Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models

Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and changes to anatomy and physiology. Here, we characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome - the caecilian Ichthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model sys-tem because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diver-sity indices commonly applied in community ecology. We synthesize previous models that integrate TE abundance, diversity, and activity, and test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.

Automated summary

Transposable elements (TEs) play a major role in determining eukaryotic genome size, with their collective properties reflecting the evolutionary dynamics of TE/host interactions. The amphibian caecilian Ichthyophis bannanicus, with its giant genome size, exhibits unique TE landscape composition compared to other giant amphibians, but shares similarities in ectopic recombination-mediated deletion rate. TE activity in the caecilian is characterized by high somatic transcription levels, suggesting active TE superfamilies. Comparing TE diversity across vertebrates of varying genome sizes highlights the importance of thorough TE characterization for future comparative analyses, with potential implications for understanding shared features of TE/host genome evolutionary dynamics in convergent gigantic genomes.