Comparative Analysis of Transposable Element Evolution in Crustaceans

Transposable elements (TEs) are pivotal in driving genome evolution, playing a significant role in generating genetic diversity, modulating genome size, and inducing chromosome structural changes. Despite extensive research in model species, studies on TE evolution and structure in crustaceans are notably limited. This study offers an in-depth analysis of TEs diversity and its impact on representative crustacean genomes' genome structure and function. Our results revealed substantial variation in TE content among crustacean species, with levels ranging from 16.19% in Daphnia pulex to a high of 63.36% in Procambarus clarkii. Notably, species with larger genomes, such as P. clarkii and Homarus americanus, show a higher proportion of TEs, which implies that TE proliferation may be a major factor in the expansion of genome size. Analysis of sequence divergence across multiple TE subfamilies reveals 2 distinct peaks, suggesting that most crustacean species may have experienced at least 2 separate periods of TE expansion. The second peak, characterized by divergence rates between 0% and 5%, indicates a more recent episode of TE proliferation and implies potential ongoing activity. Phylogenetic signal analysis revealed distinct evolutionary dynamics among TEs: terminal inverted repeat (TIR) transposon elements initially contracted then expanded, long terminal repeat retrotransposon (LTR) and short interspersed nuclear element (SINE) elements consistently expanded, with TIRs evolving at significantly lower rates. Chronological analysis of LTR transposons in crustaceans revealed the recent proliferation of Bel-Pao, Copia, and Ty3 subfamilies, with species-specific patterns of diversification. Furthermore, the molt stage-specific expression of TEs in Eriocheir sinensis and Penaeus vannamei throughout the molting process suggests that TEs may play a role in regulating this periodic event. Generally, these results deepen our understanding of the role of TEs in crustacean genome evolution and hint at their possible involvement in regulating biological processes within these species.