Data for: Mobilomes of four flower-breeding Drosophila species

Understanding the mechanisms that shape the architecture, diversity and adaptations of genomes and their ecological and genetic interfaces is of utmost importance to understand biological evolution. Transposable elements (TEs) play an important role in genome evolution, due to their ability to transpose within and between genomes, providing sites of non-allelic recombination. Here we investigate patterns and processes of TE driven genome evolution associated with niche diversification. Specifically, we compared TE content, TE landscapes, and frequency of horizontal transposon transfers (HTTs) across genomes of five flower-breeding Drosophila (FBD) with different levels of specialization on flowers. Further, we investigated whether niche breadth, and ecological and geographical overlaps are associated with potential for HTT rates. Mobilome landscapes recovered for all species presented a bell-shaped curve, revealing an equilibrium between transposition and excision over evolutionary hist..., A de novo search for repetitive elements was performed using the raw filtered Illumina reads on the Galaxy platform (Afgan et al., 2016) through the RepeatExplorer 2.0 tool (Novák et al., 2013). This algorithm makes TE discovery and characterization easier by using graph-based sequence clustering and then evaluating the similarity of each hit to reference databases (Novák et al., 2020). As a first step, FASTQ paired-end reads were preprocessed on the Galaxy platform, through interlacing and quality filtering. The file thus obtained was then employed as input for the graph-based clustering. After, the detected read similarities were used to build a virtual graph that is partitioned into clusters, returning contigs related to individual repeat superfamilies. In addition, supplementary information was also obtained for each supercluster, as the proportions of shared paired-end reads among clusters. To detect and remove false overlaps, a second contig assembly was performed with the results..., Molecular Evolutionary Genetics Analysis - MEGA software