VIRUSES
crossm Genome Sequence of Grapevine Virus T, a Novel Foveavirus Infecting Grapevine Yeonhwa Jo,a Myung-Kyu Song,b Hoseong Choi,a Jae-Seong Park,b Jae-Wung Lee,b Sen Lian,c Bong Choon Lee,d Won Kyong Choa Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Koreaa; Grape Research Institute, Chungbuk Agricultural Research and Extension Services, Okcheon, Republic of Koreab; College of Crop Protection and Agronomy, Qingdao Agricultural University, Qingdao, Shandong, Chinac; Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, Republic of Koread
Here, we report the genome sequence of grapevine virus T (GVT), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVT is 8,701 nucleotides in length and encodes five open reading frames. GVT is a putative member of the genus Foveavirus in the family Betaflexiviridae.
ABSTRACT
G
rapevines (Vitis vinifera) are commercially important fruit crops worldwide. Grapevines are cultivated for the production of wine or table grapes. A wide range of pathogens, including viruses, can threaten the quality and quantity of grapevine production. To date, more than 70 plant viruses infecting grapevines have been reported (1). With the advancement of next-generation sequencing (NGS) techniques, numerous plant viruses, including novel viruses, have been identified (2, 3). NGS techniques facilitate not only the identification of known and novel viruses but also the assembly of viral genomes (4, 5). For example, eight viruses and two viroids have been identified from the transcriptome data of a single grapevine cultivar (6). In the search for viruses and viroids infecting grapevine using transcriptome data, a novel virus has been identified from a transcriptome of the grapevine cultivar Teroldego (7). Detailed information for the plant sample and library preparation can be found in the previous study (7). To summarize, the total mRNA was extracted by pooling three individual grape berry samples from a single cultivar. The library, prepared using the Illumina TruSeq RNA kit was single-end (85 bp) sequenced using the Illumina GAIIx platform. We downloaded the raw data (2.5 Gb) for grapevine cultivar Teroldego deposited in the Sequence Read Archive (SRA) database (GenBank accession number ERR923264). The raw sequence reads were de novo assembled with Trinity version 2.0.6 with default parameters (8). A BLAST search of the assembled transcriptome of Teroldego was completed against the NCBI viral reference database (https:// www.ncbi.nlm.nih.gov/genome/viruses). From the transcriptome of Teroldego, we identified 86 contigs associated with viruses and viroids. Of them, two contigs were associated with a novel virus named grapevine virus T (GVT) isolate Cho (GenBank accession number MF095096). The genome of GVT is composed of positive single-stranded RNA with a length of 8,701 nucleotides (nt). The obtained GVT genome sequence is a nearly full-length genome containing sequences of the 5= and 3= untranslated regions (61 and 246 nt in length, respectively). The GVT encodes five open reading frames (ORFs), replicase (ORF1), three triple-gene blocks (TGB1, TGB2, and TGB3), and coat protein (ORF5). The BLASTp search against NCBI’s nonredundant protein database revealed that the five ORFs of GVT shared the following sequence similarities with grapevine rupestris stem pittingVolume 5 Issue 37 e00995-17
Received 9 August 2017 Accepted 14 August 2017 Published 14 September 2017 Citation Jo Y, Song M-K, Choi H, Park J-S, Lee J-W, Lian S, Lee BC, Cho WK. 2017. Genome sequence of grapevine virus T, a novel foveavirus infecting grapevine. Genome Announc 5:e00995-17. https://doi.org/10.1128/ genomeA.00995-17. Copyright © 2017 Jo et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Won Kyong Cho, [email protected].
genomea.asm.org 1
Jo et al.
associated virus (GRSPaV): 52% identity with replicase, 62% identity with TGB1, 53% identity with TGB2, 48% identity with TGB3, and 53% identity with coat protein. Based on the BLASTp results, we proposed that the identified GVT is a putative member of the genus Foveavirus in the family Betaflexiviridae. Taken together, we report a novel virus, GVT, which is a potential member of the genus Foveavirus, from the grapevine transcriptome. Accession number(s). The full-genome sequence of grapevine virus T isolate Cho has been submitted to GenBank under the accession number MF095096. ACKNOWLEDGMENTS This work was carried out with the support of the “Cooperative Research Program for Agriculture Science and Technology Development” (project no. PJ01186102) conducted by the Rural Development Administration, Republic of Korea. This work is dedicated to the memory of Tae Jin Cho (1946 –2015).
REFERENCES 1. Martelli GP. 2014. Directory of virus and virus-like diseases of the grapevine and their agents. J Plant Pathol 96:1–136. https://doi.org/10.4454/ JPP.V96I1SUP. 2. Barba M, Czosnek H, Hadidi A. 2014. Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6:106 –136. https://doi.org/10.3390/v6010106. 3. Al Rwahnih M, Daubert S, Golino D, Rowhani A. 2009. Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology 387:395– 401. https://doi.org/10.1016/j.virol.2009.02.028. 4. Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. 2016. Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus. BMC Genomics 17:579. https://doi.org/10.1186/s12864-016-2994-6. 5. Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. 2017. The pepper virome:
Volume 5 Issue 37 e00995-17
natural co-infection of diverse viruses and their quasispecies. BMC Genomics 18:453. https://doi.org/10.1186/s12864-017-3838-8. 6. Jo Y, Choi H, Cho JK, Yoon JY, Choi SK, Cho WK. 2015. In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data. Sci Rep 5:15841. https://doi.org/10.1038/srep15841. 7. Potenza E, Racchi ML, Sterck L, Coller E, Asquini E, Tosatto SC, Velasco R, Van de Peer Y, Cestaro A. 2015. Exploration of alternative splicing events in ten different grapevine cultivars. BMC Genomics 16:706. https://doi .org/10.1186/s12864-015-1922-5. 8. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. 2013. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nat Protoc 8:1494 –1512. https://doi.org/10.1038/nprot.2013.084.
genomea.asm.org 2
crossm Genome Sequence of Grapevine Virus T, a Novel Foveavirus Infecting Grapevine Yeonhwa Jo,a Myung-Kyu Song,b Hoseong Choi,a Jae-Seong Park,b Jae-Wung Lee,b Sen Lian,c Bong Choon Lee,d Won Kyong Choa Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Koreaa; Grape Research Institute, Chungbuk Agricultural Research and Extension Services, Okcheon, Republic of Koreab; College of Crop Protection and Agronomy, Qingdao Agricultural University, Qingdao, Shandong, Chinac; Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, Republic of Koread
Here, we report the genome sequence of grapevine virus T (GVT), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVT is 8,701 nucleotides in length and encodes five open reading frames. GVT is a putative member of the genus Foveavirus in the family Betaflexiviridae.
ABSTRACT
G
rapevines (Vitis vinifera) are commercially important fruit crops worldwide. Grapevines are cultivated for the production of wine or table grapes. A wide range of pathogens, including viruses, can threaten the quality and quantity of grapevine production. To date, more than 70 plant viruses infecting grapevines have been reported (1). With the advancement of next-generation sequencing (NGS) techniques, numerous plant viruses, including novel viruses, have been identified (2, 3). NGS techniques facilitate not only the identification of known and novel viruses but also the assembly of viral genomes (4, 5). For example, eight viruses and two viroids have been identified from the transcriptome data of a single grapevine cultivar (6). In the search for viruses and viroids infecting grapevine using transcriptome data, a novel virus has been identified from a transcriptome of the grapevine cultivar Teroldego (7). Detailed information for the plant sample and library preparation can be found in the previous study (7). To summarize, the total mRNA was extracted by pooling three individual grape berry samples from a single cultivar. The library, prepared using the Illumina TruSeq RNA kit was single-end (85 bp) sequenced using the Illumina GAIIx platform. We downloaded the raw data (2.5 Gb) for grapevine cultivar Teroldego deposited in the Sequence Read Archive (SRA) database (GenBank accession number ERR923264). The raw sequence reads were de novo assembled with Trinity version 2.0.6 with default parameters (8). A BLAST search of the assembled transcriptome of Teroldego was completed against the NCBI viral reference database (https:// www.ncbi.nlm.nih.gov/genome/viruses). From the transcriptome of Teroldego, we identified 86 contigs associated with viruses and viroids. Of them, two contigs were associated with a novel virus named grapevine virus T (GVT) isolate Cho (GenBank accession number MF095096). The genome of GVT is composed of positive single-stranded RNA with a length of 8,701 nucleotides (nt). The obtained GVT genome sequence is a nearly full-length genome containing sequences of the 5= and 3= untranslated regions (61 and 246 nt in length, respectively). The GVT encodes five open reading frames (ORFs), replicase (ORF1), three triple-gene blocks (TGB1, TGB2, and TGB3), and coat protein (ORF5). The BLASTp search against NCBI’s nonredundant protein database revealed that the five ORFs of GVT shared the following sequence similarities with grapevine rupestris stem pittingVolume 5 Issue 37 e00995-17
Received 9 August 2017 Accepted 14 August 2017 Published 14 September 2017 Citation Jo Y, Song M-K, Choi H, Park J-S, Lee J-W, Lian S, Lee BC, Cho WK. 2017. Genome sequence of grapevine virus T, a novel foveavirus infecting grapevine. Genome Announc 5:e00995-17. https://doi.org/10.1128/ genomeA.00995-17. Copyright © 2017 Jo et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Won Kyong Cho, [email protected].
genomea.asm.org 1
Jo et al.
associated virus (GRSPaV): 52% identity with replicase, 62% identity with TGB1, 53% identity with TGB2, 48% identity with TGB3, and 53% identity with coat protein. Based on the BLASTp results, we proposed that the identified GVT is a putative member of the genus Foveavirus in the family Betaflexiviridae. Taken together, we report a novel virus, GVT, which is a potential member of the genus Foveavirus, from the grapevine transcriptome. Accession number(s). The full-genome sequence of grapevine virus T isolate Cho has been submitted to GenBank under the accession number MF095096. ACKNOWLEDGMENTS This work was carried out with the support of the “Cooperative Research Program for Agriculture Science and Technology Development” (project no. PJ01186102) conducted by the Rural Development Administration, Republic of Korea. This work is dedicated to the memory of Tae Jin Cho (1946 –2015).
REFERENCES 1. Martelli GP. 2014. Directory of virus and virus-like diseases of the grapevine and their agents. J Plant Pathol 96:1–136. https://doi.org/10.4454/ JPP.V96I1SUP. 2. Barba M, Czosnek H, Hadidi A. 2014. Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6:106 –136. https://doi.org/10.3390/v6010106. 3. Al Rwahnih M, Daubert S, Golino D, Rowhani A. 2009. Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology 387:395– 401. https://doi.org/10.1016/j.virol.2009.02.028. 4. Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. 2016. Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus. BMC Genomics 17:579. https://doi.org/10.1186/s12864-016-2994-6. 5. Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. 2017. The pepper virome:
Volume 5 Issue 37 e00995-17
natural co-infection of diverse viruses and their quasispecies. BMC Genomics 18:453. https://doi.org/10.1186/s12864-017-3838-8. 6. Jo Y, Choi H, Cho JK, Yoon JY, Choi SK, Cho WK. 2015. In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data. Sci Rep 5:15841. https://doi.org/10.1038/srep15841. 7. Potenza E, Racchi ML, Sterck L, Coller E, Asquini E, Tosatto SC, Velasco R, Van de Peer Y, Cestaro A. 2015. Exploration of alternative splicing events in ten different grapevine cultivars. BMC Genomics 16:706. https://doi .org/10.1186/s12864-015-1922-5. 8. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. 2013. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nat Protoc 8:1494 –1512. https://doi.org/10.1038/nprot.2013.084.
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