Metagenomics-based novel Caulimoviridae virus discovery and its development of identification markers in Lilium lancifolium thunb

Plant viruses cause considerable economic losses in the lily industry due to the emergence of diverse viral mutations and novel pathogens. Effective detection and identification of these viruses are critical for controlling their spread and mitigating infections. In this study, two novel Caulimoviridae viruses, namely Lancifolium Caulimovirus A (LCaA) and Lancifolium Caulimovirus B (LCaB), were identified for the first time in Lilium lancifolium Thunb. (tiger lily) through integrated metagenomic sequencing and Sanger sequencing. The complete genomes of LCaA and LCaB were determined to be 7,542 nt and 7,582 nt in length, respectively. Among the pooled tiger lily samples, seven LCaA isolates exhibited genome sequence identities ranging from 99.59 to 99.73%, while six LCaB isolates showed identities between 98.51% and 98.91%. Leveraging these isolates genomic variations, four sets of diagnostic markers were developed to distinguish the LCa viruses (LCaA and LCaB). Specific marker combinations were employed to identify LCa, LCaA, and LCaB strains. This study reports the discovery of two novel Caulimoviridae species and establishes a robust PCR-based methodology for their detection. The developed markers provide a valuable diagnostic tool for the early detection and management of LCa viruses in lily cultivation systems.