Cold plasma-induced transcriptomic reprogramming and alternative splicing in tomato plants infected with ToBRFV

Abstract

Cold atmospheric plasma (CAP), specifically cold air glow discharge plasma (CAGDP), offers a novel approach to enhancing plant defense against viral infections. This study investigates the effects of CAGDP on alternative splicing (AS) and transcriptome-wide gene expression in tomato seedlings infected with Tomato brown rugose fruit virus (ToBRFV). Using high-throughput RNA sequencing and bioinformatics analyses via CLC Genomics Workbench, custom Python scripts, and functional enrichment tools including STRING database and KEGG REST API, we identified significant AS changes, predominantly exon skipping and intron retention, in chromosomes associated with disease resistance. These splicing alterations were linked to key biological processes such as metabolic pathways, catalytic activity, and hormone signaling. Moreover, integration of miRNA–mRNA networks predicted by psRNATarget and visualized in Cytoscape revealed a complex regulatory system involving both transcriptional and post-transcriptional mechanisms. The identification of 19 differentially expressed AS genes highlights the coordinated reprogramming induced by CAGDP to activate antiviral defenses. These findings highlight cold plasma technology as a promising, eco-friendly tool to reprogram plant molecular pathways and enhance resistance to viral pathogens.