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

In Saudi Arabia, cucurbit crops such as zucchini (<i>Cucurbita pepo</i>) and snake gourd (<i>Trichosanthes cucumerina</i>) 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.