RNA viromes of the oriental hybrid lily cultivar “Sorbonne”

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5138-3) contains supplementary material, which is available to authorized users.

Sweet potato viromes in eight different geographical regions in Korea and two different cultivars

“…Eight RNA viruses in this study possessed polyadenylate (poly(A)) tails (all except SPLCV and SPSMV). As shown in other previous studies 21,35 , virus genomes with poly(A) tails can be easily assembled. It is also not surprising that genomes of DNA viruses such as SPLCV can also be assembled from transcriptome data, as shown in our previous studies 26 .…”

“…Plant tissues and developmental stages are important factors for plant virome studies. Our previous studies demonstrated that viral RNA was enriched in grape fruits and lily flowers 24,35 . Of course, the optimal tissues for plant virome studies depend on the plant species.…”

A bushel of viruses: Identification of seventeen novel putative viruses by RNA-seq in six apple trees

“…What the frequency of viruses in the roots does highlight is the need to consider the entire host when studying plant viromes. Some virome studies have examined multiple tissues for their plant species of interest, either pooling samples or sequencing them separately [8,10,11,14]. Czotter et al [11] pooled extracts of shoot tips, young leaves, older leaves, tendrils and inflorescences of grapes for sequencing.…”

“…Roots and leaves were not always, but sometimes from the same plant [14]. Jo and Cho [8], in examining the lily virome, re-analyzed sequence data from previous studies that sequenced different tissue types. In examining different tissues, either separately or by pooling, these studies most likely provided a more complete picture of the viromes of the individual plants they examined than studies that sequenced only one tissue type.…”

“…Next generation sequencing (NGS) has enabled researchers in the last few years to assess the virome of a plant [5]. This technology has been applied to several crop species including peaches [6], lilies [7,8], barley [9], sweet pepper [10], grapevine [11,12], vanilla [13], and citrus [14]. While these studies detected known species, novel viruses were also identified [7,10,13,14].…”