High-throughput virome profiling reveals squash vein yellowing virus in bottle gourd and cucumber in India

High-throughput sequencing (HTS) was employed to characterize the virome associated with yellowing disease in bottle gourd (Lagenaria siceraria) from Varanasi, India, after conventional RT-PCR assays for known yellowing-associated viruses yielded negative results. HTS analysis of symptomatic samples revealed the presence of three viruses: squash vein yellowing virus (SqVYV; genus Ipomovirus), cucumber green mottle mosaic virus (CGMMV; genus Tobamovirus), and tomato leaf curl New Delhi virus (ToLCNDV; genus Begomovirus). The coding-complete genome of CGMMV and the complete DNA-A and DNA-B components of ToLCNDV were recovered, whereas SqVYV was initially identified as partial contigs. The full-length genome of SqVYV (~ 9.8 kb) was subsequently recovered from bottle gourd through overlapping RT-PCR amplification. Based on this information, cucumber samples collected from adjacent fields exhibiting similar symptoms were also analysed, and the full-length SqVYV genome was subsequently recovered. The characterized SqVYV isolates shared 98.5-98.8% nucleotide identity and clustered within the Asian lineage. The CGMMV isolate exhibited > 97.6% nucleotide identity with global isolates but was genetically distinct from previously reported Indian isolates. Similarly, the ToLCNDV isolate showed high nucleotide identity with Indian cucurbit-infecting isolates, confirming its close genetic relatedness. This study provides the first evidence of SqVYV infecting bottle gourd and cucumber in India and demonstrates the occurrence of mixed infections involving RNA and DNA viruses in cucurbits. These findings highlight the utility of HTS in uncovering complex viral associations and enhancing our understanding of cucurbit virus epidemiology.

The online version contains supplementary material available at 10.1007/s13205-026-04876-y.