Uncovering transposable element variants and their potential adaptive impact in urban populations of the malaria vector <i>Anopheles coluzzii</i>

A bstract Background Anopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has colonized the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments is partly due to an increased tolerance to organic pollution and insecticides. While some of the molecular mechanisms for ecological adaptation, including chromosome rearrangements and introgressions, are known, the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet. To assess the role of TEs in rapid urban adaptation, the first step is to accurately annotate TE insertions in the genomes of natural populations collected in urban settings. Results We sequenced using long-reads six An. coluzzii genomes from natural breeding sites in two major Central Africa cities. We de novo annotated the complete set of TEs in these genomes and in an additional high-quality An. coluzzii genome available and identified 64 previously undescribed TE families. TEs were non-randomly distributed throughout the genome with significant differences in the number of insertions of several superfamilies across the studied genomes. We identified seven putatively active families with insertions near genes with functions related to vectorial capacity. Moreover, we identified several TE insertions providing promoter and transcription factor binding sites to insecticide resistance and immune-related genes. Conclusions The analysis of multiple genomes sequenced using long-read technologies allowed us to generate the most comprehensive TE annotations in this species to date. We identified several TE insertions that could potentially impact both genome architecture and the regulation of functionally relevant genes in An. coluzzii . These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii .