Master 2 Internship Proposal 2024-2025

Exploration of the Influence of Geographic/Ecological Proximity on the Rate of Horizontal Transfer of Transposable Elements Between Species: The Drosophilidae as a Study Model

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

Transposable elements (TEs) are genetic entities that can move and multiply within genomes, regardless of their impact on host fitness. Hence, they are sometimes considered as genomic parasites (Hua-Van et al., 2011). All eukaryotic genomes contain varying proportions of TEs, ranging from a few percent to over 80%. While some insertions can be beneficial, leading to molecular domestication and evolutionary innovations, the invasive nature of TEs requires active measures by the host to maintain genome integrity. For example, the piRNA pathway in metazoans inhibits TE expression and then transposition. The combination of regulation and the accumulation of inactivating mutations ultimately leads to the extinction of TE families within a species. The constant battle against TEs is evident through the vast diversity of coexisting families within a genome (sometimes several thousand), most of which exist as inactive relics. However, active TE families persist in all genomes due to the recurrent invasion of new genomes by new TEs from other species, through horizontal transfer.

In eukaryotes, TEs are particularly prone to horizontal transfer between reproductively isolated species, unlike gene transfers, which are infrequent. Recent studies comparing TE sequences between phylogenetically distant species have revealed the extent of horizontal TE transfers (HTT) (Peccoud et al., 2016). The mechanistic process behind HTTs remains largely misunderstood, but bacteria or viruses could be probable vectors. Transfer opportunities primarily depend on interactions between species or between species and their shared symbionts/parasites, suggesting the involvement of ecological/geographical factors. The success of a new TE in amplifying and establishing in a new host genome also depends on various parameters, including demographic, population, and phylogenetic factors, as well as contingency elements, such as the rapid establishment of piRNA regulation.

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?

Bibliography :

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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

Desired Profile:

The project involves handling large datasets of sequences. We are looking for a motivated candidate, preferably with knowledge in bioinformatics (genomics) or proficiency in Python and/or R, and an interest in evolution (molecular evolution) and comparative genomics. Any additional expertise in genetics, population genetics, phylogeny, or Drosophila biology would be highly appreciated.

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