Survey of viruses associated with the whitefly Bemisia tabaci in cucurbits in Georgia, United States

Whiteflies ( Bemisia tabaci ) are major agricultural pests causing over $100 million in losses to vegetable production annually through the transmission of plant viruses. Characterizing the virome of B. tabaci is critical for understanding vectoring potential and identifying candidate viral biocontrol agents. In this study, B. tabaci were collected from cucurbit crops in Tifton, Georgia, across two consecutive years, 2023 and 2024. Total RNA was extracted and ribodepleted, then sequenced with 150 bp paired-end reads on the Illumina NovaSeq 6000. Bioinformatics analyses included quality-assessing raw reads, which were trimmed prior to mapping to the B. tabaci reference genome (GCF_918797505.1) on the Alabama HPC, then mapping to a viral database (viral2019-03) using the Galaxy platform. After de novo transcriptome assembly using rnaviralSPAdes, the assembled contigs were screened for viral similarity using BLAST-based searches against the NCBI non-redundant nucleotide (nt) and non-redundant protein (nr) databases. Candidate viral contigs were evaluated by read mapping, coverage assessment, taxonomic assignment, and open reading frame prediction. The analysis identified contigs representing plant, bacteriophage, and insect-associated viruses. Near-complete cucurbit chlorotic yellows virus (CCYV) RNA1 and RNA2 sequences were assembled from both years, with higher abundance in 2024. A dicistrovirus-like sequence related to Cripavirus was also detected in both years and contained both major open reading frames. CCYV and the dicistrovirus-like sequence were the only viral targets with sufficient read support for genome assembly and molecular validation in both sampling years.