The role of natural transposable element insertions in environmental adaptation

Josefa Gonzalez
Institute of Evolutionary Biology, Barcelona.

 josefa.gonzalez@ibe.upf-csic.es

Transposable elements are ubiquitous, abundant, and active components of genomes. Although most of the mutations caused by transposable elements are likely deleterious or neutral, adaptive mutations have also been repeatedly identified across species. Drosophila melanogaster is an excellent species to quantify the role of transposable elements in environmental adaptation as it has recently colonized very distinct habitats. We have generated 32 D. melanogaster reference genomes using long-read sequencing of flies collected in arid, cold, and temperate environments. The in depth annotation of these genomes has allowed us to discover three new transposable element families in this well-studied species. We have also generated RNA-seq data for 25 of these genomes to investigate the role of transposable elements in expression quantitative trait loci variation and more specifically in desiccation, oxidative, and heavy-metal stress resistance. Our results will allow us to quantify the role of transposable elements in environmental adaptation and to generate testable hypothesis for follow-up functional validation studies.

Recent publications:

1 Rech, G.E. et al Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genetics, 15(2): e1007900, 2019.

2 Villanueva-Cañas et al. Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in D. melanogaster. Nuc Acids Res, 47 (13): 6842–6857 2019

3 Bogaerts-Márquez, M. T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data. Bioinformatics, https://doi.org/10.1093/bioinformatics/btz727. 2019