In Silico Virome Analysis of Chinese Narcissus Transcriptomes Reveals Diverse Virus Species and Genetic Diversity at Different Flower Development Stages

SIMPLE SUMMARY: In this study, we analyzed Chinese narcissus flowers at different stages of development to determine the presence of viruses. We identified seven viral species, including narcissus common latent virus (NCLV), narcissus mottling-associated virus (NMaV), and narcissus symptomless virus (NSV) from the genus Carlavirus. We also found contigs associated with cucumber mosaic virus (CMV) and three viruses from the genus Potyvirus: narcissus degeneration virus (NDV), narcissus late season yellow virus (NLSYV), and narcissus yellow stripe virus (NYSV). NCLV was the most abundant among these viruses, followed by NYSV and NMaV. The composition of viruses varied between white tepal plants and yellow tepal plants. White tepal plants harbored six viruses, whereas yellow tepal plants harbored seven viruses, including CMV. The number of viral reads increased as flowers developed in white tepal plants; however, the difference in yellow tepal plants was not statistically significant. NDV was the most common virus in the white tepal samples, whereas NDV and NYSV were prominent in the yellow tepal samples. The viruses showed distinct genetic groups based on phylogenetic analysis, and genetic diversity analysis revealed variations in sequence similarities and differences within each virus. This study provides valuable insights into the identification, abundance, composition, and genetic diversity of Chinese narcissus flowers at different developmental stages. ABSTRACT: Viromes of Chinese narcissus flowers were explored using transcriptome data from 20 samples collected at different flower development stages. Quality controlled raw data underwent de novo assembly, resulting in 5893 viral contigs that matched the seven virus species. The most abundant viruses were narcissus common latent virus (NCLV), narcissus yellow stripe virus (NYSV), and narcissus mottling-associated virus (NMaV). As flower development stages advanced, white tepal plants showed an increase in the proportion of viral reads, while the variation in viral proportion among yellow tepal plants was relatively small. Narcissus degeneration virus (NDV) dominated the white tepal samples, whereas NDV and NYSV prevailed in the yellow tepal samples. Potyviruses, particularly NDV, are the primary infectious viruses. De novo assembly generated viral contigs for five viruses, yielding complete genomes for NCLV, NDV, narcissus late season yellow virus (NLSYV), and NYSV. Phylogenetic analysis revealed genetic diversity, with distinct NCLV, NMaV, NDV, NLSYV, and NYSV groups. This study provides valuable insights into the viromes and genetic diversity of viruses in Chinese narcissus flowers.