Abstract
BackgroundThe lily is a perennial flowering plant belonging to the genus Lilium in the family Liliaceae. Most cultivated lily plants are propagated by bulbs. Therefore, numerous lily bulbs are frequently infected by diverse viruses causing viral diseases. To date, no study has examined the viromes of plants of one type with identical genetic backgrounds collected from different geographical regions.ResultsHere, we examined different viromes of the lily cultivar “Sorbonne” using 172 gigabytes of transcriptome data composed of 23 libraries from four different projects for the cultivar “Sorbonne.” We identified 396 virus-associated contigs from all but one library. We identified six different viruses, including Plantago asiatica mosaic virus (PlAMV), Cucumber mosaic virus (CMV), Lily symptomless virus (LSV), Tulip virus X (TVX), Lily mottle virus (LMoV), and Tobacco rattle virus (TRV). Of them, PlAMV was the most common virus infecting the lily. Scale and flower samples possessed a high number of virus-associated reads. We assembled 32 nearly complete genomes for the six identified viruses possessing the polyadenylate tails. Genomes of all six viruses were highly conserved in the lily cultivar “Sorbonne” based on mutation analysis. We identified defective RNAs from LSV, TVX, and PlAMV localized in the triple gene block region. Phylogenetic analyses showed that virus genomes are highly correlated with geographical regions and host plants.ConclusionsWe conducted comprehensive virome analyses of a single lily cultivar, “Sorbonne,” using transcriptome data. Our results shed light on an array of lily virome-associated topics, including virus identification, the dominant virus, virus accumulation in different plant tissues, virus genome assembly, virus mutation, identification of defective RNAs, and phylogenetic relationships of identified viruses. Taken together, we provide very useful methods and valuable results that can be applied in other virome-associated studies.
Highlights
The lily is a perennial flowering plant belonging to the genus Lilium in the family Liliaceae
We carried out an in silico study of different viromes for the lily cultivar “Sorbonne.” Taking advantage of transcriptome data followed by bioinformatics analyses, we addressed diverse questions associated with lily viromes in this study
Identification of viruses infecting lilies A total of 23 RNA-Sequencing (RNA-Seq) datasets derived from four different projects were associated with the lily cultivar “Sorbonne” (Fig. 1a)
Summary
The lily is a perennial flowering plant belonging to the genus Lilium in the family Liliaceae. Most cultivated lily plants are propagated by bulbs. Numerous lily bulbs are frequently infected by diverse viruses causing viral diseases. Lilies are tall perennial herbaceous flowering plants, which are members of the genus Lilium in the family Liliaceae [1]. In order to keep the genetic characteristics of lily flowers, lilies are usually clonally propagated using bulbs and scaling, which involves detaching scales from the bulb and planting individual scales to make new bulbs [4]. Due to the clonal propagation of lilies, most lily cultivars are frequently infected by diverse pathogenic microorganisms [5]. Viruses infecting lily species cause serious damage to the quality and quantity of lily production. Since the first report of the three major viruses infecting the lily in 1944 (i.e., Lily symptomless virus (LSV) in the genus Carlavirus, Lily mottle virus (LMoV) in the genus Potyvirus, and Cucumber mosaic virus (CMV) in the genus Cucumovirus [6]), more than 20 viruses infecting the lily have been reported [7]
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