Genome size evolution in the diverse insect order Trichoptera

Abstract

Background Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. Results We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). Conclusion Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.

Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes

“…proportion of repetitive sequence supports previous studies, which suggest that repetitive element expansion occurred in lineages of tube case-making caddisflies, such as the closely related genera Agrypnia and Hesperophylax[9,41]. In contrast, a total of 31.94% of the P. interpunctella genome assembly was masked as repeats.…”

Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

“…Despite recent analyses showing no evidence of whole-genome duplication in caddisflies(Heckenhauer et al 2022), the findings in this study may be an indication of tetraploidy. Future research should be done to further examine these patterns.The P. interpunctella assembly represents a substantial improvement to existing, publicly available genome assemblies (Table2).…”

“…Of the repeats that were classified, retroelements were the most abundant, comprising 15.35% (of which 14.55% are LINEs) of the genome. The relatively high proportion of repetitive sequence supports previous studies which suggest that repetitive element expansion occurred in lineages of tube case-making caddisflies, such as the closely related genera Agrypnia and Hesperophylax [9, 35]. In contrast, a total of 31.94% of the P. interpunctella genome assembly was masked as repeats.…”

600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges

“…Investigating the diversity of insect models with varying genome sizes and complexity can expand our perspectives on genome evolution. For example, in caddisflies (Trichoptera), clades containing large genomes show higher species diversity and ecological breadth than small-genome lineages, raising the potential for adaptive advantages of maintaining high repeat loads (27, 38). With high species diversity and broad distributions in nearly all habitat types, insects may be particularly useful for understanding factors driving temporal dynamics of TE activity including population demographics (39) and environmental stress (40, 41).…”