High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.

The advent of long-read sequencing technologies has allowed the generation of multiple high-quality de novo genome assemblies for multiple species, including well-known model species such as Drosophila melanogaster. Genome assemblies for multiple individuals of the same species are key to discover the genetic diversity present in natural populations, especially the one generated by transposable elements, the most common type of structural variant. Despite the availability of multiple genomic datasets for D. melanogaster populations, we lack an efficient visual tool to display different genomes assemblies simultaneously. In this work, we present DrosOmics, a population genomics-oriented browser for 52 high-quality reference genomes of D. melanogaster, including annotations from a highly reliable set of transposable elements, and functional transcriptomics and epigenomics data for 26 genomes. DrosOmics is based on JBrowse 2, a highly scalable-platform, which allows the visualization of multiple assemblies at once, key to unraveling structural and functional features of D. melanogaster natural populations. DrosOmics is open access and freely available at http://gonzalezlab.eu/drosomics.

The advent of long-read sequencing technologies has allowed the generation of multiple high-quality de novo genome assemblies for multiple species including well-known model species such as Drosophila melanogaster. Genome assemblies for multiple individuals of the same species are key to unravel the genetic diversity present in natural populations, especially the one generated by transposable elements, the most common type of structural variant. Despite the availability of multiple genomic datasets for D. melanogaster populations, we lack an efficient visual tool to display different genomes assemblies simultaneously and compare how homologous regions differ in terms of the structural variation composition. In this work, we present DrosOmics, a comparative genomics-oriented browser for 52 high-quality reference genomes of D. melanogaster, spanning 32 locations worldwide and including annotations from a highly reliable set of transposable elements. DrosOmics is based on JBrowse 2, a highly scalable and user-friendly platform that allows the visualization of multiple assemblies at once. In this browser, we have also compiled functional -omics data for half of the populations, including transcriptomics and epigenomics data. We believe that this resource will be key for unraveling structural and functional features of D. melanogaster natural populations and will open the door for exploring new evolutionary biology hypotheses.