Thesis subject

Gene regulatory networks controlling developmental transitions

Extensive information about the genes and their connections in gene regulatory networks (GRNs) underlying developmental processes has been obtained for several model species. This species-centric approach only provides a static picture of the network making difficult to distinguish the selective pressures on each regulatory element necessary to understand its functional relevance. Moreover, how to translate this knowledge to other species with a higher economical potential where this genomic information is much more limited or non-existent?

The goal of this project is to analyze developmental GRNs from an evo-devo perspective, comparing cross-species global gene expression in a phylogenetic context. As proof of concept, we focus on the plant seed germination GRN as (1) all seeded plants share the same definition of the process, allowing a direct comparison between very distant species; and (2) this phase transition is important for the adaptive value for plant species and a significant impact on crop yield. A kingdom-wide phylotranscriptomics comparison should address fundamental questions as 1) how to normalize the same developmental process between different species despite their different parameters (e.g. timescale); 2) assign the role and the relevance for each component within the GRN; 3) define the role of selection and neutrality shaping the GRNs assessing conservation and divergence in circuitry architecture for the same developmental output.

Used skills: Programming, genomics

Requirements: INF-22306 Programming in Python, BIF-30806 Advanced bioinformatics, ABG-30306 Genomics