Investigating the Role of Transposable Elements in the Evolution of Host Genomic Complexity

The extent that TEs contribute to host evolution remains an open question. Comparative genomic studies can evaluate TE contributions to host genome evolution and elucidate processes underlying variation in TE abundance and diversity. Mass annotation of TEs requires effective automated methodologies. Thus, we developed a new automated TE curation and annotation pipeline 'Earl Grey', to address problems associated with poorly-defined TE boundaries, redundant consensus sequences in TE libraries, and fragmented or overlapping annotations. Earl Grey outperforms other widely-used tools, is user-friendly, and generates summary plots, promoting accessibility among non-specialists. Recent assemblies for the monarch butterfly genus (Danaus) were used to explore how TEs shape host genomes, by analysing TE expansion, removal and host gene interactions. Novel patterns were identified in TE content, expansion, turnover, and hotspots, demonstrating considerable impacts on host genomic change. 21 available aphid assemblies were analysed to explore if TEs contribute genomic novelty for host evolution. TEs were significantly enriched at xenobiotic resistance loci (XRL) and housekeeping genes. Unlike housekeeping genes where TE hotspots are likely due to constitutive expression and open chromatin, TE hotspots at XRL (not expressed in germline cells) may be due to selection for resistance evolution. Supporting this, TEs are enriched at cytochrome P450 genes with known functions in synthetic insecticide detoxification in 3 agriculturally important aphids. 88 butterfly assemblies were analysed to identify determinants of TE content variation (6%-68%). Strong phylogenetic signal was found in TE abundance and diversity, indicating these are good indicators of evolutionary past. 3 life history traits were strongly negatively correlated with TE abundance, and 2 were strongly negatively correlated with TE diversity, confirming one hypothesis, but challenging understanding for others.