Padilla, K. A. | bioRxiv Science

bioRxiv2025

Host-Specific Adaptations and Global Transmission Potential of a Mexican ToBRFV Isolate: Insights from Genomic Analysis

The tomato brown rugose fruit virus (ToBRFV) poses a severe global threat to tomato and pepper production due to its high transmissibility and genetic adaptability. This study provides an in-depth characterization of a Mexican ToBRFV isolate, integrating genomic variability analysis, host-specific investigations, and seed transmission studies to better understand the viruss adaptability and dissemination pathways. Phylogenetic analysis places this Mexican isolate in close genetic proximity to strains from Israel and China, suggesting cross-regional transmission potentially facilitated by agricultural trade. Genomic comparison with 100 ToBRFV isolates revealed a notable balance between genomic stability and host-specific adaptations, particularly within the 126-kDa replicase domain proteins critical for viral replication. Specific single nucleotide variants (SNVs) were identified in these regions, exhibiting host-dependent patterns; Solanum lycopersicum (tomato) isolates maintained consistent profiles, whereas isolates from Capsicum annuum (pepper) and Citrullus lanatus (watermelon) displayed unique substitutions. These variations suggest distinct selection pressures across hosts, potentially optimizing viral replication and survival in specific plant environments. Experimental bioassays confirmed that the Mexican isolate could infect additional species, including Physalis ixocarpa, and Solanum melongena, thereby expanding the known host range of ToBRFV. Seed transmission studies conducted on N. rustica revealed a 30% reduction in germination rates for infected seeds compared to healthy controls, highlighting the viruss impact on seed viability and underscoring the necessity of stringent biosecurity protocols. This comprehensive analysis enhances our understanding of the Mexican ToBRFV isolate genetic diversity, host specificity, and transmission dynamics.

microbiology↗

bioRxiv2022

An integrative approach: using transcriptomic data and network analysis of transcriptional reprogramming in tomato response to PSTVd variants

Viroids are minimal pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global molecular mechanisms of host response, we implemented an omics approach to identify master transcription regulators (MTRs) and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Overall, our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling regulation and hormone-related processes. Strikingly, a member of the bHLH-TF family have a potential specific role as a microprotein involved in the post-translational regulation of hormone signaling events. For the severe variant, ERF-MTRs are characteristic, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.

systems biology↗