Mots-Clés
Evolutionary biology
Agronomy
Horizontal gene transfer
Comparative genomics
Description
Context
How species evolve and adapt to changing conditions remains a central question in biology. In addition to single-nucleotide mutations and structural variations in their own DNA, species can acquire foreign genes from other species 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 is less frequent; however, numerous robust cases have been reported across multiple lineages, including those of multicellular organisms. Many of these HGTs likely contributed to rapid evolutionary transitions by conferring new adaptive functions on recipient species [1]. These gains are particularly well illustrated in insects, where multiple horizontally acquired genes have been reported that 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]. For example, 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, there is an increasing interest in identifying horizontally acquired genes and their functions in insect pests. These genes may serve as targets for developing new biocontrol strategies, thereby contributing to more sustainable pest management within an agroecological framework [4].
Objectives
B. tabaci (whiteflies; family Aleyrodidae) is a complex of cryptic species comprising some of the world’s most harmful horticultural pests. It is notable for harboring approximately 200 HGT-derived genes, initially identified in the MEAM1 species (Middle East - Asia Minor 1), acquired from bacteria, fungi, and plants. Many plant-derived genes in MEAM1 are conserved in two other whitefly species, MED1 (Mediterranean 1) and SSA1 (Sub-Saharan Africa 1), and a few in the basal Aleyrodidae species, Trialeurodes vaporariorum [5]. However, the timing of HGT events in whitefly, the ongoing nature of these events, and the potential vectors for these transfers remain unknown. During this internship, you will use an established pipeline to search for HGT events across 17 whitefly species with a broad geographical range, in addition to the Aleyrodidae species T. vaporariorum and Aleurodicus rugioperculatus. You will perform protein clustering and BLAST searches to address the presence-absence of transferred genes across whitefly species and the other two Aleyrodidae species to create a detailed chronology of HGT events in whiteflies. You will build phylogenetic trees for each family of transferred genes and infer the taxonomy of their donor species. You will then perform functional prediction and selection analyses of transferred genes. If time allows, you will examine the flanks of transferred genes to search for viral sequences and transposable elements that could represent footprints of active transfers.
Expected profile
We are looking for a motivated candidate with a background in bioinformatics and a keen interest in biodiversity and species evolution.
You will join the Jean-Pierre Bourgin Institute in Versailles in the AGIPP team, which studies plant-parasite interactions through genomic analyses.
References
1. Keeling, P.J. Horizontal gene transfer in eukaryotes: aligning theory with data. Nat Rev Genet 2024.
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. Azad, R.B.; et al. Horizontal Gene Transfer in Plants and Implications for Biotechnology. Plant Environ Interact 2025.
5. Gilbert, C.; et al. Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci. Genome Biol Evol 2022.