Transcriptomic and Phytohormone Metabolomics Provide Insight into the Changes in Citrus limon Infected by Citrus yellow vein clearing virus

Background: Citrus yellow vein-clearing virus (CYVCV) is a Mandarivirus that causes great economic losses in lemon production. CYVCV infection is associated with obvious yellow vein-clearing disease symptoms and is directly regulated by plant hormone responses. Methods: To understand how lemon plants respond to CYVCV infection, we performed transcriptomic and phytohormone metabolomics. Results: A total of 936 differentially expressed genes were identified, and 773 were downregulated. Salicylic acid and auxin levels increased after CYVCV infection, and phytohormone regulatory systems were also explored. Jasmonic acid and auxin levels decreased after the CYVCV challenge, and jasmonic acid and auxin signaling pathway components were mostly downregulated. The differentially expressed genes (DEGs) involved in the immune response to viral infection, including those related to cell wall integrity, lectin, microtubules, and mildew resistance locus O (MLO), may also provide new candidate targets for CYVCV control. Conclusions: Our findings provide new insights into the molecular changes underlying the pathogenesis of CYVCV in lemon plants.