Reanalysis of the Tomato Transcriptome Revealed Host Responses to Southern Tomato Virus Infection

Abstract A previous study reported that Southern tomato virus (STV)-infected tomato plants were taller, had higher fruit yields. Here, it was aimed to reanalyze the same dataset with updated genomic resources and a bioinformatics pipeline to validate and expand upon those findings.The raw single-end RNA-Seq reads were remapped to the latest tomato reference genome (SL3.0) using Rsubread for alignment and featureCounts for gene quantification. Differential expression was assessed with DESeq2, applying rigorous filtering (FDR < 0.05, |log₂ fold-change| ≥ 1). The results revealed no genes meeting the criteria for differential expression (FDR < 0.05, fold-change ≥ 2). In contrast to the original report, and the host transcriptome remains largely unchanged by STV infection. The few transcripts with the largest expression differences included those in the ethylene biosynthesis and signaling pathway, which were slightly lower in STV-infected plants, mirroring the trends reported previously. Our reanalysis using a RNA-Seq workflow finds that STV infection causes at changes in tomato leaf gene expression, notably slight downregulation of ethylene-related genes, but no broad transcriptomic reprogramming. These results temper the earlier claims of significant transcriptomic effects of STV, instead supporting the notion that STV exerts a minimal and possibly cultivar-specific influence on the host. This study underlines the importance of updated genomic references and statistical approaches. Future studies with larger sample sizes or different developmental stages will be valuable.