Mots-Clés
Génomique comparée
Evolution
Phylogénie
Éléments transposables
Description
Why is transposable element genomic content so diverse?
Background:
Comparative genomics is a scientific field aimed at understanding genome organization
across a broad phylogenetic scale. It combines computational methods (bioinformatics) with
modern sequencing technologies, which enable the compilation of high-quality genomic
sequences from thousands of species across the tree of life. This powerful approach allows
researchers to explore new biological questions related to systematic patterns of
genome-scale evolution.
Transposable Elements (TEs) are duplicated sequences capable of colonizing genomes,
sometimes constituting over half of the total DNA. They are a major driver of genome
evolution, though their impact on species evolution remains poorly understood. TEs
comprise multiple families, differing in their transposition mechanisms and interactions with
host species. Both the total TE content and the preferential composition of TE families can
vary significantly across species. Some TE families proliferate into hundreds or thousands of
copies, while others remain rare, with only a few active sequences. Some species
accumulate vast amounts of TE-related DNA, whereas closely related species may exhibit
far less. To date, the observed diversity in TE content lacks a formal explanation: Does it
primarily depend on TE-specific mechanisms, species properties, individual TE-species
interactions, or randomness?
Project:
This master project aims to address this question through a large-scale bioinformatic
approach. The student will use automated procedures to build a database of TE success by
counting detectable copies across a wide variety of TE families, sampled from all known TE
groups in multiple species from well-sequenced model clades, such as Drosophila, with over
300 sequenced genomes, and fish, with over 400 genomes. Statistical models will then
determine the relative effects of TE family versus host species on TE success, accounting
for phylogenetic correlations at both TE and host levels. This approach may uncover exciting
research avenues: What characteristics drive successful TEs (e.g., size, transposition
mechanism, or anti-regulation features)? Which biological or ecological factors are
associated with TE-rich species?
During the internship, the student will learn to access specialised databases to download
genomes and genome annotations, use generic bioinformatics tools, and design simple
pipelines (e.g., bash, Nextflow). They will also explore specific algorithms for TE detection
and annotation. Pipelines will run on Linux servers, requiring basic resource management
(CPU, RAM, disk space). Phylogenetic analyses and statistical modeling will be conducted in
R, adhering to reproducible science practices. The internship involves regular oral
presentations during group meetings, and the production of a final scientific report.Implementation:
The 6-month internship will take place at EGCE, part of IDEEV (Institute for Biodiversity,
Ecology, and Evolution) at Université Paris-Saclay (35 km south of Paris). The hosting
group, “Pôle Génome,” has a long-standing expertise in transposable element genetics and
genome evolution. This project is funded by an ANR research grant on TE evolution and
phylogenetic distribution. The student will be supervised by Arnaud Le Rouzic (CNRS
researcher) and co-supervised by project collaborators (Antoine Branca, Ian Dewan,
Clément Gilbert, and Aurélie Hua-Van).
Student Background:
We seek a master’s student with training in bioinformatics, genomics, and evolutionary
biology. An interest in computer science, theoretical approaches, and statistics is a plus.
The starting date is flexible (preferentially January - March 2027). The application will
remain open until the position is filled up.