In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data.
Viruses are ubiquitous and present in a wide range of settings, from living organisms to various environments. Although viruses are regarded as important pathogens in higher plants, viral populations in specific host plants have not yet been fully examined. This study revealed viral populations in grape berries obtained from a cultivar from a single vineyard using currently available grapevine transcriptomes. Eight viruses and two viroids were identified using 11 grapevine libraries. Virus-associated sequences in each transcriptome ranged from 0.2% (seed) to 8.8% (skin). The amount of viral RNAs and virus copy numbers was quantified, thus revealing the dominant virus or viroid in each individual library. In addition, five viral genomes were successfully assembled de novo using transcriptome data. Phylogenetic analyses revealed that the viruses and viroids might have originated from Europe, along with the host. Single nucleotide variation studies revealed the quasispecies of RNA viruses. Taken together, this study defines complex viral populations in three different grape tissues from a single vineyard.
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Yeonhwa
Y
Jo
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Hoseong
H
Choi
Department of Fruit Tree, Korea National College of Agriculture and Fisheries, Jeonju, 560-500, Republic of Korea.
Jin Kyong
JK
Cho
Virology Unit, Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wan-Ju, 565-852, Republic of Korea.
Ju-Yeon
JY
Yoon
Virology Unit, Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wan-Ju, 565-852, Republic of Korea.
Seung-Kook
SK
Choi
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Won Kyong
WK
Cho
D003198:Computer Simulation; D005060:Europe; D015723:Gene Library; D016679:Genome, Viral / Q000235:genetics; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D018515:Plant Leaves / Q000821:virology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012328:RNA Viruses / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D014772:Viroids / Q000235:genetics; D027843:Vitis / Q000821:virology*
D012367:RNA, Viral