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 antagonism in
gigantic genomes produces stochastic TE accumulation, reflecting noisy
intermolecular interactions in huge genomes and cells.