1 |
Adams, I. P., Glover, R. H., Monger, W. A., Mumford, R., Jackeviciene, E., Navalinskiene, M., Samuitiene, M. and Boonham, N. 2009. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol. Plant Pathol. 10:537-545.
DOI
|
2 |
Al Rwahnih, M., Daubert, S., Urbez-Torres, J. R., Cordero, F. and Rowhani, A. 2011. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Arch. Virol. 156:397-403.
DOI
|
3 |
Card, S. D., Pearson, M. N. and Clover, G. R. G. 2007. Plant pathogens transmitted by pollen. Australas. Plant Pathol. 36:455-461.
DOI
|
4 |
Czotter, N., Molnar, J., Szabo, E., Demian, E., Kontra, L., Baksa, I., Szittya, G., Kocsis, L., Deak, T., Bisztray, G., Tusnady, G. E., Burgyan, J. and Varallyay, E. 2018. NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards. Front. Microbiol. 9:122.
DOI
|
5 |
Grisoni, M., Marais, A., Filloux, D., Saison, A., Faure, C., Julian, C., Theil, S., Contreras, S., Teycheney, P.-Y., Roumagnac, P. and Candresse, T. 2017. Two novel alphaflexiviridae members revealed by deep sequencing of the vanilla (Orchidaceae) virome. Arch. Virol. 162:3855-3861.
DOI
|
6 |
Hadidi, A., Flores, R., Candresse, T. and Barba, M. 2016. Next-generation sequencing and genome editing in plant virology. Front. Microbiol. 7:1325.
DOI
|
7 |
Hull, R. 2002. Transmission 2: Mechanical, seed, pollen and epidemiology. In: Mathew's plant virology, ed. by R. Hull, pp. 533-581. Academic Press, New York, USA.
|
8 |
Jakovljevic, V., Otten, P., Berwarth, C. and Jelkmann, W. 2017. Analysis of the apple rubbery wood disease by next generation sequencing of total RNA. Eur. J. Plant Pathol. 148:637-646.
DOI
|
9 |
Jo, Y. and Cho, W. K. 2018. RNA viromes of the oriental hybrid lily cultivar "Sorbonne". BMC Genomics 19:748.
DOI
|
10 |
Jo, Y., Choi, H., Kim, S.-M., Kim, S.-L., Lee, B. C. and Cho, W. K. 2017. The pepper virome: natural co-infection of diverse viruses and their quasispecies. BMC Genomics 18:453.
DOI
|
11 |
Hull, R., 2013. Plant virology. Academic Press, San Diego, CA, USA. 1118 pp.
|
12 |
Kim, N.-Y., Lee, H-.J., Kim, H.-S., Lee, S.-H., Moon, J.-S. and Jeong, R.-D. 2021. Identification of plant viruses infecting pear using RNA sequencing. Plant Pathol. J. 37:258-267.
DOI
|
13 |
Akinyemi, I. A., Wang, F., Zhou, B., Qi, S. and Wu, Q. 2016. Ecogenomic survey of plant viruses infecting tobacco by next generation sequencing. Virol. J. 13:181.
DOI
|
14 |
Isogai, M., Shimoda, R., Nishimura, H. and Yaegashi, H. 2022. Pollen grains infected with apple stem grooving virus serve as a vector for horizontal transmission of the virus. J. Gen. Plant Pathol. 88:81-87.
DOI
|
15 |
Al Rwahnih, M., Daubert, S., Golino, D. and 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.
DOI
|
16 |
Blouin, A. G., Pearson, M. N., Chavan, R. R., Woo, E. N. Y., Lebas, B. S. M., Veerakone, S., Ratti, C., Biccheri, R., Mac-Diarmid, R. M. and Cohen, D. 2013. Viruses of kiwifruit (Actinidia species). J. Plant Pathol. 95:221-235.
|
17 |
Desvignes, J. C. 1985. Peach latent mosaic and its relation to peach mosaic and peach yellow mosaic virus diseases. Acta Hortic. 193:51-58.
DOI
|
18 |
Hernandez, C. and Flores, R. 1992. Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures. Proc. Natl. Acad. Sci. U. S. A. 89:3711-3715.
DOI
|
19 |
Osman, F., Hodzic, E., Kwon, S.-J., Wang, J. and Vidalakis, G. 2015. Development and validation of a multiplex reverse transcription quantitative PCR (RT-qPCR) assay for the rapid detection of citrus tristeza virus, citrus psorosis virus, and citrus leaf blotch virus. J. Virol. Methods 220:64-75.
DOI
|
20 |
Massart, S., Olmos, A., Jijakli, H. and Candresse, T. 2014. Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus Res. 188:90-96.
DOI
|
21 |
Jonghe, K. D., Haegeman, A., Foucart, Y. and Maes, M. 2018. The use of high-throughput sequencing for the study and diagnosis of plant viruses and viroids in pollen. Methods Mol. Biol. 17446:131-149.
|
22 |
Jo, Y., Bae, J.-Y., Kim, S.-M., Choi, H., Lee, B. C. and Cho, W. K. 2018a. Barley RNA viromes in six different geographical regions in Korea. Sci. Rep. 81:13237.
|
23 |
Jo, Y., Choi, H., Lian, S., Cho, J. K., Chu, H. and Cho, W. K. 2020. Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing. PeerJ 8:e9588.
DOI
|
24 |
Jo, Y., Song, M.-K., Choi, H., Park, J.-S., Lee, J.-W., Cho, W. K. and Kim, K.-H. 2018c. In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome. J. Plant Pathol. 100:91-96.
DOI
|
25 |
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P. and Drummond, A. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647-1649.
DOI
|
26 |
Kim, M.-K., Kwak, H.-R., Lee, S.-H., Kim, J.-S., Kim, K.-H., Cha, B. and Choi, H.-S. 2011. Characteristics of cucumber mosaic virus isolated from Zea mays in Korea. Plant Pathol J. 27:372-377.
DOI
|
27 |
Kim, N.-K., Lee, H.-J., Kim, S.-M. and Jeong, R.-D. 2022. Identification of viruses infecting oats in Korea by metatranscriptomics. Plants 11:256.
DOI
|
28 |
Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I. and Simon, R. 2009. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology 388:1-7.
DOI
|
29 |
Martin, R. R., Constable, F. and Tzanetakis, I. E. 2016. Quarantine regulations and the impact of modern detection methods. Annu. Rev. Phytopathol. 54:189-205.
DOI
|
30 |
Maliogka, V. I., Minafra, A., Saldarelli, P., Ruiz-Garcia, A. B., Glasa, M., Katis, N. and Olmos, A. 2018. Recent advances on detection and characterization of fruit tree viruses using high-throughput sequencing technologies. Viruses 10:436.
DOI
|
31 |
Malandraki, I., Beris, D., Isaioglou, I., Olmos, A., Varveri, C. and Vassilakos, N. 2017. Simultaneous detection of three Pome fruit tree viruses by one-step multiplex quantitative RT-PCR. PLoS ONE 12:e0180877.
DOI
|
32 |
Li, Y., Jia, A., Qiao, Y., Xiang, J., Zhang, Y. and Wang, W. 2018. Virome analysis of lily plants reveals a new potyvirus. Arch. Virol. 163:1079-1082.
DOI
|
33 |
Lopez, M. M., Bertolini, E., Olmos, A., Caruso, P., Gorris, M. T., Llop, P., Penyalver, R. and Cambra, M. 2003. Innovative tools for detection of plant pathogenic viruses and bacteria. Int. Microbiol. 64:233-243.
|
34 |
Lu, Y., Yao, B., Wang, G. and Hong, N. 2018. The detection of ACLSV and ASPV in pear plants by RT-LAMP assays. J. Virol. Methods 252:80-85.
DOI
|
35 |
Osaki, H., Yamaguchi, M., Sato, Y., Tomita, Y., Kawai, Y., Miyamoto, Y. and Ohtsu, Y. 1999. Peach latent mosaic viroid isolated from stone fruits in Japan. Ann. Phytopathol. Soc. Jpn. 65:3-8.
DOI
|
36 |
Matsumura, E. E., Coletta-Filho, H. D., Nouri, S., Falk, B. W., Nerva, L., Oliveira, T. S., Dorta, S. O. and Machado, M. A. 2017. Deep sequencing analysis of RNAs from citrus plants grown in a citrus sudden death-affected area reveals diverse known and putative novel viruses. Viruses 9:92.
DOI
|
37 |
Huang, B., Jennison, A., Whiley, D., McMahon, J., Hewitson, G., Graham, R., De Jong, A. and Warrilow, D. 2019. Illumina sequencing of clinical samples for virus detection in a public health laboratory. Sci. Rep. 9:5409.
DOI
|
38 |
Morgulis, A., Coulouris, G., Raytselis, Y., Madden, T. L., Agarwala, R. and Schaffer, A. A. 2008. Database indexing for production MegaBLAST searches. Bioinformatics 24:1757-1764.
DOI
|
39 |
Massart, S., Candresse, T., Gil, J., Lacomme, C., Predajna, L., Ravnikar, M., Reynard, J.-S., Rumbou, A., Saldarelli, P., Skoric, D., Vainio, E. J., Valkonen, J. P. T., Vanderschuren, H., Varveri, C. and Wetzel, T. 2017. A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologies. Front. Microbiol. 8:45.
|
40 |
Mink, G. I. 1993. Pollen and seed-transmitted viruses and viroids. Annu. Rev. Phytopathol. 31:375-402.
DOI
|
41 |
Radford, A. D., Chapman, D., Dixon, L., Chantrey, J., Darby, A. C. and Hall, N. 2012. Application of next-generation sequencing technologies in virology. J. Gen. Virol. 93:1853-1868.
DOI
|
42 |
Roossinck, M. J., Martin, D. P. and Roumagnac, P. 2015. Plant virus metagenomics: advances in virus discovery. Phytopathology 105:716-727.
DOI
|
43 |
Nabi, S. U., Baranwal, V. K., Rao, G. P., Mansoor, S., Vladulescu, C., Raja, W. H., Jan, B. L. and Alansi, S. 2022. High-throughput RNA sequencing of mosaic infected and non-infected apple (Malus × domestica Borkh.) cultivars: from detection to the reconstruction of whole genome of viruses and viroid. Plants 11:675.
DOI
|
44 |
Qian, Y., Xu, Y., Zhou, Q. and Zhou, X. 2014. Application of next-generation sequencing technology for plant virus identification. Sci. Sin. Vitae 44:351-363.
DOI
|
45 |
Rivarez, M. P. S., Vucurovic, A., Mehle, N., Ravnikar, M. and Kutnjak, D. 2021. Global advances in tomato virome research: current status and the impact of high-throughput sequencing. Front. Microbiol. 12:671925.
DOI
|
46 |
Shamloul, A. M., Minafra, A., Hadidi, A., Waterworth, H. E., Giunchedi, L. and Allam, E. K. 1994. Peach latent mosaic viroid: nucleotide sequence of an Italian isolate, sensitive detection using RT-PCR and geographic distribution. Acta Hortic. 386:522-530.
DOI
|
47 |
Shim, H., Min, Y., Hong, S., Kwon, M., Kim, D., Kim, H., Choi, Y., Lee, S. and Yang, J. 2004. Nucleotide sequences of a Korean isolate of apple stem grooving virus associated with black necrotic leaf spot disease on pear (Pyrus pyrifolia). Mol. Cells 18:192-199.
|
48 |
Thompson, J. D., Gibson, T. J. and Higgins, D. G. 2003. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinformatics 2:2.3.1-2.3.22.
|
49 |
Torrance, L. and Jones, R. A. C. 1981. Recent developments in serological methods suited for use in routine testing for plant viruses. Plant Pathol. 30:1-24.
DOI
|
50 |
Shaffer, C., Gress, J. C. and Tzanetakis, I. E. 2019. First report of cycas necrotic stunt virus and lychnis mottle virus in peony in the United States. Plant Dis. 103:1048.
|
51 |
Wright, A. A., Cross, A. R. and Harper, S. J. 2020. A bushel of viruses: identification of seventeen novel putative viruses by RNA-seq in six apple trees. PLoS ONE 15:e0227669.
DOI
|
52 |
Wylie, S. J., Li, H., Saqib, M. and Jones, M. G. K. 2014. The global trade in fresh produce and the vagility of plant viruses: a case study in garlic. PLoS ONE 98:e105044.
|
53 |
Zhang, P., Liu, Y., Liu, W., Cao, M., Massart, S. and Wang, X. 2017. Identification, characterization and full-length sequence analysis of a novel polerovirus associated with wheat leaf yellowing disease. Front. Microbiol. 8:1689.
DOI
|
54 |
Jo, Y., Lian, S., Chu, H., Cho, J. K., Yoo, S.-H., Choi, H., Yoon, J.-Y., Choi, S.-K., Lee, B. C. and Cho, W. K. 2018b. Peach RNA viromes in six different peach cultivars. Sci. Rep. 8:1844.
DOI
|
55 |
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
DOI
|
56 |
Villamor, D. E. V., Ho, T., Al Rwahnih, M., Martin, R. R. and Tzanetakis, I. E. 2019. High throughput sequencing for plant virus detection and discovery. Phytopathology 109:716-725.
DOI
|
57 |
Yoo, R. H., Zhao, F., Lim, S., Igori, D., Lee, S.-H. and Moon, J. S. 2015. The complete nucleotide sequence and genome organization of lychnis mottle virus. Arch. Virol. 160:2891-2894.
DOI
|