The Plant Pathology Journal

The Korean Society of Plant Pathology (한국식물병리학회)
권호 표지
DOI QR코드

DOI QR Code

Deep Sequencing Analysis of Apple Infecting Viruses in Korea

  • Cho, In-Sook (Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Igori, Davaajargal (Molecular Biofarming Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Lim, Seungmo (Molecular Biofarming Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Choi, Gug-Seoun (Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Hammond, John (Floral and Nursery Plants Unit, United States National Arboretum, United States Department of Agriculture-Agricultural Research Service) ;
  • Lim, Hyoun-Sub (Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Moon, Jae Sun (Molecular Biofarming Research Center, Korea Research Institute of Bioscience and Biotechnology)
  • Received : 2016.04.24
  • Accepted : 2016.05.23
  • Published : 2016.10.01
Download PDF
⟨ Previous Next ⟩

Abstract

Deep sequencing has generated 52 contigs derived from five viruses; Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV), Apple green crinkle associated virus (AGCaV), and Apricot latent virus (ApLV) were identified from eight apple samples showing small leaves and/or growth retardation. Nucleotide (nt) sequence identity of the assembled contigs was from 68% to 99% compared to the reference sequences of the five respective viral genomes. Sequences of ASPV and ASGV were the most abundantly represented by the 52 contigs assembled. The presence of the five viruses in the samples was confirmed by RT-PCR using specific primers based on the sequences of each assembled contig. All five viruses were detected in three of the samples, whereas all samples had mixed infections with at least two viruses. The most frequently detected virus was ASPV, followed by ASGV, ApLV, ACLSV, and AGCaV which were withal found in mixed infections in the tested samples. AGCaV was identified in assembled contigs ID 1012480 and 93549, which showed 82% and 78% nt sequence identity with ORF1 of AGCaV isolate Aurora-1. ApLV was identified in three assembled contigs, ID 65587, 1802365, and 116777, which showed 77%, 78%, and 76% nt sequence identity respectively with ORF1 of ApLV isolate LA2. Deep sequencing assay was shown to be a valuable and powerful tool for detection and identification of known and unknown virome in infected apple trees, here identifying ApLV and AGCaV in commercial orchards in Korea for the first time.

Keywords

References

  1. Adams, M. J., Antoniw, J. F., Bar-Joseph, M., Brunt, A. A., Candresse, T., Foster, G. D., Martelli, G. P., Milne, R. G., Zavriev, S. K. and Fauquet, C. M. 2004. The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch. Virol. 149:1045-1060.
  2. 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. https://doi.org/10.1016/j.virol.2009.02.028
  3. Al Rwahnih, M., Dave, A., Anderson, M., Uyemoto, J. K. and Sudarshana, M. R. 2012. Association of a circular DNA virus in grapevines affected by red blotch disease in California. In: Proceedings of the 17th Congress of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine (ICVG), ed by B. Ferguson, pp. 104-105. October 7-14, 2012, Foundation Plant Services, University of California, Davis, CA, USA.
  4. Barba, M., Czosnek, H. and 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
  5. Candresse, T., Marais, A., Faure, C. and Gentit, P. 2013. Association of Little cherry virus 1 (LChV1) with the Shirofugen stunt disease and characterization of the genome of a divergent LChV1 isolate. Phytopathology 103:293-298. https://doi.org/10.1094/PHYTO-10-12-0275-R
  6. Cho, I. S. 2015. New approaches of the molecular assays and the surveys of fruit tree viruses in commercial orchards. Ph.D. thesis. Chungnam National University, Daejeon, Korea.
  7. Coetzee, B., Freeborough, M. J., Maree, H. J., Celton, J. M., Rees, D. J. and Burger, J. T. 2010. Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 400:157-163. https://doi.org/10.1016/j.virol.2010.01.023
  8. Gadiou, S., Kundu, J. K., Paunovic, S., Garcia-Diez, P., Komorowska, B., Gospodaryk, A., Handa, A., Massart, S., Birisik, N., Takur, P. D. and Polischuk, V. 2010. Genetic diversity of Flexiviruses infecting pome fruit trees. J. Plant Pathol. 92:685-691.
  9. Giampetruzzi, A., Roumi, V., Roberto, R., Malossini, U., Yoshikawa, N., La Notte, P., Terlizzi, F., Credi, R. and Saldarelli, P. 2012. A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris. Virus Res. 163:262-268. https://doi.org/10.1016/j.virusres.2011.10.010
  10. Howell, W. E., Thompson, D. and Scott, S. 2011. Virus-like disorders of fruit trees with undetermined etiology. In: Virus and virus-like diseases of pome and stone fruits, eds. by A. Hadidi, M. Barba, T. Candresse and W. Jelkmann, pp. 259-265. The American Phytopathological Society Press, St. Paul, MN, USA.
  11. James, D., Varga, A., Jesperson, G. D., Navratil, M., Safarova, D., Constable, F., Horner, M., Eastwell, K. and Jelkmann, W. 2013. Identification and complete genome analysis of a virus variant or putative new foveavirus associated with apple green crinkle disease. Arch. Virol. 158:1877-1887. https://doi.org/10.1007/s00705-013-1678-7
  12. Komatsu, K., Yamaji, Y., Ozeki, J., Hashimoto, M., Kagiwada, S., Takahashi, S. and Namba, S. 2008. Nucleotide sequence analysis of seven Japanese isolates of Plantago asiatica mosaic virus (PlAMV): a unique potexvirus with significantly high genomic and biological variability within the species. Arch. Virol. 153:193-198. https://doi.org/10.1007/s00705-007-1078-y
  13. Komorowska, B., Siedlecki, P., Kaczanowski, S., Hasiow-Jaroszewska, B. and Malinowski, T. 2011. Sequence diversity and potential recombination events in the coat protein gene of Apple stem pitting virus. Virus Res. 158:263-267. https://doi.org/10.1016/j.virusres.2011.03.003
  14. Li, R., Gao, S., Hernandez, A. G., Wechter, W. P., Fei, Z. and Ling, K. S. 2012. Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS One 7:e37127. https://doi.org/10.1371/journal.pone.0037127
  15. Lim, H. S., Vaira, A. M., Reinsel, M. D., Bae, H., Bailey, B. A., Domier, L. L. and Hammond, J. 2010. Pathogenicity of Alternanthera mosaic virus is affected by determinants in RNA-dependent RNA polymerase and by reduced efficacy of silencing suppression in a movement-competent TGB1. J. Gen. Virol. 91:277-287. https://doi.org/10.1099/vir.0.014977-0
  16. Magome, H., Yoshikawa, N. and Takahashi, T. 1999. Singlestrand conformation polymorphism analysis of apple stem grooving capillovirus sequence variants. Phytopathology 89:136-140. https://doi.org/10.1094/PHYTO.1999.89.2.136
  17. Maroon-Lango, C. J., Guaragna, M. A., Jordan, R. L., Hammond, J., Bandla, M. and Marquardt, S. K. 2005. Two unique US isolates of Pepino mosaic virus from a limited source of pooled tomato tissue are distinct from a third (European-like) US isolate. Arch. Virol. 150:1187-1201. https://doi.org/10.1007/s00705-005-0495-z
  18. Martelli, G. P., Agranovsky, A. A., Bar-Joseph, M., Boscia, D., Candresse, T., Coutts, R. H. A., Dolja, V. V., Duffus, J. D., Falk, B. W., Gonsalves, D., Jelkmann, W., Karasev, A., Minafra, A., Murant, A. F., Namba, S., Niblett, C. L., Vetten, H. J. and Yoshikawa, N. 2000. Genus Capillovirus. In: Virus taxonomy: seventh report of the International Committee on Taxonomy of Viruses, eds. by M. H. V. van Regenmortel, C. M. Fauquet and D. H. L. Bishop, pp. 952-959. Academic Press, San Diego, CA, USA.
  19. Mathews, D. M. 2010. Optimizing detection and management of virus diseases of plants and emerging tree diseases in Southern California. In: Proceedings of the Landscape Disease Symposium, pp. 10-20. October 14, 2010, Camarillo, CA, USA.
  20. Nemchinov, L. G., Shamloul, A. M., Zemtchik, E. Z., Verderevskaya, T. D. and Hadidi, A. 2000. Apricot latent virus: a new species in the genus Foveavirus. Arch. Virol. 145:1801-1813. https://doi.org/10.1007/s007050070057
  21. Nemeth, M. V. 1986. Virus, mycoplasma, and rickettsia diseases of fruit trees. Kluwer Academic, Hingham, MA, USA.
  22. Nisar, A. D. 2013. Apple stem grooving virus-a review article. Int. J. Modern Plant Anim. Sci. 1:28-42.
  23. Patel, R. K. and Jain, M. 2012. NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 7:e30619. https://doi.org/10.1371/journal.pone.0030619
  24. Rowhani, A., Maningas, M. A., Lile, L. S., Daubert, S. D. and Golino, D. A. 1995. Development of a detection system for viruses of woody plants based on PCR analysis of immobilized virions. Phytopathology 85:347-352. https://doi.org/10.1094/Phyto-85-347
  25. Saade, M., Aparicio, F., Sanchez-Navarro, J. A., Herranz, M. C., Myrta, A., Di Terlizzi, B. and Pallas, V. 2000. Simultaneous detection of the three ilarviruses affecting stone fruit trees by nonisotopic molecular hybridization and multiplex reversetranscription polymerase chain reaction. Phytopathology 90:1330-1336. https://doi.org/10.1094/PHYTO.2000.90.12.1330
  26. Sastry, K. S. 2013. Plant virus and viroid diseases in the tropics volume-1: introduction of plant viruses and sub-viral agents, classification, assessment of loss, transmission and diagnosis. Springer, New York, NY, USA.
  27. 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. https://doi.org/10.1093/molbev/msr121
  28. Yoshikawa, N., Sasamoto, K., Sakurada, M., Takahashi, T. and Yanase, H. 1996. Apple stem grooving and citrus tatter leaf capilloviruses obtained from a single shoot of Japanese pear (Pyrus serotina). Jpn. J. Phytopathol. 62:119-124. https://doi.org/10.3186/jjphytopath.62.119
  29. Yoshikawa, N. and Takahashi, T. 1988. Properties of RNAs and proteins of Apple stem grooving and Apple chlorotic leafspot viruses. J. Gen. Virol. 69:241-245. https://doi.org/10.1099/0022-1317-69-1-241
  30. Yoshikawa, N., Yamagishi, N., Yaegashi, H. and Ito, T. 2012. Deep sequence analysis of viral small RNAs from a green crinkle-diseased apple tree. Petria 22:292-297.
  31. Youssef, F., Marais, A., Faure, C., Barone, M., Gentit, P. and Candresse, T. 2011. Characterization of Prunus-infecting Apricot latent virus-like Foveaviruses: evolutionary and taxonomic implications. Virus Res. 155:440-445. https://doi.org/10.1016/j.virusres.2010.11.013
  32. Yozwiak, N. L., Skewes-Cox, P., Stenglein, M. D., Balmaseda, A., Harris, E. and DeRisi, J. L. 2012. Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl. Trop. Dis. 6:e1485. https://doi.org/10.1371/journal.pntd.0001485
  33. Zerbino, D. R. and Birney, E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829. https://doi.org/10.1101/gr.074492.107

Cited by

  1. First report of apple luteovirus 1 and apple rubbery wood virus 1 on apple tree rootstocks in Korea pp.0191-2917, 2019, https://doi.org/10.1094/PDIS-08-18-1351-PDN
  2. Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies vol.10, pp.8, 2018, https://doi.org/10.3390/v10080436