosiphon pisum) that develop in either one or the other alternative phenotype: viviparous parthenogenetic females or oviparous sexual females. The challenge is to develop and use innovative techniques in modeling, centered in formal concept analyses, to construct, visualize, annotate and simplify networks. The output of these networks will be to define new hypotheses on putative candidate genes that could be then targeted for further functional analyses. This project is thus within the general paradigm of the ENCODE initiatives, applied to non-model species of high ecological impact (see Tagu et al. 2014 BMC Genomics 2014, 15:490).