Virome identification in wheat in the Czech Republic using small RNA deep sequencing

doi:10.1016/S2095-3119(19)62805-4

Journal of Integrative Agriculture ›› 2020, Vol. 19 ›› Issue (7): 1825-1833.DOI: 10.1016/S2095-3119(19)62805-4

所属专题：植物病理合辑Plant Protection—Plant Pathology；植物病毒合辑Plant Virus

收稿日期:2019-05-30 出版日期:2020-07-01 发布日期:2020-05-24

Virome identification in wheat in the Czech Republic using small RNA deep sequencing

<div style="line-height: 150%"><a href="https://www.chinaagrisci.com/Jwk_zgnykxen/EN/article/advancedSearchResult.do?searchSQL=(((Khushwant SINGH[Author]) AND 1[Journal]) AND year[Order])" target="_blank">Khushwant SINGH</a>1, Jana JARO&Scaron;<a href="https://www.chinaagrisci.com/Jwk_zgnykxen/EN/article/advancedSearchResult.do?searchSQL=(((OV&Aacute[Author]) AND 1[Journal]) AND year[Order])" target="_blank">OV&Aacute</a>;1, Jan FOUSEK1, CHEN Huan2, Jiban Kumar KUNDU1</div>

¹ Plant Virus and Vector Interactions Group, Division of Crop Protection and Plant Health, Crop Research Institute, Prague 16106, Czech Republic
² Zhejiang Tianke High-Technology Development Co., Ltd., Hangzhou 310012, P.R.China

Received:2019-05-30 Online:2020-07-01 Published:2020-05-24
Contact: Correspondence Jiban Kumar Kundu, E-mail: jiban@vurv.cz
Supported by:
This work was supported by a grant from the Technology Agency of the Czech Republic (TF02000056).

摘要/Abstract

Abstract:

High-throughput deep-sequencing technology and bioinformatics analysis of the small RNA (sRNA) population isolated from plants allows universal virus detection and complete virome reconstruction for a given sample. In the present sRNA deep-sequencing analysis of virus-infected wheat samples in the Czech Republic, samples were firstly tested for barley yellow dwarf viruses (BYDVs), wheat streak mosaic virus (WSMV) and wheat dwarf virus (WDV) using ELISA, RT-PCR and PCR. Subsequent sRNA sequencing of these samples yielded more than ~60 million single-end 50-bp reads with high confidence for nine field samples of wheat. Overall, 16.5% of reads were virus-specific and 83.5% were mapped to the host. More 21-nt reads (~7.7E+06 reads) were found than 24-nt (~6.20E+06 reads) or 22-nt (~4.30E+06 reads) reads. De novo assembly of the high-quality contigs revealed the presence of three earlier reported viruses in the Czech Republic: BYDVs (31.48%), WSMV (24.23%) and WDV (26.66%). We also showed the presence of cereal yellow dwarf virus (14.33%; two species CYDV-RPS and CYDV-RPV (family Luteoviridae/Polerovirus) and wheat yellow dwarf virus (WYDV, 3.30%; Luteoviridae). Phylogenetic analysis showed CYDV and WYDV grouped separately from BYDVs. Furthermore, several recombination breakpoints were found among the groups of yellow dwarf viruses (BYDVs, CYDV, and WYDV). Using RNA deep sequencing, we confirmed the presence of the three known viruses (BYDVs, WSMV, and WDV) and the first record of two species of CYDV and WYDV in wheat in the Czech Republic.

Key words: NGS , sRNA , BYDVs , CYDV , WSMV , WYDV , WDV

. [J]. Journal of Integrative Agriculture, 2020, 19(7): 1825-1833.

Khushwant SINGH, Jana JAROŠOVÁ, Jan FOUSEK, CHEN Huan, Jiban Kumar KUNDU. Virome identification in wheat in the Czech Republic using small RNA deep sequencing[J]. Journal of Integrative Agriculture, 2020, 19(7): 1825-1833.

参考文献

Adams I P, Glover R H, Monger W A, Mumford R, Jackeviciene E, Navalinskiene M. 2009. Next-generation sequencing and metagenomics analysis: A universal diagnostic tool in plant virology. Molecular Plant Pathology, 10, 537–545.
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, 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.
Barba M, Czosnek H, Hadidi A. 2014. Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses, 6, 106–136.
Beoni E, Chrpová J, Jarošová J, Kundu J K. 2016. Survey of Barley yellow dwarf virus incidence in winter cereal crops, and assessment of wheat and barley resistance to the virus. Crop & Pasture Science, 67, 1054–1063.
Bi Y, Tugume A K, Valkonen J P T. 2012. Small-RNA deep sequencing reveals Arctium tomentosum as a natural host of Alstroemeria virus X and a new putative Emaravirus. PLoS ONE, 7, e42758.
Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R. 2014. Methods in virus diagnostics: From ELISA to next generation sequencing. Virus Research, 186, 20–31.
Boulila M. 2011. Selective constraints, molecular recombination structure and phylogenetic reconstruction of isometric plant RNA viruses of the families Luteoviridae and Tymoviridae. Biochimie, 93, 242–253.
Chalupniková J, Kundu J K, Singh K, Bartaková P, Beoni E. 2017. Wheat streak mosaic virus: Incidence in field crops, potential reservoir within grass species and uptake in winter wheat cultivars. Journal of Integrative Agriculture, 16, 523–531.
Chen S, Huang Q, Wu L, Qian Y. 2015. Identification and characterization of a maize-associated mastrevirus in China by deep sequencing small RNA populations. Virology Journal, 12, 156.
Chen S, Jiang G, Wu J, Liu Y, Qian Y, Zhou X. 2016. Characterization of a novel polerovirus infecting maize in China. Viruses, 8, 120.
Ding S, Voinnet O. 2007. Antiviral immunity directed by small RNAs. Cell, 130, 413–426.
Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer K F, Aranda M A, Llave C. 2009. Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology, 392, 203–214.
Deb M, Anderson J M. 2008. Development of a multiplexed PCR detection method for Barley and Cereal yellow dwarf viruses, Wheat spindle streak virus, Wheat streak mosaic virus and Soil-borne wheat mosaic virus. Journal of Virological Methods, 148, 17–24.
Dráb T, Svobodová E, Ripl J, Jarošová J, Rabenstein F, Melcher U, Kundu J K. 2014. SYBR green I based RT-qPCR assays for the detection of RNA viruses of cereals and grasses. Crop & Pasture Science, 65, 1323–1328.
Gray S, Gildow F E. 2003. Luteovirus-aphid interactions. Annual Review of Phytopathology, 41, 539–566.
Hadi B A R, Flanders K L, Bowen K L, Murphy J F, Blount A R. 2012. Survey of Barley yellow dwarf virus and Cereal yellow dwarf virus on three perennial pasture grasses in Florida. Journal of Entomolcial Science, 47, 1–9.
Ibaba J D, Laing M D, Gubba A. 2017. Pepo aphid-borne yellows virus: A new species in the genus Polerovirus. Virus Genes, 53, 134–136.
Jarošová J, Chrpová J, Šíp V, Kundu J K. 2013. A comparative study of the Barley yellow dwarf virus species PAV and PAS: Distribution, virus accumulation and host resistance. Plant Pathology, 62, 436–443.
Jarošová J, Kundu J K. 2010. Validation of reference genes as internal control for studying viral infections in cereals by quantitative real-time PCR. BMC Plant Biology, 10, 146.
Jarošová J, Ripl J, Fousek J, Kundu J K. 2018. TaqMan multiplex real-time qPCR assays for the detection and quantification of Barley yellow dwarf virus, Wheat dwarf virus and Wheat streak mosaic virus and the study of their interactions. Crop & Pasture Science, 69, 755–764.
Kashif M, Pietilä S, Artola K, Jones R A C, Tugume A K, Mäkinen V, Valkonen T P J. 2012. Detection of viruses in sweet potato from Honduras and Guatemala augmented by deep-sequencing of small-RNAs. Plant Disease, 96, 1430–1437.
Kreuze J, Perez A, Untveros M, Quispe D, Fuentes S, Barker I. 2009. Complete viral genome sequence and discovery of novel viruses by deep-sequencing of small RNAs: A generic method for diagnosis, discovery and sequence of viruses. Virology, 388, 1–7.
Krueger E N, Beckett R J, Gray S M, Miller W A. 2013. The complete nucleotide sequence of the genome of Barley yellow dwarf virus-RMV reveals it to be a new Polerovirus distantly related to other yellow dwarf viruses. Frontier in Microbiology, 4, 205.
Kundu J K, Gadiou S, ?ervená G. 2009a. Discrimination and genetic diversity of Wheat dwarf virus in the Czech Republic. Virus Genes, 38, 468–474.
Kundu J K, Jarošová J, Gadiou S, ?ervená G. 2009b. Discrimination of three BYDV species by one-step RT-PCR-RFLP and sequence based methods in cereal plants from the Czech Republic. Cereal Research Communications, 37, 541–550.
Lapierre H, Signoret P A. 2004. Viruses and Virus Diseases of Poaceae (Gramineae). Editions Quae, Paris, France.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
Massart S, Candresse T, Gil J, Lacomme C, Predajna L, Ravnikar M. 2017. A framework for the evaluation of biosecurity, commercial, regulatory and scientific impacts of plant viruses and viroids identified by NGS technologies. Frontiers in Microbiology, 8, 45.
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, et al. 2019. Virus detection by high-throughput sequencing of small RNAs: large scale performance testing of sequence analysis strategies. Phytopathology, 109, 488–497.
McKirdy S J, Jones R A C. 2002. Quantification of yield losses caused by Barley yellow dwarf virus in wheat and oats. Plant Disease, 86, 769–773.
Milgate A, Adorada D, Cxhambers G, Terras M A. 2016. Occurrence of winter cereal viruses in New South Eales, Australia, 2006 to 2014. Plant Disease, 100, 313–317.
Pagán I, Holmes E C. 2010. Long-term evolution of the Luteoviridae: Time scale and mode of virus speciation. Journal of Virology, 84, 6177–6187.
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.
Pooggin M M. 2018. Small RNA-omics for plant virus identification, virome reconstruction, and antiviral defense characterization. Frontiers in Microbiology, 9, 2779.
Robinson M D, Murray T D. 2013. Genetic variation of Wheat streak mosaic virus in the United States Pacific Northwest. Phytopathology, 103, 98–104.
Roossinck M J, Martin D P, Roumagnac P. 2015. Plant virus metagenomics: Advances in virus discovery. Phytopathology, 105, 716–727.
Santala J, Valkonen P T J. 2018. Sensitivity of small RNA-based detection of plant viruses. Frontiers in Microbiology, 9, 939.
Singh K, Kundu J K. 2017. Variations in coat protein sequence of Wheat streak mosaic virus among crop and non-crop hosts. Crop and Pasture Science, 68, 328–336.
Singh K, Wegulo S N, Skoracka A, Kundu J K. 2018. Wheat streak mosaic virus: A century old virus with rising importance worldwide. Molecular Plant Pathology, 19, 2193–2206.
Tr?bicki P, Nancarrow N, Cole E, Bosque-Pérez N A, Constable FE, Freeman A J, Rodoni B, Yen A L, Luck J E, Fitzgerald G J. 2015. Virus disease in wheat predicted to increase with a changing climate. Global Change Biology, 9, 3511–3519.
Tr?bicki P, Vandegeer R K, Bosque-Pérez N A, Powell A, Kevin S, Dader B, Freeman A J, Yen A L, Fitzgerald G J, Luck J E. 2016. Virus infection mediates the effects of elevated CO2 on plants and vectors. Scientific Reports, 6, 22785.
Turco S, Golyaev V, Seguin J, Gilli C, Farinelli L, Boller T, Schumpp O, Pooggin M M. 2018. Small RNA-omics for virome reconstruction and antiviral defense characterization in mixed infections of cultivated Solanum plants. Molecular Plant Microbe Interaction, 31, 707–723.
Walls J III, Rajotte E, Rosa C. 2019. The past, present, and future of Barley yellow dwarf management. Agriculture, 9, 23.
Wylie S J, Li H, Saqib M, Jones M G K. 2014. The global trade in fresh produce and the vagility of plant viruses: A case study in garlic. PLoS ONE, 9, e105044.
Yang X, Huang J, Liu C, Chen B, Zhang T, Zhou G. 2017. Rice stripe mosaic virus, a novel cytorhabdovirus infecting rice via leafhopper transmission. Frontiers in Microbiology, 7, 2140.
Zhang P, Liu Y, Liu W, Cao M, Massart S, Wang X. 2017. Identification, characterization and full-length sequence analysis of a novel Polerovirus associated with Wheat leaf yellowing disease. Frontiers in Microbiology, 8, 1689.
Zhang W, Cheng Z, Xu L, Wu M, Waterhouse P, Zhou G, Li S. 2009. The complete nucleotide sequence of the barley yellow dwarf GPV isolate from China shows that it is a new member of the genus Polerovirus. Archives of Virology, 154, 1125–1128.
Zheng Y, Gao S, Padmanabhan C, Li R, Galvez M, Gutierrez D, Fuentes S, Ling K S, Kreuze J, Fei Z. 2017. VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology, 500, 130–138.

Virome identification in wheat in the Czech Republic using small RNA deep sequencing

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