Transposable element and host silencing activity in gigantic genomes

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Transposable elements (TEs) contribute to genome size variation through an evolutionary arms race with host silencing mechanisms.
• Extremely large animal genomes (>10 Gb) present unique questions about the efficacy of TE silencing pathways.

Purpose of the Study:

• To investigate TE silencing mechanisms, specifically the piRNA pathway and KRAB-ZFP transcriptional repression, in the male and female gonads of *Ranodon sibiricus*, a salamander with a ~21 Gb genome.
• To correlate TE silencing pathway gene expression with genome size across 15 vertebrate species.

Main Methods:

• Quantification of genomic TE diversity, TE expression, and small RNA expression in *Ranodon sibiricus* gonads.
• Analysis of TE silencing pathway gene expression in *R. sibiricus* and 14 other vertebrates with varying genome sizes.

Main Results:

• A significant relationship was observed between piRNA expression and their targeted TEs in both ovaries and testes, indicating effective piRNA-mediated silencing.
• No association was found between TE silencing pathway gene expression and genome size across the studied vertebrates.
• The gigantic *R. sibiricus* genome harbors at least 19 active TE superfamilies, all targeted by the piRNA pathway proportionally to their expression levels.
• Male gonads (testes) exhibited higher TE expression than female gonads (ovaries).

Conclusions:

• The piRNA pathway effectively silences numerous active transposable elements in the large genome of *Ranodon sibiricus*, despite extensive TE accumulation.
• The absence of correlation between silencing pathway gene expression and genome size suggests that the host-TE dynamic, rather than pathway capacity, influences TE load in large genomes.
• Testes may play a larger role in the accumulation of TEs in the *R. sibiricus* genome.