# Dynamic Coordination of Alternative Splicing and Subgenome Expression Bias Underlies Rusty Root Symptom Response in Panax ginseng

## TL;DR

This study explores how alternative splicing and subgenome expression changes help Panax ginseng respond to rusty root symptoms, offering insights for disease-resistant crop breeding.

## Contribution

The study reveals dynamic coordination between alternative splicing and subgenome expression bias in ginseng's defense against rusty root symptoms.

## Key findings

- Alternative splicing frequency sharply increases in reddened lesion core tissue, with intron retention being predominant.
- 671 genes are under dual regulation by alternative splicing and transcription, involved in stress response and chromatin remodeling.
- The B subgenome disproportionately contributes stress-responsive transcripts in diseased ginseng tissue.

## Abstract

Ginseng rusty root symptoms (GRSs) compromise the yield and quality of Panax ginseng. While transcriptomic analyses have demonstrated extensive remodeling of stress signaling networks, the post-transcriptional defense circuitry remains obscure. We profiled alternative splicing (AS) in three phloem tissues, the healthy phloem (AG), the non-reddened phloem neighboring lesions (BG), and the reddened lesion core (CG), to delineate AS reprogramming during GRS progression. The frequency of AS was sharply elevated in CG, with intron retention predominating. Extensive gains and losses of splice events indicate large-scale rewiring of the splice network. Overlapping differentially alternative spliced genes (DAGs) identified in both CG vs AG and CG vs BG contrasts were significantly enriched for RNA–spliceosome assembly and stress–response pathways, revealing a conserved post-transcriptional response associated with lesion formation. Integrative analysis of differentially expressed genes uncovered 671 loci under dual regulation; functional classification categorized these genes in receptor-like kinase signaling and chromatin-remodeling modules, underscoring the synergy between AS and transcriptional control. Moreover, the B subgenome disproportionately contributed stress-responsive transcripts in diseased tissue, suggesting an adaptive, subgenome-biased strategy. These findings demonstrate that dynamic AS remodeling and subgenome expression bias jointly orchestrate ginseng defense against GRS and provide a framework for breeding disease-resilient crops.