Sekwencjonowanie następnej generacji (NGS) jako uniwersalna metoda wykrywania i różnicowania wirusów roślinnych
Next generation sequencing (NGS) as a multipurpose method for detection and differentiation of plant viruses
Agata Kaczmarek, e-mail: a.kaczmarek@ihar.edu.pl
Instytut Hodowli i Aklimatyzacji Roślin – Państwowy Instytut Badawczy, Radzików, 05-870 Błonie, PolskaKrzysztof Treder, e-mail: k.treder@ihar.edu.pl
Instytut Hodowli i Aklimatyzacji Roślin – Państwowy Instytut Badawczy, Radzików, 05-870 Błonie, PolskaStreszczenie |
Niniejsza praca opisuje wykorzystanie sekwencjonowania następnej generacji (NGS) w badaniach nad wirusami roślin. Pomimo iż, NGS nie jest jeszcze rutynowo stosowane, coraz częściej jest adaptowane w diagnostyce oraz genomice fitopatogenów. Techniki NGS umożliwiają jednoczesne wykrycie wielu wirusów obecnych w zakażonym materiale. Dzięki nim możliwe jest nie tylko stwierdzenie, jakie wirusy są obecne w jednej badanej próbie, ale również ich zróżnicowanie genetyczne. Jednoczesna identyfikacja wielu wirusów, możliwość wczesnego wykrywania ognisk choroby, śledzenie rozwoju epidemii oraz monitorowanie zmian genetycznych zachodzących w populacji patogenów wirusowych w trakcie rozwoju epidemii sprawiają, że NGS staje się uniwersalnym narzędziem badawczym umożliwiającym nie tylko detekcję, ale również zrozumienie mechanizmów molekularnych pozwalających wirusom adaptować się do zmian środowiskowych (genotypu rośliny – gospodarza, wektora, obecności innych patogenów).
This paper describes the application of next generation sequencing (NGS) in plant virus research. Although NGS has not been routinely used yet, it is increasingly adopted in diagnostics and genomics of phytopathogens. NGS technics enable the simultaneous detection of multiple viruses present in infected material. This makes it possible not only to determine which viruses are present in a single sample but also to determine their concentration and genetic diversity. The simultaneous identification of many viruses, the possibility of early detection of disease outbreaks as well as tracking and monitoring of epidemic development, make NGS a universal research tool that enables not only the detection but also the understanding of molecular mechanisms allowing viruses to adapt to environmental changes (host plant genotype, vector, presence of other pathogens). |
Słowa kluczowe |
diagnostyka; fitopatologia; NGS; sekwencjonowanie; wirusy roślin; diagnostics; plant pathology; sequencing; plant viruses |
Referencje |
Adams I., Fox A. 2016. Diagnosis of plant viruses using next-generation sequencing and metagenomic analysis. s. 323–335. W: Current Research Topics in Plant Virology (A. Wang, X. Zhou, red.). Springer, Cham. DOI: 10.1007/978-3-319-32919-2_14
Adams I.P., Glover R.H., Monger W.A., Mumford R., Jackeviciene E., Navalinskiene M., Samuitiene M., Boonham N. 2009. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Molecular Plant Pathology 10 (4): 537–545. DOI: 10.1111/j.1364-3703.2009.00545.x
Adams I.P., Skelton A., Macarthur R., Hodges T., Hinds H., Flint L., Nath P.D., Boonham N., Fox A. 2014. Carrot yellow leaf virus is associated with carrot internal necrosis. PLOS ONE 9: 109–125. DOI: 10.1371/journal.pone.0109125
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 (2): 395–401. DOI: 10.1016/j.virol.2009.02.028
Atsumi G., Sekine K.T., Kobayashi K. 2015. A new method to isolate total dsRNA. s. 27–37. W: Plant Virology Protocols. Methods in Molecular Biology (Methods and Protocols), vol. 1236 (I. Uyeda, C. Masuta C., red.). Humana Press, New York, NY. DOI: 10.1007/978-1-4939-1743-3_3
Barba M., Czosnek H., Hadidi A. 2014. Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6 (1): 106–136. DOI: 10.3390/v6010106
Bayley H. 2015. Nanopore sequencing: from imagination to reality. Clinical Chemistry 61 (1): 25–31. DOI: 10.1373/clinchem.2014.223016
Bayley H., Cremer P.S. 2001. Stochastic sensors inspired by biology. Nature 413: 226–230. DOI: 10.1038/35093038
Bronzato Badial A., Sherman D., Stone A., Gopakumar A., Wilson V., Schneider W., King J. 2018. Nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues. Plant Disease 102 (8): 1648–1652. DOI: 10.1094/PDIS-04-17-0488-RE
Della Bartola M., Byrne S., Mullins E. 2020. Characterization of potato virus Y isolates and assessment of nanopore sequencing to detect and genotype potato viruses. Viruses 12 (4): 478. DOI: 10.3390/v12040478
Dodds J.A., Morris T.J., Jordan R.L. 1984. Plant viral double-stranded RNA. Annual Review of Phytopathology 22: 151–168. DOI: 10.1146/annurev.py.22.090184.001055
Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., Peluso P., Rank D., Baybayan P., Bettman B., Bibillo A., Bjornson K., Chaudhuri B., Christians F., Cicero R., Clark S., Dalal R., deWinter A., Dixon J., Foquet M., Gaertner A., Hardenbol P., Heiner C., Hester K., Holden D., Kearns G., Kong X., Kuse R., Lacroix Y., Lin S., Lundquist P., Ma C., Marks P., Maxham M., Murphy D., Park I., Pham T., Phillips M., Roy J., Sebra R., Shen G., Sorenson J., Tomaney A., Travers K., Trulson M., Vieceli J., Wegener J., Wu D., Yang A., Zaccarin D., Zhao P., Zhong F., Korlach J., Turner S. 2009. Real-time DNA sequencing from single polymerase molecules. Science 323 (5910): 133–138. DOI: 10.1126/science.1162986
Elbeaino T., Giampetruzzi A., De Stradis A., Digiaro M. 2014. Deep-sequencing analysis of an apricot tree with vein clearing symptoms reveals the presence of a novel betaflexivirus. Virus Research 181: 1–5. DOI: 10.1016/j.virusres.2013.12.030
Filloux D., Fernandez E., Loire E., Claude L., Galzi S., Candresse T., Winter S., Jeeva M., Makeshkumar T., Martin D.P. 2018. Nanopore-based detection and characterization of yam viruses. Scientific Reports 8: 17879. DOI: 10.1038/s41598-018-36042-7
Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. 1998. Potent and specific genetic interference by doublestranded RNA in Caenorhabditis elegans. Nature 391: 806–811. DOI: 10.1038/35888
Fox A., Adams I., Hany U., Hodges T., Forde S., Jackson L., Skelton A., Barton V. 2015. The application of next-generation sequencing for screening seeds for viruses and viroids. Seed Science and Technology 43 (3): 531–535. DOI: 10.15258/sst.2015.43.3.06
Goodwin S., McPherson J.D., McCombie W.R. 2016. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics 17: 333–351. DOI: 10.1038/nrg.2016.49
Hamilton A.J., Baulcombe D.C. 1999. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286 (5441): 950–952. DOI: 10.1126/science.286.5441.950
Hwang Y.T., Kalischuk M., Fusaro A.F., Waterhouse P.M., Kawchuk L. 2013. Small RNA sequencing of Potato leafroll virusinfected plants reveals an additional subgenomic RNA encoding a sequence-specific RNA-binding protein. Virology 438 (2): 61–69. DOI: 10.1016/j.virol.2012.12.012
Jones S., Baizan-Edge A., MacFarlane S., Torrance L. 2017. Viral diagnostics in plants using next generation sequencing: computational analysis in practice. Frontiers in Plant Sciewnce 8: 1770. DOI: 10.3389/fpls.2017.01770
Kreuze J.F., Perez A., Untiveros M., Quispe D., Fuentes S., Barker I., 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): 1–7. DOI: 10.1016/j.virol.2009.03.024
Kutnjak D., Rupar M., Gutierrez-Aguirre I., Curk T., Kreuze J.F., Ravnikar M. 2015. Deep sequencing of virus-derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscapes of a plant virus population. Journal of Virology 89 (9): 4760–4769. DOI: 10.1128/JVI.03685-14
Maliogka V., Minafra A., Saldarelli P., Ruiz-García A., Glasa M., Katis N., Olmos A. 2018. Recent advances on detection and characterization of fruit tree viruses using high-throughput sequencing technologies. Viruses 10 (8): 436. DOI: 10.3390/v10080436
Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.-J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L.I., Jarvie T.P., Jirage K.B., Kim J.-B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., Rothberg J.M. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376–380. DOI: 10.1038/nature03959
Massart S., Chiumenti M., De Jonghe K., Glover R., Haegeman A., Koloniuk I., Komínek P., Kreuze J., Kutnjak D., Lotos L., Maclot F., Maliogka V., Maree H.J., Olivier T., Olmos A., Pooggin M.M., Reynard J.S., Ruiz-García A.B., Safarova D., Schneeberger P.H.H., Sela N., Turco S., Vainio E.J., Varallyay E., Verdin E., Westenberg M., Brostaux Y., Candresse T. 2019. Virus detection by high-throughput equencing of small RNAs: large-scale performance testing of sequence analysis strategies. Phytopathology 109 (3): 488–497. DOI: 10.1094/PHYTO-02-18-0067-R
Minicka J., Zarzyńska-Nowak A., Budzyńska D., Borodynko-Filas N., Hasiów-Jaroszewska B. 2020. High-throughput sequencing facilitates discovery of new plant viruses in Poland. Plants 9 (7): 820. DOI: 10.3390/plants9070820
Mullis K., Faloona F., Scharf S., Saiki R., Horn G., Erlich H. 1986. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. W: Cold Spring Harbor Symposia on Quantitative Biology 51: 263–273. DOI: 10.1101/SQB.1986.051.01.032
Noceń J., Puchta M., Czembor J.H. 2018. Wykorzystanie nowoczesnych technologii sekwencjonowania DNA (NGS) w bankach genów i hodowli roślin. Praca przeglądowa. [Using the next generation DNA sequencing (technology NGS) in gene banks and plant breeding. A review]. Agronomy Sciences 73 (1): 5–17. DOI: 10.24326/asx.2018.1.1
Okada R., Kiyota E., Moriyama H., Fukuhara T., Natsuaki T. 2015. A simple and rapid method to purify viral dsRNA from plant and fungal tissue. Journal of General Plant Pathology 81: 103–107. DOI: 10.1007/s10327-014-0575-6
Pecman A., Kutnjak D., Gutiérrez-Aguirre I., Adams I., Fox A., Boonham N., Ravnikar M. 2017. Next generation sequencing for detection and discovery of plant viruses and viroids: comparison of two approaches. Frontiers in Microbiology 8: 1998. DOI: 10.3389/fmicb.2017.01998
Roossinck M.J., Martin D.P., Roumagnac P. 2015. Plant virus metagenomics: advances in virus discovery. Phytopathology 105 (6): 716–727. DOI: 10.1094/PHYTO-12-14-0356-RVW
Sanger F., Brownlee G.G., Barrell B.G. 1965. A two-dimensional fractionation procedure for radioactive nucleotides. Journal of Molecular Biology 13 (2): 373–398. DOI: 10.1016/S0022-2836(65)80104-8
Sanger F., Nicklen S., Coulson A.R. 1977. DNA sequencing with chain-terminating inhibitors. Proccedings of the National Academy of Sciences of the United States of America 74 (12): 5463–5467. DOI: 10.1073/pnas.74.12.5463
Santala J., Valkonen J.P.T. 2018. Sensitivity of small RNA-based detection of plant viruses. Frontiers in Microbiology 9: 939. DOI: 10.3389/fmicb.2018.00939
Smith L.M., Sanders J.Z., Kaiser R.J., Hughes P., Dodd C., Connell C.R., Heiner C., Kent S.B., Hood L.E. 1986. Fluorescence detection in automated DNA sequence analysis. Nature 321: 674–679. DOI: 10.1038/321674a0
Stoddart D., Heron A.J., Mikhailova E., Maglia G., Bayley H. 2009. Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proccedings of the National Academy of Sciences of the United States of America 106 (19): 7702–7707. DOI: 10.1073/pnas.0901054106
Villamor D.E., Pillai S.S., Eastwell K.C. 2017. High throughput sequencing reveals a novel fabavirus infecting sweet cherry. Archives of Virology 162: 811–816. DOI: 10.1007/s00705-016-3141-z
Watson J.D., Crick F.H. 1953. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171 (4356): 737–738. DOI: 10.1038/171737a0
Żmieńko A., Satyr A. 2020. Sekwencjonowanie nanoporowe i jego zastosowanie w biologii. Postępy Biochemii/Advances in Biochemistry 66 (3): 193–204. DOI: 10.18388/pb.2020_328 |
Progress in Plant Protection (2021) 61: 269-277 |
Data pierwszej publikacji on-line: 2021-10-08 11:06:47 |
http://dx.doi.org/10.14199/ppp-2021-029 |
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