My research focus on the study of the population dynamics and evolution of the transposable elements (TEs), one type of repeats, mainly in insect genomes (Petrov et al, MBE 2011; Barron et al, Annual Review of Genetics 2014; Maumus et al, Current opinion in Insect Science 2015). I am also particularly interested in the impact of such repetitive elements on genome adaptation (Kelley et al Nature Comm. 2014). Another interest of my research is to assess the veracity of short and long read sequencing technologies and develop tools for the annotation and analyze of these repeats (McCoy et al. 2014, PLoS One; Fiston-Lavier et al NAR 2011, 2014).
Detection of DNA repeats in assembled and non-assembled data
Transposable elements (TEs). TEs are ubiquitous repetitive elements of genomes representing a large part of genomes. As more and more studies highlight the implication of these elements in the evolution and adaptation of genomes, the annotation of TEs is still a huge challenge. In my research, I developed computational approaches and tools for the detection and annotation of TE insertions in genome sequencing from individuals and pooled data (https://github.com/asfistonlavie/T-lex3; Fiston-Lavier et al NAR 2011, Fiston-Lavier et al NAR 2014; Bogaerts et al Bioinformatics 2019). The accuracy of the detection depends on biologic and technic variables. My current interest is to (1) optimize existing TE detection approaches and (2) assess the impact of repeats on the quality of genome assemblies.
As TEs may represent a large fraction of genomes, a clear and thorough understanding of how TEs evolve is essential for a full comprehension of genome evolution. In previous work, we showed that most of TE insertions are deleterious and subject to purifying selection. This selection varies predictably with recombination rate, length of individual TEs, and copy number and length of other TEs from the same family. However, the effect of each factor is not the same for all TE families (Petrov et al MBE 2011). To take into account the biology TE families, I am currently investigating the TE insertion bias and the effect of piRNA pathway a mechanism that represses transposition. Bridlin Barckmann, a post-doc in the lab, members from the Chambeyron team and I tracked novel TE insertions over generations after stress and show (Barckmann et al NAR 2018).
Impact of TEs on genome evolution and adaptation
Another major part of my work consists assessing the impact of TEs on genome evolution and adaptation. I currently interesting understanding the impact of TEs on rearrangments, such as inversion and duplications of known genes involved in pesticide resistance in mosquitoes (Assogba et al PLoS Biology 2016) and in climate adaptation in antartic species (Kelley et al Nature Comm. 2014).
Recombination rate estimation
Recombination rate is a key evolutionary parameter that determines the degree to which genomic regions or genes are linked. Estimating recombination rates is thus of crucial importance for population genetic and molecular evolutionary studies. Several approaches can be used to estimate the recombination rate along the chromosome(s). Fine-scale recombination estimates are starting to be available for few organisms. However, the approaches used are time and cost-consuming. One aspect of my research is dedicated developing statistic and computational tools for the recombination rate estimation based on genetic and physical maps (Fiston-Lavier et al Gene 2010; Mansour et al 2020).