Mots-Clés
co-expression, regulatory network, gene expression, lncRNA, mRNA, coevolution, adaptation
Description
Coevolutionary interactions, from the delicate co-dependency in mutualistic interactions to the antagonistic relationship of hosts and parasites, are a ubiquitous driver of adaptation. Surprisingly, little is known about the genomic processes underlying coevolution (Cornille et al 2022).
From public health, food production to conservation, coevolution of hosts and parasite is central to addressing contemporary scientific challenges. Here we used ‘dual RNA-seq’ approach to profile RNA expression simultaneously in parasite and host during Dysaphis plantaginea infestations of the wild and cultivated apples. The aim of the internship will be to investigate the gene co-expression between the host and the parasite to detect genes involved in coevolution. Note that several genotypes of aphids and apples were studied, which will allow testing for a Ghost*Gparasite interaction at the molecular level.
The intern will use short read Illumina data already available for both the aphid and the apple. The intern will trim the reads, map them to reference genomes of both the host and the pest, count the genes and statistically analyzed 1) differentially expressed genes, and 2) modules co-expressed genes depending on the aphid and apple genotypes. This will require to run and adapt bioinformatics pipelines available in the ECLECTIC group (Dicoexpress, Magniette et al 2020). The students will also investigate whether differentially expressed genes in the promoters of the genes show transposable elements insertion. Transposable elements (TEs) are indeed considered to be key players in the adaptation of populations to stress, and to which extent TE insertions can be associated with changes in gene expression in the host and the parasite remain unknown.
Note that all coded workflow and data that will be generated for the project will be publicly available through open access platforms (Github, forgemia, Dryad) at the end of the project, providing transparency, reproducibility and replicability of the research. The results will be submitted to journals with Open Access to provide transparency for readers and allow other researchers to build directly and efficiently on primary work. Of course, sufficient contributions to the project will involve co-authorship.
Expected skills
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Familiar in coding in shell / python or perl, know how to access to bioinformatic cluster, basic code in R. Concept in evolutionary genomics, gene regulatory network evolution and an interest in plant-pest interaction will be a plus.
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Other details
Access to bioinformatic clusters: local in the GQE-Le Moulon, Genotoul (http://bioinfo.genotoul.fr), Migale (https://migale.inrae.fr), IFB-core (https://www.france-bioinformatique.fr/cluster-ifb-core/)
References
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Cornille A.*, Ebert D., Stukenbrock E., Rodríguez de la Vega R., Tiffin P., Croll D., Tellier A. Unraveling coevolutionary dynamics using ecological genomics. *corresponding author. Trends in Genetics.Accepted.
A. J. Westermann, L. Barquist, J. Vogel, Resolving host–pathogen interactions by dual RNA-seq. PLOS Pathog. 13, e1006033 (2017).
A. J. Westermann, S. A. Gorski, J. Vogel, Dual RNA-seq of pathogen and host. Nat. Rev. Microbiol. 10, 618–630 (2012).
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