Mots-Clés
Genomics
Evolutionary biology
Bioinformatics
Ecology
Description
We are looking for a candidate to present to the SDSV doctoral school 2026 competition on the following topic.
If the scholarship is awarded, the thesis will be co-supervised by Clément Gilbert (EGCE, CNRS) and Florian Maumus (IJPB, INRAE)
Summary
Horizontal gene transfer (HGT) is an intriguing process in which genes with established functions in one organism are transferred to another, often with significant biological consequences. While HGT is a major driving force behind the evolution and adaptation of prokaryotes, several studies indicate it also plays a role in eukaryotic evolution, though this is less common, and the underlying mechanisms are largely unknown. In insects, HGT has been documented multiple times and shown to confer functions that can greatly influence their biology and their ability to feed on various plants. This project aims to identify HGT events across a large, diverse collection of insect genomes to assess global patterns of HGT and its potential role in facilitating phytophagy.
Context
The question of how species evolve and adapt to new conditions remains central to biology. In addition to mutations in their DNA, genome comparisons revealed that species also evolve through the lateral acquisition of genes by means other than reproduction, a process known as horizontal gene transfer (HGT). The patterns, mechanisms, and vectors of HGT are well characterized in prokaryotes, where these transfers are ubiquitous and a major source of innovation. In eukaryotes, HGT has often been viewed as anecdotal or controversial due to barriers to transfer and the potential for artifacts or contamination. However, recent studies using high-quality genomes and transcriptomes have confirmed many instances of gene and transposable element transfers among various eukaryotic organisms [1]. These findings provide compelling evidence that horizontal gene transfer also occurs in eukaryotes and contributes to rapid evolutionary transitions by conferring new functions to recipient species.
These gains are particularly well illustrated in insects, where multiple horizontally acquired genes have been reported. Remarkably, many of these transfers directly impact insect interactions with plant hosts by conferring functions involved in resistance to plant toxic compounds, assimilation of plant products, or degradation of plant cell walls [2]. While most of these genes were transferred from bacteria and viruses, some have reportedly been acquired from other eukaryotes, including fungi and plants. For instance, the whitefly Bemisia tabaci (Hemiptera) acquired a malonyl-transferase gene through HGT from plants, enabling it to overcome plant defenses by neutralizing ingested toxic phenolic glucosides, thereby greatly expanding the host range of this major crop pest [3]. Therefore, characterizing HGT in insects provides significant insights into the evolution of the insect gene repertoire and can reveal key genes potentially involved in phytophagy that have facilitated insect adaptation to plant hosts.
Objectives
How many HGTs have occurred during insect evolution and from which sources? Are there over-represented predicted functions among horizontally acquired genes in insects, and if so, which ones? To address these questions, we will systematically identify HGT among insects. A recent study focusing on 218 insect species identified as many as 1340 horizontally acquired genes [4]. This study marked an important milestone but had two main limitations. First, a parallel survey focusing on B. tabaci, which utilized a horizontal gene transfer (HGT) mining approach we developed, showed greater sensitivity than the methods used by Li et al. [5]. Second, this study did not aim to identify HGT events between different insect species, as suitable methodologies for detecting HGT within the same phylum were unavailable. This suggests that the number of HGT events in insects may be underestimated, while recently released insect genomes have not been analyzed at all.
In this thesis, we will conduct a comprehensive study of horizontal gene transfer (HGT) across all insect species with annotated genomes available in public databases. As of October 2025, this includes 418 species in NCBI. We will utilize two complementary approaches. The first approach will help us identify genes that insects have acquired from non-metazoan lineages, which include prokaryotes, viruses, plants, and fungi. The second approach employs a specialized workflow we recently developed to detect intraphylum transfers, enabling us to perform the first large-scale search for HGT events between insect species. This method has previously been successful in identifying transfers among fish species {Policarpo, 2025 #485}. Together, these approaches will facilitate the identification of HGT from any donor and provide insights into HGT patterns across insects. We will then submit each horizontally acquired gene to functional prediction and evolutionary analysis, including the dating of HGT events, characterization of the selection regime acting on these genes, and identification of signatures hinting at potential HGT mechanisms in the donor and receiving species genomes.
Altogether, this work will advance our understanding of the pervasiveness and potential impact of HGT on insect evolution. Specific attention will be dedicated to addressing which of these transfers are likely to constitute genetic determinants that have influenced plant-insect evolutionary arms races.
Expected profile
We are looking for a motivated candidate with a background in bioinformatics and a keen interest in biodiversity and species evolution.
References
1. Van Etten, J.; et al. Horizontal Gene Transfer in Eukaryotes: Not if, but How Much? Trends Genet 2020.
2. Wybouw, N.; et al. Horizontal Gene Transfer Contributes to the Evolution of Arthropod Herbivory. Genome Biol Evol 2016.
3. Xia, J.; et al. Whitefly hijacks a plant detoxification gene that neutralizes plant toxins. Cell 2021.
4. Li, Y.; et al. HGT is widespread in insects and contributes to male courtship in lepidopterans. Cell 2022.
5. Gilbert, C.; et al. Sidestepping Darwin: horizontal gene transfer from plants to insects. Current Opinion in Insect Science 2023.
6. Policarpo, M.; et al. Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes. Mol Biol Evol 2025.