Comparative analysis of transposable elements in jellyfish and hydroid species (Cnidaria: Medusozoa)

Abstract Background Transposable elements (TEs) are repetitive genetic elements that can jump to new loci causing genome expansions, structural rearrangements, and can, ultimately, propel the evolution of genomes. Despite their significance, the role of TEs in the evolution of genomes and phylogenetic groups remains largely understudied in early diverging lineages. Further, the extent of TE content variation and diversity remains unresolved in some understudied taxa. Medusozoa, a group within Cnidaria encompassing jellyfish and hydroids, exhibits an exceptional diversity of life history strategies, body plans, and physiological capabilities. These characteristics, along with its early-diverging phylogenetic position, establish Medusozoa as an ideal system for investigating the composition and evolutionary history of TEs within the group. Results We generated a custom repeat library built from annotations of 26 cnidarian genomes and used it to characterize TEs in Medusozoa. Repetitive element percentage and genome size displayed a strong, positive relationship even among large genomes (> 3 Gb). Examining TE proliferations in these large genomes revealed different mechanisms that may be driving genome size increases. Intra-genus comparisons revealed a surprising degree of differences in TE dynamics; expansions of specific elements were observed within genera, indicating TE proliferation after divergence. Proliferations also occurred differently across genomes. In some cases, proliferation was driven by a single or a few elements and in others, proliferation was much more even across elements. Interestingly, most genomes showed evidence of recent TE expansions, suggesting ongoing activity in many medusozoan species. Conclusion We present the first comparative analysis of TEs across all medusozoan classes. Our results elucidate the relationship between TEs and genome characteristics and highlight cases of TE expansions that vary between lineages. The approaches used in this research provide a framework for comparing TE dynamics across groups. Additionally, this data fills important gaps about TE contribution to the evolution and diversification of early diverging animal lineages.