Transcriptomic Validation of the Infectious Full-Length Clone of Citrus Tristeza Virus for Its Use as a Viral Vector

Citrus tristeza virus (CTV) infection can induce significant changes in growth patterns and cellular differentiation in citrus species, with severe strains causing visible symptoms and damage. In contrast, mild strains may result in asymptomatic infections. The mild strain CTV-T36 was used to build an infectious clone. However, the effects of the CTV-T36-based infectious clone on the foliar transcriptome of citrus plants were not investigated. We studied the impact of the infectious clone on the leaf transcriptome of Citrus macrophylla. High-quality RNA sequencing data were generated, yielding a total of 20,531 differentially expressed genes. Among these, only 218 genes were upregulated, and 383 genes were downregulated in plants inoculated with the CTV-T36-based infectious clone. Gene Ontology analysis highlighted significant enrichment in pathways related to oxidative stress response, redox regulation, and metal ion transport. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed key pathways affected by inoculation, including phenylpropanoid biosynthesis, plant hormone signal transduction, and glycerophospholipid metabolism. Significant changes in gene expression were observed in several categories, including photosynthesis, carbohydrate metabolism, cell division, and cell wall biosynthesis. A comprehensive analysis of stress-related genes revealed adaptive responses, including increased expression of systemic acquired resistance-related proteins. Transcription factors involved in stress responses, development, and regulatory pathways were also differentially expressed. Overall, these alterations are limited (2.93% of gene reads) and thus validate the use of the infectious clone as an expression vector and/or for virus-induced gene silencing, at least for concept proofing.