M2 - Genomics-enabled analysis of the microevolution of jumping genes

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<p>RD10, route de Saint Cyr, 78000 Versailles</p>

Maumus Florian
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<p><strong>Genomics-enabled analysis of the microevolution of jumping genes</strong></p><p><strong>Context</strong></p><p>Transposable elements (TEs), also called jumping genes, are mobile genetic sequences that can contribute a predominant fraction of eukaryotic genomes (about 50% in mammals and up to 90% in plants). They are considered selfish genetic elements because their function is to replicate themselves. While TE activity is in general deleterious, they mediate key evolutionary transitions and they have co-evolved with their hosts for billions of years. Although the duration of this co-evolution is impressive, the evolutionary trajectories of TEs remain poorly understood. It has been very challenging to address the microevolution of TEs in the past, mostly because TEs are rapidly evolving sequences and the plants which genomes are available often belong to branches that are too divergent to identify conserved TE families across two or more species. As a result, when identifying a TE sequence, it is difficult to understand what regions are constrained, novel, or lost besides protein-coding ones. Indeed, conservation can only be revealed in the light of evolution so that it is necessary to compare several sequences from one TE family to allow addressing evolutionary trends.</p><p><strong>Objectives</strong></p><p>In the frame of the genome sequencing and comparative analysis of 32 Brassicaceae relatives (cousins of Arabidopsis thaliana), we have discovered exceptional cases of conservation of TE families. TE sequences are minted by a complex assortment of evolutionary constraints to subsist such as those imposed by epigenetic, transcriptional, post-transcriptional, and translational regulations. Our data offers for the first time the opportunity to study various facets of TE evolution at fine scale. During this project, the candidate will make the most of Brassicaceae genomic data using computational approaches to address key features in the microevolution of TEs, both in protein-coding genes and in regulatory elements. Methods employed should include the generation of multiple sequence alignments, phylogenetic analyses, search for conserved motifs and quantifying evolutionary constraints.</p><p><strong>Expected profile</strong></p><p>Candidates should be curious about evolutionary biology and have a good background in bioinformatics. Highly motivated candidates will be supported to apply for a PhD fellowship in the lab.</p><p><strong>Host lab</strong></p><p>The host lab is a transdisciplinary unit dedicated to genome analysis and data integration. It is composed of over 20 permanent members, including several developers and researchers. The genome analysis team is internationally recognized for his expertise in the annotation and analysis of selfish genetic elements, including transposable elements and endogenous viruses. URGI will provide a friendly and formative environment to the trainee. The INRA Versailles Centre may rent temporary on-site institutional accommodation in guest house under specific conditions.</p><br/>
Laboratoire: Unité de recherche en génomique-info