High-Throughput Sequencing Reveals Regional Diversification of Cucurbit-Infecting Begomoviruses in Eastern Saudi Arabia

In Saudi Arabia, cucurbit crops such as zucchini (Cucurbita pepo) and snake gourd (Trichosanthes cucumerina) are major vegetables and key dietary components, yet their associated viral threats remain poorly understood. We surveyed symptomatic cucurbit samples from greenhouses and open fields in the Al-Ahsa and Qatif regions. The detection methods employed included PCR, RCA, and Illumina NGS. Based on nucleotide sequence comparisons and maximum-likelihood phylogenetic analysis, we identified three viruses, i.e., TYLCV, WmCSV, and ToLCPalV, present as both single and mixed infections. Sequence analyses revealed a novel strain, TYLCV-Hasa, representing a distinct lineage of TYLCV. Analysis revealed that recombination occurred solely in the DNA-A components of the identified viruses, while DNA-B segments showed no evidence of recombination. Notably, no DNA satellites were detected, suggesting cucurbits may act as independent reservoirs of begomovirus diversity. These results provide a comprehensive genomic insight into cucurbit-infecting begomoviruses in Eastern Saudi Arabia. The discovery of TYLCV-Hasa and evidence of recombination raise concerns about the emergence of novel viral variants that could pose risks to cucurbit cultivation. The results establish a foundation for advanced molecular surveillance and breeding strategies, contributing to improved food security and supporting Saudi Arabia’s Vision 2030 goals for sustainable agriculture.