Reanalysis of the tomato transcriptome revealed host responses to Southern tomato virus infection

Prior work reported that tomato plants infected with Southern tomato virus (STV) displayed increased height and higher fruit yield. Here, we aimed to re-examine that original dataset using an updated bioinformatics pipeline and the latest genomic resources to verify and extend those results. Raw single-end RNA-Seq reads were re-aligned to the current tomato reference genome (SL3.0) with Rsubread, and gene-level counts were obtained using featureCounts. Differential expression analysis was performed with DESeq2 under stringent thresholds (FDR < 0.05, |log 2 FC| ≥ 1, corresponding to a FC ≥ 2). No genes satisfied these criteria. In contrast to the earlier report, the host transcriptome remained largely unaltered by STV infection. Among the transcripts showing the largest effect sizes, the ethylene biosynthesis gene ACO1 (Solyc07g049530) showed a Wald log 2 FC of − 1.70 (shrunk − 1.47, adjusted P -value = 0.225) and the ethylene-responsive transcription factor ERF16 (Solyc12g009240) showed a Wald log 2 FC of − 1.25 (shrunk − 1.12, adjusted P -value = 0.083), but neither passed the pre-specified criterion of BH-adjusted P -value < 0.05 and |log 2 FC| ≥ 1.The same results held when the pipeline was run against the SL4.0 and SL6.0 tomato reference assemblies. Zero host genes satisfied BH-adjusted P -value < 0.05 and |log 2 FC| ≥ 1 under any reference. Our RNA-Seq reanalysis reveals that STV infection causes minimal changes in tomato leaf gene expression, most notably a subtle downregulation of ethylene-related genes, without broad transcriptomic reprogramming. These results temper prior claims of extensive transcriptomic effects and instead support the view that STV exerts a minor, possibly cultivar-dependent influence on its host. This study highlights the importance of updated reference genomes and rigorous statistical methods. Future investigations employing larger sample sizes or different developmental stages would be valuable.