DOI: 10.5061/dryad.qz612jmjs
title: Data for: Mobilomes of four flower-breeding Drosophila species

description: 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 history. This pattern agrees with results
 previously recovered for other Drosophilidae species of the same subgenera
 studied here, suggesting that lineage-specific factors shape the mobilome
 of this lineage. Nevertheless, the abundance and richness of TE
 superfamilies was associated with niche breadth. Furthermore, the two more
 widespread species, the specialist D. incompta and the generalist D.
 lutzii, presented the highest frequency of HTT events. Our analyses also
 revealed that HTT opportunities are positively influenced by abiotic niche
 overlap but are not associated with phylogenetic relationships, niche
 breadth and biotic niche overlap. This suggests the existence of
 intermediate vectors promoting HTTs between species presenting
 non-overlapping biotic niches.
description: A <em>de novo</em>
 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 obtained
 from RepeatExplorer in the program CAP3 (Huang & Madan, 1999)
 using the parameters: -a 20 -b 20 -c 12 -d 200 -e 30 -f 20 -g 6 -m 2 -n -5
 -p 80 -r 1 -s 900 -t 300 -u 3 -v 2 -o 40. The final contigs annotated by
 superclusters were then used in a homology-based search using RMBlast
 2.10.0 against a curated TE database (Repbase v. 20181026 database) to
 evaluate TEs identity. A second homology-based search was performed
 with the draft assembled genome recovered for each species against Repbase
 v. 20181026 database, to obtain a complementary TE library. In this case,
 the best query recovered for each contig was manually selected based on
 the best bit-score number, with a threshold of at least 160 bit-score and
 a minimum length of 130bp, considering the minimum start and maximum end
 query sequences. Lastly, the combined TEs libraries of each species were
 processed by CD-HIT-est clustering algorithm, removing redundant sequences
 with more than 95% identity (Fu et al., 2012).
description: Molecular Evolutionary Genetics Analysis - MEGA software