DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions

Size evolution among gigantic genomes involves gain and loss of many gigabases of transposable elements (TEs), sequences that parasitize host genomes. Vertebrates suppress TEs using piRNA and KRAB-ZFP pathways. TEs and hosts coevolve in an arms race, where suppression strength reflects TE fitness costs. In enormous genomes, additional TE costs become miniscule. How, then, do TEs and host suppression invoke further addition of massive DNA amounts? We analyze TE proliferation histories, deletion rates, and community diversities in six salamander genomes (21.3 - 49.9 Gb), alongside gonadal expression of TEs and suppression pathways. We show that TE activity is higher in testes than ovaries, attributable to lower KRAB-ZFP suppression. Unexpectedly, genome size and expansion are uncorrelated with TE deletion rate, proliferation history, expression, and host suppression. Also, TE community diversity increases with genome size, contrasting theoretical predictions. We infer that TE-host antagon..., , # DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions

Dataset DOI: [10.5061/dryad.zpc866tkv](10.5061/dryad.zpc866tkv)

Our manuscript described differences in TE composition, TE diversity, TE proliferation history based on histograms of sequence divergence, and TE ectopic recombination-mediated deletion from the genomes of six salamander species with different genome sizes. In addition, we quantified expresion of TEs and piRNAs that target TEs, as well as genes in TE silencing pathways.

## Description of the data and file structure

The data we include here in this DRYAD submission are those that we used to generate the five figures in our manuscript. For each of the five figures, we include a folder that includes an excel spreadsheet with the relevant data, as well as the R code for producing the figure itself. When relevant, we also include tree files.

## Sharing/Access information

Genomic shotgun and transcriptome ...,