# Small RNAs regulation and genomic harmony: insights into allopolyploid evolution in marsh orchids (Dactylorhiza)

## TL;DR

This study explores how small RNAs influence genome evolution in marsh orchids, revealing shared and unique patterns in polyploid species.

## Contribution

The study identifies convergent and divergent small RNA patterns in independently formed allopolyploids, linking them to genomic stability and evolution.

## Key findings

- Allopolyploids Dactylorhiza majalis and D. traunsteineri show overlapping small RNA patterns despite independent origins.
- TE-associated 24 nt small RNAs resemble the paternal genome, while shorter ones reflect the maternal genome.
- Older D. majalis has more small RNAs near regulatory genes, while younger D. traunsteineri shows non-additive patterns.

## Abstract

Hybridization and polyploidy are major drivers of plant diversification, often accompanied by shifts in gene expression and genome composition. Small RNAs (smRNAs) are thought to influence such genomic changes, particularly through their interactions with transposable elements (TEs).We quantified smRNAs in established sibling allopolyploids Dactylorhiza majalis and D. traunsteineri and their diploid progenitors to assess how independent allopolyploidization events shaped smRNA landscapes.Despite independent origins, the allotetraploids exhibited substantial overlap in smRNA composition, including transgressive accumulation of smRNAs near genes related to transcriptional regulation, cell division, and stress response. Consistently, TE‐associated 24 nt smRNAs more closely resembled the paternal and larger genome, while shorter smRNAs typically reflected the maternal and smaller genome. Nevertheless, distinct patterns were also evident: the older D. majalis showed greater accumulation of smRNAs near genes involved in transcriptional and translational regulation, while the younger D. traunsteineri displayed stronger non‐additive patterns, suggesting ongoing resolution of post‐polyploid meiotic and mitotic instability.Our results reveal both convergence and divergence in smRNA landscapes among independently formed allopolyploids. Our study highlights the central role of smRNAs in resolving genomic conflict, with possible implications for functional divergence and ecological innovation during polyploid evolution.

Hybridization and polyploidy are major drivers of plant diversification, often accompanied by shifts in gene expression and genome composition. Small RNAs (smRNAs) are thought to influence such genomic changes, particularly through their interactions with transposable elements (TEs).

We quantified smRNAs in established sibling allopolyploids Dactylorhiza majalis and D. traunsteineri and their diploid progenitors to assess how independent allopolyploidization events shaped smRNA landscapes.

Despite independent origins, the allotetraploids exhibited substantial overlap in smRNA composition, including transgressive accumulation of smRNAs near genes related to transcriptional regulation, cell division, and stress response. Consistently, TE‐associated 24 nt smRNAs more closely resembled the paternal and larger genome, while shorter smRNAs typically reflected the maternal and smaller genome. Nevertheless, distinct patterns were also evident: the older D. majalis showed greater accumulation of smRNAs near genes involved in transcriptional and translational regulation, while the younger D. traunsteineri displayed stronger non‐additive patterns, suggesting ongoing resolution of post‐polyploid meiotic and mitotic instability.

Our results reveal both convergence and divergence in smRNA landscapes among independently formed allopolyploids. Our study highlights the central role of smRNAs in resolving genomic conflict, with possible implications for functional divergence and ecological innovation during polyploid evolution.