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RNA viromes of the oriental hybrid lily cultivar Sorbonne

Cited 6 time in Web of Science Cited 6 time in Scopus
Authors
Jo, Yeonhwa; Cho, Won Kyoung
Issue Date
2018-10-13
Publisher
BioMed Central
Citation
BMC Genomics, 19(1):748
Keywords
GenomeLilySorbonneTranscriptomeVirusVirome
Abstract
Background
The 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.

Results
Here, 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.

Conclusions
We 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.
ISSN
1471-2164
Language
English
URI
https://hdl.handle.net/10371/145161
DOI
https://doi.org/10.1186/s12864-018-5138-3
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College of Agriculture and Life Sciences (농업생명과학대학)Research Institute of Agriculture and Life Sciences (농업생명과학연구원)Journal Papers (저널논문_농업생명과학연구원)
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