In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome
Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids t...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Jo, Yeonhwa [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2018 |
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| Schlagwörter: |
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| Anmerkung: |
© Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 |
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| Übergeordnetes Werk: |
Enthalten in: Journal of plant pathology - [Cham] : Springer International Publishing, 1997, 100(2018), 1 vom: 08. März, Seite 91-96 |
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| Übergeordnetes Werk: |
volume:100 ; year:2018 ; number:1 ; day:08 ; month:03 ; pages:91-96 |
| Links: |
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| DOI / URN: |
10.1007/s42161-018-0009-y |
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| Katalog-ID: |
SPR038428687 |
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| 100 | 1 | |a Jo, Yeonhwa |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome |
| 264 | 1 | |c 2018 | |
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| 500 | |a © Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 | ||
| 520 | |a Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world. | ||
| 650 | 4 | |a Genome |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Grapevine |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Transcriptome |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Virus |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Viroid |7 (dpeaa)DE-He213 | |
| 700 | 1 | |a Song, Myung-Kyu |4 aut | |
| 700 | 1 | |a Choi, Hoseong |4 aut | |
| 700 | 1 | |a Park, Jae-Seong |4 aut | |
| 700 | 1 | |a Lee, Jae-Wung |4 aut | |
| 700 | 1 | |a Cho, Won Kyong |4 aut | |
| 700 | 1 | |a Kim, Kook-Hyung |4 aut | |
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| 912 | |a GBV_ILN_2027 | ||
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| 912 | |a GBV_ILN_2044 | ||
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| 912 | |a GBV_ILN_2050 | ||
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| 912 | |a GBV_ILN_2057 | ||
| 912 | |a GBV_ILN_2059 | ||
| 912 | |a GBV_ILN_2061 | ||
| 912 | |a GBV_ILN_2064 | ||
| 912 | |a GBV_ILN_2065 | ||
| 912 | |a GBV_ILN_2068 | ||
| 912 | |a GBV_ILN_2088 | ||
| 912 | |a GBV_ILN_2093 | ||
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| 912 | |a GBV_ILN_4305 | ||
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| 912 | |a GBV_ILN_4307 | ||
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2018 |
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2018 |
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10.1007/s42161-018-0009-y doi (DE-627)SPR038428687 (SPR)s42161-018-0009-y-e DE-627 ger DE-627 rakwb eng Jo, Yeonhwa verfasserin aut In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world. Genome (dpeaa)DE-He213 Grapevine (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Virus (dpeaa)DE-He213 Viroid (dpeaa)DE-He213 Song, Myung-Kyu aut Choi, Hoseong aut Park, Jae-Seong aut Lee, Jae-Wung aut Cho, Won Kyong aut Kim, Kook-Hyung aut Enthalten in Journal of plant pathology [Cham] : Springer International Publishing, 1997 100(2018), 1 vom: 08. März, Seite 91-96 (DE-627)504102400 (DE-600)2212051-8 2239-7264 nnns volume:100 year:2018 number:1 day:08 month:03 pages:91-96 https://dx.doi.org/10.1007/s42161-018-0009-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_161 GBV_ILN_165 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_266 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_374 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_2946 GBV_ILN_2949 GBV_ILN_2951 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4346 GBV_ILN_4393 GBV_ILN_4700 AR 100 2018 1 08 03 91-96 |
| spelling |
10.1007/s42161-018-0009-y doi (DE-627)SPR038428687 (SPR)s42161-018-0009-y-e DE-627 ger DE-627 rakwb eng Jo, Yeonhwa verfasserin aut In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world. Genome (dpeaa)DE-He213 Grapevine (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Virus (dpeaa)DE-He213 Viroid (dpeaa)DE-He213 Song, Myung-Kyu aut Choi, Hoseong aut Park, Jae-Seong aut Lee, Jae-Wung aut Cho, Won Kyong aut Kim, Kook-Hyung aut Enthalten in Journal of plant pathology [Cham] : Springer International Publishing, 1997 100(2018), 1 vom: 08. März, Seite 91-96 (DE-627)504102400 (DE-600)2212051-8 2239-7264 nnns volume:100 year:2018 number:1 day:08 month:03 pages:91-96 https://dx.doi.org/10.1007/s42161-018-0009-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_161 GBV_ILN_165 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_266 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_374 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_2946 GBV_ILN_2949 GBV_ILN_2951 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4346 GBV_ILN_4393 GBV_ILN_4700 AR 100 2018 1 08 03 91-96 |
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10.1007/s42161-018-0009-y doi (DE-627)SPR038428687 (SPR)s42161-018-0009-y-e DE-627 ger DE-627 rakwb eng Jo, Yeonhwa verfasserin aut In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world. Genome (dpeaa)DE-He213 Grapevine (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Virus (dpeaa)DE-He213 Viroid (dpeaa)DE-He213 Song, Myung-Kyu aut Choi, Hoseong aut Park, Jae-Seong aut Lee, Jae-Wung aut Cho, Won Kyong aut Kim, Kook-Hyung aut Enthalten in Journal of plant pathology [Cham] : Springer International Publishing, 1997 100(2018), 1 vom: 08. März, Seite 91-96 (DE-627)504102400 (DE-600)2212051-8 2239-7264 nnns volume:100 year:2018 number:1 day:08 month:03 pages:91-96 https://dx.doi.org/10.1007/s42161-018-0009-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_161 GBV_ILN_165 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_266 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_374 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_2946 GBV_ILN_2949 GBV_ILN_2951 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4346 GBV_ILN_4393 GBV_ILN_4700 AR 100 2018 1 08 03 91-96 |
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10.1007/s42161-018-0009-y doi (DE-627)SPR038428687 (SPR)s42161-018-0009-y-e DE-627 ger DE-627 rakwb eng Jo, Yeonhwa verfasserin aut In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world. Genome (dpeaa)DE-He213 Grapevine (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Virus (dpeaa)DE-He213 Viroid (dpeaa)DE-He213 Song, Myung-Kyu aut Choi, Hoseong aut Park, Jae-Seong aut Lee, Jae-Wung aut Cho, Won Kyong aut Kim, Kook-Hyung aut Enthalten in Journal of plant pathology [Cham] : Springer International Publishing, 1997 100(2018), 1 vom: 08. März, Seite 91-96 (DE-627)504102400 (DE-600)2212051-8 2239-7264 nnns volume:100 year:2018 number:1 day:08 month:03 pages:91-96 https://dx.doi.org/10.1007/s42161-018-0009-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_161 GBV_ILN_165 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_266 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_374 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_2946 GBV_ILN_2949 GBV_ILN_2951 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4346 GBV_ILN_4393 GBV_ILN_4700 AR 100 2018 1 08 03 91-96 |
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10.1007/s42161-018-0009-y doi (DE-627)SPR038428687 (SPR)s42161-018-0009-y-e DE-627 ger DE-627 rakwb eng Jo, Yeonhwa verfasserin aut In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world. Genome (dpeaa)DE-He213 Grapevine (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Virus (dpeaa)DE-He213 Viroid (dpeaa)DE-He213 Song, Myung-Kyu aut Choi, Hoseong aut Park, Jae-Seong aut Lee, Jae-Wung aut Cho, Won Kyong aut Kim, Kook-Hyung aut Enthalten in Journal of plant pathology [Cham] : Springer International Publishing, 1997 100(2018), 1 vom: 08. März, Seite 91-96 (DE-627)504102400 (DE-600)2212051-8 2239-7264 nnns volume:100 year:2018 number:1 day:08 month:03 pages:91-96 https://dx.doi.org/10.1007/s42161-018-0009-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_161 GBV_ILN_165 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_266 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_374 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_2946 GBV_ILN_2949 GBV_ILN_2951 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4346 GBV_ILN_4393 GBV_ILN_4700 AR 100 2018 1 08 03 91-96 |
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Jo, Yeonhwa @@aut@@ Song, Myung-Kyu @@aut@@ Choi, Hoseong @@aut@@ Park, Jae-Seong @@aut@@ Lee, Jae-Wung @@aut@@ Cho, Won Kyong @@aut@@ Kim, Kook-Hyung @@aut@@ |
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Jo, Yeonhwa |
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Jo, Yeonhwa misc Genome misc Grapevine misc Transcriptome misc Virus misc Viroid In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome |
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In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome Genome (dpeaa)DE-He213 Grapevine (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Virus (dpeaa)DE-He213 Viroid (dpeaa)DE-He213 |
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in silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome |
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In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome |
| abstract |
Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world. © Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 |
| abstractGer |
Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world. © Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 |
| abstract_unstemmed |
Abstract Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world. © Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 |
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| title_short |
In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome |
| url |
https://dx.doi.org/10.1007/s42161-018-0009-y |
| remote_bool |
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| author2 |
Song, Myung-Kyu Choi, Hoseong Park, Jae-Seong Lee, Jae-Wung Cho, Won Kyong Kim, Kook-Hyung |
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Song, Myung-Kyu Choi, Hoseong Park, Jae-Seong Lee, Jae-Wung Cho, Won Kyong Kim, Kook-Hyung |
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| doi_str |
10.1007/s42161-018-0009-y |
| up_date |
2024-07-03T18:03:22.024Z |
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| score |
7.3974886 |