Cross-Kingdom Multi-Omics Harmonization Uncovers Coordinated Host Defense and Vector Small RNA Regulatory Networks in Begomovirus Transmission

Begomoviruses present severe threats to global crop production through complex vector-mediated transmission by the whitefly Bemisia tabaci to host plants such as tomato (Solanum lycopersicum). Unraveling the molecular dialogue between host immune activation and vector non-coding RNA networks is essential for identifying key drivers of virus persistence and transmission. Public host transcriptomic (GSE309527) and vector small RNA (sRNA) sequencing datasets (GSE111343) were processed through a multi-omics harmonization and signal calibration pipeline. Differential expression analysis was performed using empirical Bayes moderated linear models, followed by non-parametric Spearman rank correlation modeling ({rho}) to infer cross-kingdom co-expression dynamics and pathway enrichment profiling across host and vector bio-systems. Harmonized principal component analysis showed clear separation by infection status across host plant and vector cohorts. Differential expression analysis identified 138 significantly altered host genes (69 upregulated, 69 downregulated) and 130 differentially expressed vector sRNAs (65 upregulated, 65 downregulated). Host responses were dominated by significant upregulation of gene-silencing machinery, including Suppressor of Gene Silencing 3 (SGS3; log2 FC = 3.67, q = 7.47 x 10-5), and pathway enrichment in Jasmonate defense (q = 0.0004) and RNA Interference & Silencing (q = 0.0001). Vector sRNAs exhibited targeted dynamic alterations, with pathway enrichment in Salivary Gland Secretion ($q = 0.0030) and Gut Endosymbiont Response (q = 0.0210). Cross-kingdom correlation modeling revealed two distinct, highly anticorrelated regulatory modules (mean |{rho}| = 0.76). Host SGS3 expression strongly correlated with vector sRNA VEC_0080 ({rho} = 0.9762) and virus-derived siRNA Bt-vsiRNA-01 ({rho} = 0.7619). These findings demonstrate a tightly synchronized tripartite molecular crosstalk between host antiviral immunity, viral siRNA accumulation, and vector small RNA remodeling. These cross-kingdom regulatory modules highlight promising targets for dual-action RNA interference strategies aimed at controlling Begomovirus transmission.