Investigating Horizontal Transfer of Transposable Elements in Drosophilidae Genomes
Contact:
Aurélie Hua-Van (Equipe Evolution et Génome) aurelie.hua-van@universite-paris-saclay.fr
Laboratoire Evolution, Génomes, Comportement, Ecologie – Université-Paris-Saclay- CNRS – Gif-sur-Yvette
Keywords : Transposable elements, Genomics, Evolution, Horizontal transfer, Drosophila
Background:
Transposable elements (TEs) are mobile genetic elements capable of moving and multiplying within host genomes, often independently of the host’s fitness. Due to their selfish and invasive nature, TEs are frequently considered genomic parasites (Hua-Van et al., 2011). All eukaryotic genomes harbor TEs, sometimes constituting over 80% of their total DNA content. While some TE insertions can be co-opted by the host and contribute to evolutionary innovations, the majority are neutral or deleterious. To mitigate their impact, host organisms have evolved regulatory mechanisms—such as the piRNA pathway in metazoans—that suppress TE activity and limit transposition (Brennecke et al. 2007). Over time, these control mechanisms and the accumulation of mutations lead to the inactivation and eventual extinction of TE families.
Despite this, all eukaryotic genomes retain active TE families, largely due to repeated horizontal transfer of TEs (HTT) between species. Unlike conventional genes, TEs can move between reproductively isolated species, and comparative genomic studies have revealed extensive HTT events, even between phylogenetically distant taxa (Peccoud et al., 2016). While the precise mechanisms of HTT remain unclear, bacterial or viral vectors are suspected. These transfer events are thought to be facilitated by ecological and geographic interactions, such as shared environments, hosts, or symbionts.
Objective of the Internship:
The goal of this internship is to assess the influence of geographic, ecological and phylogenetic proximity on the rate and success of TE horizontal transfers. Using a comparative genomics and bioinformatics approach, the intern will work with a unique and exceptionally rich dataset comprising genome assemblies from over 300 Drosophilidae species (Kim et al., 2023). This dataset represents an unparalleled resource in terms of phylogenetic diversity, ecological breadth, and genomic quality, offering a powerful framework for studying TE dynamics at an evolutionary scale.
The aim of the internship is to evaluate the importance of geographic or ecological proximity on the HTT rate and the establishment of TEs in new genomes using a bioinformatics and comparative genomics approach applied to a set of genomes assembled from over 300 Drosophilidae species (Kim et al., 2023). TE sequences will first be identified in the genomes and classified into families based on similarity. For each TE family shared between multiple species, we will apply a statistical method (Wallau et al., 2016) to detect horizontal transfers (i.e., TE sequences are too similar compared to species divergence based on diversity). Finally, the geographical distribution of species, their phylogenetic relationships, the geographic origin of their phylogenetic clade, and the type of oviposition site will be analyzed to determine whether these parameters are independent of the obtained horizontal transfer profile or not. For instance, are horizontal transfers more frequent between species sharing the same geographic area than between geographically distant species?
Tasks will include:
- Identifying and annotating TE sequences within Drosophilidae genomes.
- Grouping TEs into families based on sequence similarity.
- Applying statistical methods (e.g., from Wallau et al., 2016) to detect putative HT events by comparing TE divergence to host species divergence.
- Investigating correlations between HT events and ecological or geographical factors, such as species distributions, phylogenetic relationships, clade origins, and oviposition site preferences.
This project will address key questions such as: Are horizontal transfers more frequent between species that coexist geographically? Do ecological traits influence the likelihood of TE transmission between species?
Candidate Profile:
We are looking for a motivated student with:
- A background in evolutionary biology, genomics, or bioinformatics.
- Basic proficiency in scripting languages (e.g., Python, R, or Bash).
- Familiarity with sequence alignment and phylogenetic tools is a plus.
- Interest in genome evolution, mobile elements, and species interactions.
Bibliography :
- Brennecke et al. 2007. Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila. Cell 128, 1089–1103. https://doi.org/10.1016/j.cell.2007.01.043
- Hua-Van et al. 2011. The struggle for life of the genome’s selfish architects. Biol Direct 6, 19. https://doi.org/10.1186/1745-6150-6-19
- Peccoud et al. 2017. Massive horizontal transfer of transposable elements in insects. Proc Natl Acad Sci U S A 114, 4721–4726. https://doi.org/10.1073/pnas.1621178114
- Wallau et al. 2016. VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila. Mol Biol Evol 33, 1094–109. https://doi.org/10.1093/molbev/msv341
- Kim et al. 2023. Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. bioRxiv 2023.10.02.560517. https://doi.org/10.1101/2023.10.02.560517