The Worldwide Invasion of Drosophila suzukii Is Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions
2021
Mérel, Vincent | Gibert, Patricia | Buch, Inessa | Rodriguez Rada, Valentina | Estoup, Arnaud | Gautier, Mathieu | Fablet, Marie | Boulesteix, Matthieu | Vieira, Cristina | Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE) ; Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS) | Centre de Biologie pour la Gestion des Populations (UMR CBGP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [Occitanie])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro) | Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE) ; Centre Inria de l'Université Grenoble Alpes ; Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria) | This work was supported by the French National Research Agency (ANR-16-CE02-0015, SWING) and performed using the computing facilities of the CC LBBE/PRABI. | ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016)
The reference assembly used in this article is available on NCBI website (https://www.ncbi.nlm.nih.gov/genome/18317?genome_assembly_id=910956) (Paris et al. 2020). Population sequencing data are available online (SRA repository under the BioProject accession number PRJNA576997) (Olazcuaga et al. 2020). The generated TE database and scripts are available in a github (https://github.com/vmerel/Dsu-TE).
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Afficher plus [+] Moins [-]anglais. Transposable elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we characterized the TE content of the spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequences de novo and found that TEs occupy 47% of the genome and are mostly located in gene-poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied the variation of TE abundance in genomic data from 16 invasive and six native populations of D. suzukii. We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversity θw^ a proxy of effective population size. We did not find any correlation between TE contents and bioclimatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 2,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g., transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.
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