Transposable Elements in Anopheles Species: Refining Annotation Strategies Towards Population Genomics Analyses

Abstract

Mosquitoes from the Anopheles genus have been extensively studied given their role as vectors of several human infectious diseases. While the genomes of 27 species are available, only a few of them have been studied from a population genomics perspective. Additionally, most of these studies have relied on single nucleotide polymorphisms while other genetic variants, including transposable element (TE) insertions have been neglected. TEs are important players in genome function, structure, and evolution. Indeed, given their capacity to generate mutations and to respond to environmental changes, TEs have been shown to play an important role in adaptation. However, given their repetitive nature they remain challenging to annotate. In this work, we aim at summarizing the current knowledge on TE content and TE diversity in anopheline genomes as the necessary first step to include these relevant genetic variants in population genomics studies. The comparison of the TE content obtained using different annotation strategies in three anopheline species suggests that combining strategies is essential to fully characterize the TE repertoire. As a first approach to the characterization of the TE repertoire in all 27 available anopheline genomes, we used TEfam, a database specialized in mosquitoes TEs, to annotate them. We found that the TE content, and its composition, varied among anopheline species, with some TE families restricted to specific phylogenetic groups. Furthermore, we showed that using all the available libraries allowed us to uncover the TE diversity to a larger extent. The ongoing efforts to improve the already available genome sequences together with the generation of new population genomic resources should allow us to assess in the near future the role of TE insertions in the evolution and function of anopheline genomes.