Abstract
<title>Abstract</title> <p> Background. Citrus bark cracking viroid (CBCVd, <italic>Cocadviroid rimocitri</italic> ) causes severe stunting in hop ( <italic>Humulus lupulus</italic> L.), but the host response has rarely been resolved across disease stages. We asked how the hop transcriptome changes between early and late season and how this relates to the whole-plant phenotype. Results. In a 2 × 2 factorial RNA-seq experiment (CBCVd-infected vs. healthy control × two post-dormancy timepoints, sampled in spring [May, 18 months post-inoculation] and August [21 months]; 16 libraries), with differential expression cross-validated against a second hop genome and validated by RT-qPCR and Sanger sequencing, the response was broader in May (169 differentially expressed genes, DEGs) than in August (42 DEGs), although biomass loss was far greater at the later timepoint; only 11 genes responded at both timepoints, with two high-affinity nitrate-transporter (NRT2.5-like) loci and a dehydrin (DHN1) as the persistent core. Viroid titre was high at both timepoints. At the whole-plant level, infected plants showed a season-wide leaf-chlorophyll deficit and near-zero biomass accumulation, converging with the transcriptome. GSEA identified coordinated suppression of photosynthesis and chloroplast function together with nitrate assimilation as the dominant signature at both timepoints, alongside repressed starch, sucrose and ascorbate metabolism. Cytosolic ribosome and translation programmes were suppressed in May but rebounded by August, pointing to a temporal switch even as photosynthetic and nitrogen deficits persisted. Conclusions. Our data suggest that at the two analysed timepoints the CBCVd-associated stunting is driven by an early, coordinated loss of carbon- and nitrogen-acquiring capacity rather than the immune-signalling-dominated response reported in other viroid studies. The dysregulation starts in spring and consolidates into irreversible biomass loss. The two NRT2.5-like loci are the most robust molecular correlate and a candidate early marker, so monitoring and intervention may be most effective in the pre-symptomatic spring window. </p>