Société Française de Bioinformatique

Mots-Clés

bioinformatics transposable elements insects symbiosis

Description

Project: The aim of this PhD project is to investigate the interactions between transposable elements (TEs),
endosymbionts, and weevil genomes. Sitophilus spp., including Sitophilus oryzae (rice weevil), are some of the most
destructive cereal pests, causing up to 80% of cereal loss in certain conditions. Our model species, Sitophilus oryzae,
harbors an intracellular bacterium Sodalis pierantonius, housed within specialized host cells called bacteriocytes that
form an organ, the bacteriome. Unlike ancient mutualistic endosymbionts, S. pierantonius has only recently
established its association with S. oryzae and retains a relatively large genome enriched in mobile genetic elements,
as well as genes involved in host–microbe interactions. On the host side, the S. oryzae genome is extraordinarily rich
in repeats, with more than 70% of its content composed of TEs, many of which remain transcriptionally active. This
combination of a TE-dense host genome and a recently acquired endosymbiont provides a unique model to explore
how symbiotic processes influence genome dynamics. Preliminary transcriptomic analyses comparing symbiotic and
experimentally obtained aposymbiotic individuals indicate that the presence of the bacterium is associated with the
upregulation of multiple TE families. Furthermore, small RNA sequencing data reveal that symbiotic and
aposymbiotic weevils display distinct small RNA profiles. The PhD candidate will take advantage of these
transcriptomic and small RNA datasets to dissect how the endosymbiont influences TE dynamics. This work will be
supported by collaborations with molecular biologists, who will perform functional assays to test selected
hypotheses.

Fellow: The PhD fellow has a solid knowledge in genomics and bioinformatics along with molecular biology and we
encourage candidates with omics background to apply. Experience in the TE field is appreciated but not necessary.
Some experience with programming (R, Python, bash) for data analysis is preferred. The candidate is highly
motivated, curious and organized. We seek someone open minded and capable of working in a small and very
interactive research team.

Lab: The PhD student will be supervised by Rita Rebollo and Nicolas Parisot from the BF2i laboratory and Marie
Fablet from LBBE. BF2i is affiliated to both INRAE and the INSA Lyon. The lab research work focuses on the biology
of different types of interactions involving insects and their symbiotic bacteria. It also aims at investigating emerging
technologies required for insect pest control. The successful applicant will benefit from fully equipped laboratories
for genomics, molecular biology, biochemistry and histology research, from the computing facilities of the
LBBE/PRABI cluster, soon to be included in the Lyon-Tech LaDoua Data Center along with a long-term expertise in
TE biology, and especially in the analysis of TEs from high throughput sequencing data. This PhD will also be
performed in close collaboration with Clément Goubert who is responsible of the current TE annotation.

Environment: Lyon is built around the Rhône and Saône rivers. It is the second economic French city and its rich
history and architecture made it part of the Unesco World Heritage. The city is also culturally very dynamic. Within
France, Lyon has a strategic geographical position, close to the Alps and the Mediterranean coast, Switzerland and
Italy. Paris is only two hours away by TGV. Last but not the least, Lyon is considered the French capital of gastronomy,
offering a wide variety of food and wine from the surrounding areas.