Transposable element dynamics in Arthropoda genomes and their impacts on the evolution of functional genes

BACKGROUND: Transposable elements (TEs) are critical in shaping genomic architecture and evolutionary processes, driving genome size expansion and functional innovation. TE dynamics and their contribution to genome expansions have been reported extensively; yet, there is a gap in information regarding their role in gene family expansions and the evolution of new genes, particularly in arthropods. RESULTS: In this study, we examine the TE dynamics across 80 species from all four major subphyla in Arthropoda, revealing a substantial variation in TE contents and their significant impacts on genome expansion. Our analysis of protein-coding transcripts demonstrates that TEs were frequently integrated into protein-coding regions, with an average of 15.1% of protein-coding transcripts harboring TE-derived fragments. We reported the dynamics of retrocopies in selected species and highlighted the role of retroposition in driving the expansion and diversification of key protein families. We find that certain species-specific key protein families such as Calreticulin-like, Acaloleptin-A, and Ctenidins proteins have undergone substantial expansion and structural diversification. CONCLUSIONS: Our study provides new insights into the impact of TEs on genome evolution, exonization of TEs into host genes, and TE-aided retroposition for gene family expansion.