Metatranscriptome analysis and reverse transcription polymerase chain reaction diagnostics were conducted to investigate viral disease in 75 Narcissus samples, resulting in the detection of snowdrop virus Y (SVY). The complete genome sequence of the SVY isolate SA66 was 10,560 nt in length, and sequence analysis revealed a typical genome structure for Potyvirus. Electron microscopy revealed filamentous rod particles approximately 800 nm long in the infected samples. In the bioassay involving 19 test plants, no SVY infection was confirmed. The coat protein sequences of 10 SVY isolates from various samples were determined, showing nucleotide identities of 99.3-99.8% and amino acid identities of 98.9-99.6% when compared with three previously reported isolates. The complete genome sequence shared 99.6% nucleotide identity and 99.7% amino acid identity with the reported isolate. SVY was detected in 10 of the collected samples, specifically showing partial detection in all four cultivars from the Sinan region, while it was not detected in the other three regions. This study is the first report of SVY in Korea and is expected to contribute to the quarantine of Narcissus bulbs and to the production of virus-free bulbs.

High-throughput RNA sequencing reveals plant viromes, but library preparation methods may bias viral detection. Here, we compared rRNA-depleted total RNA-seq and poly(A)-selected mRNA-seq using field-collected pepper leaves (Anseong and Jincheon) and garlic cloves (Hoengseong) from Korean commercial fields. rRNA-depleted total RNA-seq consistently recovered more viruses, longer contigs, and complete multipartite DNA virus genomes (e.g., milk vetch dwarf virus components, tomato spotted wilt virus segments), while mRNA-seq was dominated by highly expressed polyadenylated viruses like broad bean wilt virus 2. In Jincheon pepper, mRNA-seq missed hot pepper endornavirus, pepper cryptic virus 2, and multiple milk vetch dwarf virus segments revealed by total RNA-seq. Garlic libraries showed similar patterns, with total RNA-seq additionally detecting low-titer RNA viruses likely representing contamination. rRNA-depleted total RNA-seq provides a more complete, less biased view of plant viromes and is recommended for comprehensive virus discovery and genome reconstruction, while mRNA-seq remains useful for polyadenylated virus quantification and host gene expression analysis alongside virome profiling.

Adzuki bean (Vigna angularis), a major grain legume in Asia, is susceptible to infection by cucumber mosaic virus (CMV), which threatens crop productivity. Here, we characterized the CMV-Pa3 isolate from adzuki bean and investigated the role of specific amino acid residues in the viral 2a protein influencing systemic infection of legumes. Phylogenetic analysis demonstrated that CMV-Pa3 is genetically distinct from other legume-infecting isolates. Inoculation assays revealed that CMV-Pa3 causes systemic infection in adzuki bean, cowpea, soybean, and pea, whereas the control isolate CMV-Rs1 is restricted to inducing local necrotic lesions in cowpea and adzuki bean. Site-directed mutagenesis targeted two conserved amino acid positions (631 and 641) in the 2a protein of CMV-Rs1. Functional analysis showed that residue 631 (Tyr) facilitates systemic infection across all tested legumes, while alteration at position 641 (Ser) alone enables systemic infection in cowpea and pea. These findings identify amino acid determinants in the CMV 2a protein critical for overcoming host restrictions and mediating systemic infection in various leguminous species. This work offers new insights into the molecular mechanisms underlying CMV pathogenicity and host specificity.

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.