Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models

Abstract

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 system 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 diversity 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.

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

“…After the masking of the draft genome, about 75% of the sequences were classified as repetitive elements. This result is in accordance with what was previously reported in the literature, namely that the expansion of gigantic genomes has been driven by the proliferation of transposable elements [ 23 , 24 ]. Indeed, also due to the sequencing of short-libraries (270 bp), the huge amount of repetitive content hampered the assembly procedures and biased some assembly metrics.…”

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

“…This hypothesis is supported by a faster decay of non-LTR retrotransposon insertions caused by large deletions in reptiles and fish than in mammals [67,79]. Consistent with the hypothesis above, the gigantic genome of some salamanders and caecilian is characterised by an extremely reduced rate of DNA loss and ectopic recombination [56,80,81]. Interestingly, the rate of transposition and the rate of DNA loss can counteract each other perfectly, resulting in the long-term stability in genome size observed in birds and mammals, a process termed the "accordion" model of genome evolution [82].…”

“…Birds, for instance, have a relatively conserved genome size [52] possibly because of the metabolic cost associated with active flight [53], despite the fact that TEs are active in most bird lineages [54,55]. Salamanders, on the other hand, have experienced extreme and independent TE amplification resulting in gigantic genomes, ranging from 14,000 to 120,000 Mbp [56][57][58]. [45,46,56,[59][60][61][62][63][64].…”

“…Salamanders, on the other hand, have experienced extreme and independent TE amplification resulting in gigantic genomes, ranging from 14,000 to 120,000 Mbp [56][57][58]. [45,46,56,[59][60][61][62][63][64].…”

Caecilian genomes reveal the molecular basis of adaptation, and convergent evolution of limblessness in snakes and caecilians

“…These relative proportions differ from those found in the large genomes of other amphibians: a genomic lowcoverage shotgun analysis of the caecilian Ichthyophis bannanicus (genome size 12.2 Gb) revealed the prevalent presence of DIRSs followed by LINEs 8 , while salamander genomes are dominated by LTRs, and DIRSs never surpass 7% of the genomes 2,9 . These results reinforce the notion that repeated instances of extreme TE accumulation in amphibians do not reflect a failure to control a specific type of TE 8 .…”