Yeni Nesil Dizileme Teknolojilerinin Mikovirolojide Uygulanması

Yeni nesil yüksek verimli DNA dizileme analizleri 21. yüzyılın başlarında kullanılabilir hale gelmiştir. Bu dizileme teknolojisi genom karakterizasyonu, metagenetik, metilasyon analizi, kromatinlerin analizi, mRNA'ların profillenmesi gibi birçok amaç için kullanılmaktadır. 2009 yılından sonra, yeni nesil dizileme (YND) teknolojileri, virüs /viroid genom dizilemesi, keşfi ve tanısı, ekoloji ve epidemiyoloji, replikasyon ve transkripsiyon dahil olmak üzere çeşitli bitki virüslerinde uygulanmıştır. Son yıllarda bu teknoloji sayesinde araştırıcılar birçok yeni mikovirüsün tanılanmasını yapmışlardır. Bu derlemede, bazı yeni mikovirüslerin karakterizasyonu ve tanılanmasında yeni nesil dizileme teknolojisi (YND) nin kullanılmasıyla ilgili konular ele alınmıştır.

Anahtar Kelimeler:

DNA dizileme, Virüs, Mikovirüs

Application of Next Generation Sequencing Technologies in Mycovirology

High-throughput next generation DNA sequencing analysis became available at the onset of the 21st century. The sequencing technologies offer novel and rapid ways for genome-wide characterization and profiling of mRNAs, small RNAs, transcription factor regions, structure of chromatin and DNA methylation patterns, microbiology and metagenomics. After 2009, new generation sequencing (YND) technologies have been applied in various plant virology, including virus/viroid genome sequencing, discovery and diagnosis, ecology and epidemiology, replication and transcription. In recent years, researchers have identified many new mycoviruses through this technology. In this review, topics related to the use of new generation sequencing technology (YND) in characterization and identification of some new mycoviruses are discussed.

Keywords:

DNA sequencing, Virus, Mycovirus,

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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. Molecular Plant Pathology, 10(4): 537-45.
Adams, I. P., Miano, D. W., Kinyua, Z. M., Wangai, A., Kimani, E., Phiri, N., Reeder, R., Harju, V., Glover, R., Hany, U., Souza-Richards, R., Deb Nath, P., Nixon, T., Fox, A., Barnes, A., Smith, J., Skelton, A., Thwaites, R., Mumford, R., and Boonham, N. 2013. Use of next-generation sequencing for the identification and characterization of Maize chlorotic mottle virus and Sugarcane mosaic virus causing maize lethal necrosis in Kenya. Plant Pathology, 62: 741–749.
Aday Kaya, A. G., Doğmuş-Lehtijarvi, H. T., and Lehtijarvi, A. 2015. Mikovirüslerin orman patojenlerine karşı kullanım olanakları. Journal of the Faculty of Forestry Istanbul University, 65(1): 60-71.
Akbudak, N., Tezcan, H. 2006. Bitkisel Üretimde ve Bitki Korumada Yeni Bir Etken Madde: Harpin. Bursa Uludag Üniv. Ziraat Fak. Derg. 2(21): 39-43.
Ansorge, W., Sproat, B., Stegemann, J., Schwager, C., and Zenke, M. 1987. Automated DNA Sequencing: Ultrasensitive detection of fluorescent bands during electrophoresis. Nucleic Acid Research, 15: 4593–4602.
Al Rwahnih, M., Daubert, S., rbez-Torres, J. R. U., Cordero, F., and Rowhani, A. 2011. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Archives Virology, 156: 397–403.
Arjona-Lopez, J. M., Telengech, P., Jamal, A., Hisano, S., Kondo, H., Yelin, M. D., Arjona-Girona, I., Kanematsu, S., Lopez-Herrera, K., and Suzuki, N. 2018. Novel diverse RNA viruses from Mediterranean isolates of the phytopathogenic fungus, Rosellinia necatrix: insights into evolutionary biology of fungal viruses. Environmental Microbiology, 20(4): 1464–1483.
Bartholomaus, A., Wibberg, D., Winkler, A., hler, A. P., Schlüter, A., and Varrelmann, M. 2016. Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV. PLOS ONE 11(11): e0165965.
Buck, K.W., 1986. Fungal virology – an overview. In: Buck, K.W (Ed.), Fungal virology. CRC Press. Boca Raton, FL, pp. 1-84.
Chun, J., Yang, H., and Kim, D. 2018. Identification and Molecular Characterization of a Novel Partitivirus from Trichoderma atroviride NFCF394. Viruses Journal, 10: 578.
Cock, P.J. A., Fields, C. J., Goto, N., Heuer, M. L., and Rice, P. M. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, 38(6): 1767–1771.
Coetzee, B., Freeborough, M. J., Maree, H. J., Celton, J. M., Rees, D. J. G., and Burger, J. T. 2010. Deep Sequencing Analysis of Viruses Infecting Grapevines: Virome of a Vineyard. Virology, 400(2): 157-63.
Dawe, A. L., Nuss, D. L. 2001. Hypoviruses and chestnut blight: exploiting viruses to understand and modulate fungal pathogenesis. Annual Review of Genetics, 35: 1 –29.
Donaire, L., Pagán, I., and Ayllón, M. A. 2016. Characterization of Botrytis cinerea negative-stranded RNA virus 1, a new mycovirus related to plant viruses, and a reconstruction of host pattern evolution in negative-sense ssRNA viruses. National Center for Biotechnology Information, 499: 212-218.
Dönmez, D., Şimşek, Ö., ve Aka Kaçar, Y. 2015. Yeni Nesil DNA Dizileme Teknolojileri ve Bitkilerde Kullanımı. Türk Bilimsel Derlemeler Dergisi, 8 (1): 30-37.
Eriksson, J., Gharizadeh, B., Nordström, B. T., and Nyrén, P. 2004. Pyrosequencing technology at elevated temperature Electrophoresis. National Center for Biotechnology Information, 25: 20-27.
Espach, Y. 2013. The detection of mycoviral sequences in grapevine using next-generation sequencing. Thesis presented in partial fulfilment of the requirements for the degree Master of Science in Genetics at Stellenbosch University.
Gergerich, R. C., and Dolja, V. V. 2006. Introduction to Plant Viruses, the Invisible Foe. The Plant Health Instructor. DOI: 10.1094/PHI-I-2006-0414-01.
Ghabrial, S. A., Castón, J. R., Jiang, D., Nibert, M. L., and Suzuki, N. 2015. 50-plus years of fungal viruses. Virology. 479,: 356–368. doi: 10.1016/j.virol.2015.02.034.
Hadidi, A., Flores, R., Candresse, and T., Barba, M. 2016. Next-Generation Sequencing and Genome Editing in Plant Virology. Front. Microbiol, 7: 1325.
Heather, J. M., Chain, B. 2016. The sequence of sequencers: The history of sequencing DNA. Sponsored Document from Genomics, 107(1): 1-8.
Ion-Torrent. 2017. Ion-Torrent Next-Generation Sequencing Workflow. İnternet erişim: [http://www.thermofisher.com/tr/en/home/life-science/sequencing/next-generation-sequencing/iontorrentnext-generation-sequencing-workflow.html Erişim tarihi: 17.03.2017].
Jo, Y., Choi, H., Chu, H., Cho, and W. K. 2020. Identification of viruses from 1 fungal transcriptomes. biological-archive(bioRxiv preprint), doi: https://doi.org/10.1101/2020.02.26.966903.
Kehoe, M. A., Coutts, B. A., Buirchell, B. J., and Jones, R. A. C. 2014. Plant Virology and Next Generation Sequencing: Experiences with a Potyvirus. PLOS ONE, 9(8): e104580.
Khalifa, M. E., MacDiarmid, R. M. 2019. A Novel Totivirus Naturally Occurring in Two Different Fungal Genera. Front. Microbiology, 10: 2318.
Khalifa, M. E., Varsanib, A., Ganleye, A. R. D., and Pearsona, M. N. 2016. Comparison of Illumina de novo assembled and Sanger sequencedviral genomes: A case study for RNA viruses recovered from the plantpathogenic fungus Sclerotinia sclerotiorum. Virus Research Journal, 219: 51-57.
Kızmaz, M. Z., Paylan, İ. C., ve Erkan, S. 2017. DNA Dizilemenin Tarihsel Gelişimi. Gaziosmanpaşa Bilimsel Araştırma Dergisi, 6(2): 47-53.
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.
Kulski, J. K. 2015. Next-Generation Sequencing An Overview of the History, Tools, and “Omic” Applications: Next Generation Sequencing - Advances, Applications and Challenges, Ed: Kulski, J. K., International Technology (InTech), Croatia, pp: 3-60.
Maxam, A. M. and Gilber, W. 1977. A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America, 74(2): 560-564.
Marvelli, R. A., Hobbs, H. A., Li, Sh., McCoppin, N. K., Domier, L., Hartman, G. L., and Eastburn, D. M. 2014. Identification of novel double-stranded RNA mycoviruses of Fusarium virguliforme and evidence of their effects on virulence. Archives of Virology Journal, 159: 349-352.
Marzano, S. Y. L. and Domier, L. L. 2016. Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes. Virus Research, 213: 332-342.
Marzano, S. Y. L., and Nelson, B. D., Ajayi-Oyetunde, O., Bradley, C. A., Hughes, T. J., Hartman, G. L., Eastburn, D. M., and Domier, L. 2020. Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens. Plant Pathogens Journal Virology, 90: 6846-6863.
Milgroom, M. G. and Cortesi, P. 2004. Biological Control of Chestnut Blight with Hypovirulence: A critical analysis. Annual Review of Phytopathology, 42(1): 311-38.
Mu, F., Xie, J., Cheng, Sh., Pei, M., Barbetti, M. J., Jia, J., Wang, Q., Cheng, J., Fu, Y., Chen, T., and Jiang, D. 2018. Virome Characterization of a Collection of Sclerotinia sclerotiorum from Australia. Front. Microbiol, 8: 25-40.
Nanopore. 2017. Oxford Nanopore Technologies. İnternet erişim: [https://www.nanoporetech.com/Erişim tarihi: 17.03.2017. ]
Niu, Y., Yuan, Y., Mao, J., Yang, Z., Cao, Q., Zhang, T., Wang, Sh., and Liu, D. 2018. Characterization of two novel mycoviruses from Penicillium digitatum and the related fungicide resistance analysis. Scientific Reports, 8: 5513.
Nuss, D. L. 2011. Mycoviruses, RNA Silencing, and Viral RNA Recombination. Advances in Virus Research,80:25-48.
Nuss, D. L. 2005. Hypovirulence: mycoviruses at the Fungal-plant interface. Nature Reviews Microbiology, 3: 632 -642.
Li, P., Bhattacharje, P., Wang, Sh., Zhang, L., Ahmadi, I., and Guo, L. 2019. Mycoviruses in Fusarium Species: An Update. Frontiers in Cellular and Infection Microbiology, 9: 257
Li, Q., Huang, W., Hai, D., Wang, Y., Xie, J., and Wang, M. 2020. The complete genome sequence of a novel hypovirus infecting Bipolaris oryzae. Archives of Virology,165: 1027–1031.
Liu, Ch., Li, M., Redda, E. T., Mei, J., Zhang, J., Wu, B., and Jiang, X. 2019. A novel double-stranded RNA mycovirus isolated from Trichoderma harzianum. Virology Journal, 16: 113.
Liu, J., Xiang, Y., Sniezko, R. A., Schoettle, A. W., Williams, H., and Zamany, A. 2019. Characterization of Cronartium ribicola dsRNAs reveals novel members of the family Totiviridae and viral association with fungal virulence. Virology Journal, 16: 118.
Özkan Kahraman, Ç., Yıldız, F. 2019. Bitki Fungal Hastalıkları ile Biyolojik Savaşımda Alternatif Yaklaşımlar: Fungal Virüsler. İzlek, 2(1): 33-48.
PacBio. 2017. Pacific Biosciences. İnternet erişim: [http://www.pacb.com/] Erişim tarihi: 17.07.2017.
Pandey, B., Naidu, R. A., and Grove, G. G. 2018. Detection and analysis of mycovirus‑related RNA viruses from grape powdery mildew fungus Erysiphe necator. Archives of Virology,163: 1019-1030.
Pandey, B., Naidu, R. A., and Grove, G. G. 2018. Next generation sequencing analysis of double-stranded RNAs from sweet cherry powdery mildew fungus Podosphaera prunicola. Journal of Plant Pathology, 100: 435-446.
Prabha, K., Baranwal, V. K., and Jain, R. K. 2013. Applications of Next Generation High Throughput Sequencing Technologies in Characterization, Discovery and Molecular Interaction of Plant Viruses. Indian Journal Virology, 24(2): 157-165.
Ruiz-Martinez, M. C., Berka, J., Belenkii, A., Foret, F., Miller, A. W., and Karger, B. L. 1993. DNA sequencing by capillary electrophoresis with replaceable linear polyacrylamide and laser-induced fluorescence detection. Analytical Chemistry, 65: 2851-2858.
Sanger, F., Nicklen, S., and Coulson, A. R. 1977. DNA Sequencing With Chain-Terminating Inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 74(12): 5463-7.
Sasai, Sh., Tamura, K., Tojo, M., Herrero, M., Hoshino, T., Ohki, S. T., and Mochizuki, T. 2018. A novel non-segmented double-stranded RNA virus from an Arctic isolate of Pythium polare. Virology Journal, 522: 234- 243.
Shamsia, W., Satoa, Y., Jamala, A., Shahia, S., Kondoa, H., Suzukia, N., and Bhattib, M. F. 2019. Molecular and biological characterization of a novel botybirnavirus identified from a Pakistani isolate of Alternaria alternata. Virus Research, 263: 119-128.
Smith, L. M., Sanders, J. Z., Kaiser, R. J., Hughes, P., Dodd, Ch., Connell, Ch. R., Heiner, Ch., Kent, S. B. H., and Hood, L. E. 1986. Fluorescence detection in automated DNA sequence analysis. A Nature Research Journal, 321: 674-679.
Son, M., Yu, J., and Kim, K. H. 2015. Five Questions about Mycoviruses. Plos Pathogens Journal, 11(11): e1005172.
Taşar, O., Çınar, E., ve Onay, H. 2018. Hastalık Tanısı İçin Yeni Nesil Dizileme Verisi Analizi: Gereksinimler ve Bir Çözüm Önerisi. CERU-WS.org, 2201: 12.
Valverde, R., Nameth, S., and Jordan, S., 1990. Analysis of double-stranded RNA for plant virüs Diagnosis. Plant Disease, 74(3): 255-258.
Wang, Q., Cheng, Sh., Xiao, X., Cheng, J., Fu, Y., Chen, T., Jiang, D., and Xie, J. 2019. Discovery of Two Mycoviruses by High-Throughput Sequencing and Assembly of Mycovirus-Derived Small Silencing RNAs From a Hypovirulent Strain of Sclerotinia sclerotiorum. Frontiers in Microbiology Journal,10: 1415.
Wu, Q., Shou-Wei, D., Zhang, Y., and Zhu, Sh. 2015. Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms. Annual Review Phytopathology, 53: 425-44.
Yao, Z., Zou, Ch., Peng, N., Zhu, Y., Bao, Y., Zhou, Q., Wu, Q., Chen, B., and Zhang, M. 2020. Virome Identification and Characterization of Fusarium sacchari and F. andiyazi: Causative Agents of Pokkah Boeng Disease in Sugarcane. Frontiers in Microbiology Journal, 11:240.
Zhang, Y. Z., Shi, M., and Holmes, E. C. 2018. Using metagenomics to characterize an expanding virosphere. National Center for Biotechnology Information, 172: 1168-1172.
Zhu, J. Z., Zhu, H. J., Gao, B. D., Zhou, Q., and Zhong, J. 2018. Diverse, Novel Mycoviruses From the Virome of a Hypovirulent Sclerotium rolfsii Strain. Frontiers Plant Science Journal, 9: 1738.