Variations in coat protein sequence of Wheat streak mosaic virus among crop and non-crop hosts
Khushwant Singh A and Jiban Kumar Kundu A B
+ Author Affiliations
- Author Affiliations
A Division of Crop Protection and Plant Health, Crop Research Institute, Drnovska 507, 16106 Prague, Czech Republic.
B Corresponding author. Email: jiban@vurv.cz
Crop and Pasture Science 68(4) 328-336 https://doi.org/10.1071/CP17025
Submitted: 17 January 2017 Accepted: 4 April 2017 Published: 8 May 2017
Abstract
Wheat streak mosaic virus (WSMV) has become a re-emerging pathogen in recent years in the Czech Republic. Crop (e.g. wheat, barley, maize) and non-crop grasses from the Poaceae family are the natural hosts of the virus. Here, we report the results from coat protein (CP) gene-sequence analysis of WSMV isolates from wheat crops (four cultivars: Turondot, Bodyček, Avenue, Hymack) and three grass species (Agropyron repens, Phleum pratense, Poa pratensis). Phylogenetic reconstruction of putative CP sequences showed that all tested isolates clustered with existing type B isolates of WSMV (originating from Europe and Asia) rather than type D (originating from USA, Argentina, Australia, and Iran) and type A (originating from Mexico) isolates. Analysis of recombination events showed that Turondot and Hymack isolates recombined with P. pratense, whereas Bodyček and Avenue isolates recombined with a type B isolate (Iran_Saadat-Shahr). The grasses A. repens, P. pratense and P. pratensis share recombination events with type A (Mexico_El Batán), type B (French and German isolates) and type D (Iran_Naghadeh) isolates. The characteristic GCA (Gly276) triplet codon found in type B isolates was conserved in both the wheat and grass isolates. Notably, nucleotide variations were mainly observed at positions nt 381–389, nt 405–460 and nt 486–497 between crop and non-crop hosts. Based on our analysis, we propose that the grass isolates form subtype B1 within the type B isolates of WSMV. Putative CP amino acid sequences in the centre of the protein and in the C-terminal domain (aa 112–260) were significantly more frequently conserved in both wheat and grasses than those in the N-terminal domain (aa 11–80). Collectively, these results indicate that variations exist between crop and non-crop hosts of WSMV.
Additional keywords: cereals, RT-PCR, vector, Virus diversity, wheat curl mite.
References
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren JY, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research 37, W202–W208.| MEME SUITE: tools for motif discovery and searching.Crossref | GoogleScholarGoogle Scholar |
Brakke MK (1971). Wheat streak mosaic virus. CMI/AAB Descriptions of Plant Viruses. No. 48. Association of Applied Biologists, Wellesbourne, UK.
Chalupniková J, Kundu JK, 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.
| Wheat streak mosaic virus: incidence in field crops, potential reservoir within grass species and uptake in winter wheat cultivars.Crossref | GoogleScholarGoogle Scholar |
Choi IR, Horken KM, Stenger DC, French R (2002) Mapping of the P1 proteinase cleavage site in the polyprotein of Wheat streak mosaic virus (genus Tritimovirus). The Journal of General Virology 83, 443–450.
| Mapping of the P1 proteinase cleavage site in the polyprotein of Wheat streak mosaic virus (genus Tritimovirus).Crossref | GoogleScholarGoogle Scholar |
Coutts BA, Banovic M, Kehoe MA, Severtson DL, Jones RAC (2014) Epidemiology of Wheat streak mosaic virus in wheat in a Mediterranean-type environment. European Journal of Plant Pathology 140, 797–813.
| Epidemiology of Wheat streak mosaic virus in wheat in a Mediterranean-type environment.Crossref | GoogleScholarGoogle Scholar |
Dráb T, Svobodová E, Ripl J, Jarošová J, Rabenstein F, Melcher U, Kundu JK (2014) SYBR Green I based RT-qPCR assays for the detection of RNA viruses of cereals and grasses. Crop & Pasture Science 65, 1323–1328.
Dwyer GI, Gibb MJ, Gibbs AJ, Jones RAC (2007) Wheat streak mosaic virus in Australia: relationship to isolates from the Pacific Northwest of the USA and its dispersion via seed transmission. Plant Disease 91, 164–170.
| Wheat streak mosaic virus in Australia: relationship to isolates from the Pacific Northwest of the USA and its dispersion via seed transmission.Crossref | GoogleScholarGoogle Scholar |
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research 44, D279–D285.
| The Pfam protein families database: towards a more sustainable future.Crossref | GoogleScholarGoogle Scholar |
French R, Stenger DC (2002) Wheat streak mosaic virus. CMI/ AAB Descriptions of Plant Viruses, No. 398. Association of Applied Biologists, Wellesbourne, UK.
Gadiou S, Kudela O, Ripl J, Rabenstein F, Kundu JK, Glasa M (2009) An amino acid deletion in Wheat streak mosaic virus capsid protein distinguishes a homogeneous group of European isolates and facilitates their specific detection. Plant Disease 93, 1209–1213.
| An amino acid deletion in Wheat streak mosaic virus capsid protein distinguishes a homogeneous group of European isolates and facilitates their specific detection.Crossref | GoogleScholarGoogle Scholar |
Hadi BAR, Langham MAC, Osborne L, Tilmon KJ (2011) Wheat streak mosaic virus on wheat: biology and management. Journal of Integrated Pest Management 2, 1–5.
| Wheat streak mosaic virus on wheat: biology and management.Crossref | GoogleScholarGoogle Scholar |
Hassan M, Sirlova L, Vacke J (2014) Tall oatgrass mosaic virus (TOgMV): a novel member of the genus Tritimovirus infecting Arrhenatherum elatius. Archives of Virology 159, 1585–1592.
| Tall oatgrass mosaic virus (TOgMV): a novel member of the genus Tritimovirus infecting Arrhenatherum elatius.Crossref | GoogleScholarGoogle Scholar |
Jarošová J, Chrpová J, Šíp V, Kundu JK (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.
| A comparative study of the Barley yellow dwarf virus species PAV and PAS: distribution, virus accumulation and host resistance.Crossref | GoogleScholarGoogle Scholar |
Jones JDG, Dangl JL (2006) The plant immune system. Nature 444, 323–329.
| The plant immune system.Crossref | GoogleScholarGoogle Scholar |
Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis Version 7.0 for bigger datasets. Molecular Biology and Evolution 33, 1870–1874.
| MEGA7: Molecular evolutionary genetics analysis Version 7.0 for bigger datasets.Crossref | GoogleScholarGoogle Scholar |
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948.
| Clustal W and Clustal X version 2.0.Crossref | GoogleScholarGoogle Scholar |
Li WH (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution 36, 96–99.
| Unbiased estimation of the rates of synonymous and nonsynonymous substitution.Crossref | GoogleScholarGoogle Scholar |
Librado P, Rozas J (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452.
| DnaSP v5: A software for comprehensive analysis of DNA polymorphism data.Crossref | GoogleScholarGoogle Scholar |
Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution 1, 1–5.
| RDP4: Detection and analysis of recombination patterns in virus genomes.Crossref | GoogleScholarGoogle Scholar |
Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3, 418–426.
Prendeville HR, Tenhumberg B, Pilson D (2014) Effects of virus on plant fecundity and population dynamics. New Phytologist 202, 1346–1356.
| Effects of virus on plant fecundity and population dynamics.Crossref | GoogleScholarGoogle Scholar |
Price JA, Simmons AR, Rashed A, Workneh F, Rush CM (2014) Winter wheat cultivars with temperature-sensitive resistance to Wheat streak mosaic virus do not recover from early-season infections. Plant Disease 98, 525–531.
| Winter wheat cultivars with temperature-sensitive resistance to Wheat streak mosaic virus do not recover from early-season infections.Crossref | GoogleScholarGoogle Scholar |
Rabenstein F, Seifers DL, Schubert J, French R, Stenger DC (2002) Phylogenetic relationships, strain diversity and biogeography of Tritimoviruses. The Journal of General Virology 83, 895–906.
| Phylogenetic relationships, strain diversity and biogeography of Tritimoviruses.Crossref | GoogleScholarGoogle Scholar |
Robinson MD, Murray TD (2013) Genetic variation of Wheat streak mosaic virus in the United States Pacific Northwest. Phytopathology 103, 98–104.
| Genetic variation of Wheat streak mosaic virus in the United States Pacific Northwest.Crossref | GoogleScholarGoogle Scholar |
Schubert J, Ziegler A, Rabenstein F (2015) First detection of Wheat streak mosaic virus in Germany: molecular and biological characteristics. Archives of Virology 160, 1761–1766.
| First detection of Wheat streak mosaic virus in Germany: molecular and biological characteristics.Crossref | GoogleScholarGoogle Scholar |
Singh K, Zouhar M, Mazaková J, Ryšaněk P (2014) Genome wide identification of the immunophilin gene family in Leptosphaeria maculans: A causal agent of blackleg disease in oilseed rape (Brassica napus). Omics – A Journal of Integrative Biology 18, 645–657.
| Genome wide identification of the immunophilin gene family in Leptosphaeria maculans: A causal agent of blackleg disease in oilseed rape (Brassica napus).Crossref | GoogleScholarGoogle Scholar |
Slykhuis JT (1955) Aceria tulipae keifer (Acarina: Eriophyidae) in relation to the spread of Wheat streak mosaic. Phytopathology 45, 116–128.
Stenger DC, French R (2009) Wheat streak mosaic virus genotypes introduced to Argentina are closely related to isolates from the American Pacific Northwest and Australia. Archives of Virology 154, 331–336.
| Wheat streak mosaic virus genotypes introduced to Argentina are closely related to isolates from the American Pacific Northwest and Australia.Crossref | GoogleScholarGoogle Scholar |
Stenger DC, Seifers DL, French R (2002) Patterns of polymorphism in Wheat streak mosaic virus: Sequence space explored by a clade of closely related viral genotypes rivals that between the most divergent strains. Virology 302, 58–70.
| Patterns of polymorphism in Wheat streak mosaic virus: Sequence space explored by a clade of closely related viral genotypes rivals that between the most divergent strains.Crossref | GoogleScholarGoogle Scholar |
Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences of the United States of America 101, 11030–11035.
| Prospects for inferring very large phylogenies by using the neighbor-joining method.Crossref | GoogleScholarGoogle Scholar |
Tatineni S, French R (2014) The C-terminus of Wheat streak mosaic virus coat protein is involved in differential infection of wheat and maize through host-specific long-distance transport. Molecular Plant-Microbe Interactions 27, 150–162.
| The C-terminus of Wheat streak mosaic virus coat protein is involved in differential infection of wheat and maize through host-specific long-distance transport.Crossref | GoogleScholarGoogle Scholar |
Vacke J, Zacha V, Jokeš M (1986) Identification of virus in wheat new to Czechoslovakia. In ‘Proceeding X Czechoslovak Plant Protection Conference’. pp. 209–210. Brno, Czech Republic.
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191.
| Jalview Version 2—a multiple sequence alignment editor and analysis workbench.Crossref | GoogleScholarGoogle Scholar |
