# Splicing regulation and intron evolution in the short-intron ciliate model of endosymbiosis Paramecium bursaria

## TL;DR

This study explores how splicing regulation and intron evolution help the ciliate Paramecium bursaria adapt during endosymbiosis with algae.

## Contribution

The research identifies splicing as a key mechanism in host adaptation during endosymbiosis and reveals evolutionary traits of short introns.

## Key findings

- Splicing, especially of 5′ proximal introns, enhances gene expression in symbiotic cells.
- 883 genes with differentially spliced introns are enriched in transmembrane transporters for nutrient exchange.
- Conserved introns show efficient splicing with lower GC content and uniform length.

## Abstract

The integration of symbionts into host cells during endosymbiosis significantly alters gene expression and cell physiology. Though alternative splicing facilitates cellular adaptation through rapid modulation of gene expression and protein isoform diversity, its regulatory role during endosymbiosis remains poorly understood. Paramecium bursaria, which harbors hundreds of Chlorella variabilis algae within its cytoplasm, offers a powerful model to study splicing during endosymbiosis, especially given its exceptionally short introns (median ∼24 nt). Using time-course RNA sequencing of symbiotic and aposymbiotic cells, we found that splicing, especially of 5′ proximal introns, enhances gene expression. Moreover, we identified 883 genes with differentially spliced introns, particularly enriched in transmembrane transporters essential for establishing nutrient exchange between a host cell and algal symbionts. Splicing regulation correlated with expression changes in conserved spliceosome components, implicating that these factors act as splicing enhancers or repressors during symbiosis. By exploring intron orthology across ciliates, we found that conserved introns exhibited more efficient splicing, characterized by lower GC content and uniform length, suggesting that intron evolution favors features that optimize expression. Our study reveals how splicing contributes to host adaptation during endosymbiosis and highlights the evolutionary dynamics of short introns in eukaryotes.

Graphical Abstract