Comprehensive Virome Analysis of Commercial Lilies in South Korea by RT-PCR, High-Throughput Sequencing, and Phylogenetic Analyses

TL;DR

This study analyzed viruses in lilies from South Korea and found high infection rates, multiple virus co-infections, and identified new viral variants.

Contribution

The study provides the first comprehensive virome analysis of commercial lilies in South Korea using RT-PCR, HTS, and phylogenetic methods.

Findings

87% of lily samples were infected, with lily mottle virus and Plantago asiatica mosaic virus being the most prevalent.

Mixed infections were twice as common as single infections and caused more severe symptoms, especially in triple-virus combinations.

Phylogenetic analysis showed close relationships between Korean and Chinese isolates and host-related clustering in Plantago asiatica mosaic virus.

Abstract

Viral diseases pose a significant threat to lily (Lilium spp.) cultivation; however, large-scale assessments of virus prevalence and diversity in South Korea are limited. This study combined RT-PCR surveys, high-throughput sequencing (HTS), and analyses of 48 lily hybrid transcriptomes to characterize the lily virome. RT-PCR screening of 100 samples from 13 regions showed that 87% were infected, primarily with lily mottle virus (LMoV, 65%), Plantago asiatica mosaic virus (PlAMV, 34%), cucumber mosaic virus (CMV, 34%), and lily symptomless virus (LSV, 25%). Mixed infections were approximately twice as frequent as single infections and were associated with greater symptom severity, particularly in triple-virus combinations. High-throughput sequencing expanded detection to six viruses, including milk vetch dwarf virus (MDV) and lily virus B (LVB), the latter confirmed as a variant of strawberry latent ringspot virus (SLRSV). Near-complete genomes of several viruses were assembled and validated through RT-PCR. Transcriptome mining identified eight virus species across 26 cultivars; PlAMV was the most common, and viral loads varied significantly among hybrids. Phylogenetic analyses revealed close relationships between Korean and Chinese isolates and host-related clustering in PlAMV. These findings highlight the complexity of lily viromes in South Korea and provide essential resources for diagnostics, disease management, and biosecurity.

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