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

Volumn 62, Issue 4, 2013, Pages 741-749

  Adams, I P ^a   Miano, D W ^b   Kinyua, Z M ^b   Wangai, A ^b   Kimani, E ^c   Phiri, N ^d   Reeder, R ^e   Harju, V ^a   Glover, R ^a   Hany, U ^a   Souza Richards, R ^a,f   Deb Nath, P ^a,g   Nixon, T ^a   Fox, A ^a   Barnes, A ^a   Smith, J ^a   Skelton, A ^a   Thwaites, R ^a   Mumford, R ^a   Boonham, N ^a  

^a FOOD AND ENVIRONMENT RESEARCH AGENCY   (United Kingdom)

^b KENYA AGRICULTURAL RESEARCH INSTITUTE   (Kenya)

^c Kenya Plant Health Inspectorate Service   (Kenya)

^d CAB International   (Kenya)

^e CAB International   (United Kingdom)

^f UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^g ASSAM AGRICULTURAL UNIVERSITY   (India)

Author keywords

Diagnostics; Next generation sequencing; Virology

Indexed keywords

BIOASSAY; DATABASE; DISEASE INCIDENCE; GENOME; IDENTIFICATION METHOD; INOCULATION; MAIZE; REAL TIME; RNA; SYMPTOM; VIRAL DISEASE; VIRUS;

KENYA;

MAIZE CHLOROTIC MOTTLE VIRUS; SUGARCANE MOSAIC VIRUS; ZEA MAYS;

EID: 84880302416     PISSN: 00320862     EISSN: 13653059     Source Type: Journal    
DOI: 10.1111/j.1365-3059.2012.02690.x     Document Type: Article

References (25)

1. Adams IP, Glover RH, Monger WA, 2009. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Molecular Plant Pathology 10, 537-45.
2. Adams IP, Abidrabo P, Miano DW, 2012. High throughput real-time RT-PCR assays for specific detection of cassava brown streak disease causal viruses, and their application to testing of planting material. Plant Pathology 62, 233-42.
3. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW, 2011. GenBank. Nucleic Acids Research 39, D32-7.
4. Camacho C, Coulouris G, Avagyan V, 2009. blast+: architecture and applications. BMC Bioinformatics 10, 421.
5. Chen J, Adams MJ, 2002. Characterisation of potyviruses from sugarcane and maize in China. Archives of Virology 147, 1237-46.
6. Clark MF, Adams AN, 1977. Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. Journal of General Virology 34, 475-83.
7. Gao B, Cui X-W, Li X-D, Zhang C-Q, Miao H-Q, 2011. Complete genomic sequence analysis of a highly virulent isolate revealed a novel strain of Sugarcane mosaic virus. Virus Genes 43, 390-7.
8. Goldberg K, Brakke M, 1987. Concentration of Maize chlorotic mottle virus increases in mixed infections with Maize dwarf mosaic virus, strain B. Pytopathology 77, 162-7.
9. Handley JA, Smith GR, Dale JL, Harding RM, 1998. Sequence diversity in the coat protein coding region of twelve sugarcane mosaic potyvirus isolates from Australia, USA and South Africa. Archives of Virology 143, 1145-53.
10. Hill SA, 1984. Methods in Plant Virology. Oxford, UK: Blackwell Scientific.
11. Huson DH, Auch AF, Qi J, Schuster SC, 2007. megan analysis of metagenomic data. Genome Research 17, 377-86.
12. Kreuze JF, Perez A, Untiveros M, 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.
13. Louie R, 1980. Sugarcane mosaic virus in Kenya. Plant Disease 64, 944-7.
14. Milne I, Bayer M, Cardle L, 2010. tablet - next generation sequence assembly visualization. Bioinformatics 26, 401-2.
15. Morales FJ, Arroyave JA, Castillo J, De LC, 1999. Cytopathology of maize chlorotic mottle virus in Zea mays L. Maydica 44, 231-5.
16. Nutter RC, Scheets K, Panganiban LC, Lommel SA, 1989. The complete nucleotide sequence of the Maize chlorotic mottle virus genome. Nucleic Acids Research 17, 3163-77.
17. Pruitt KD, Tatusova T, Klimke W, Maglott DR, 2009. NCBI reference sequences: current status, policy and new initiatives. Nucleic Acids Research 37, D32-6.
18. 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, 395-401.
19. Scheets K, 2000. Maize chlorotic mottle machlomovirus expresses its coat protein from a 1·47-kb subgenomic RNA and makes a 0·34-kb subgenomic RNA. Virology 267, 90-101.
20. Stenger DC, French R, 2008. Complete nucleotide sequence of a Maize chlorotic mottle virus isolate from Nebraska. Archives of Virology 153, 995-7.
21. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, 2011. mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731-9.
22. Uyemote J, Claflin L, Wilson D, Raney R, 1981. Maize chlorotic mottle and Maize dwarf mosaic viruses: effect of single and double inoculations on symptomatology and yield. Plant Disease 65, 39-41.
23. Valverde R, Nameth S, Jordan R, 1990. Analysis of double-stranded RNA for plant virus diagnosis. Plant Disease 74, 255-8.
24. Xie L, Zhang J, Wang Q, Meng C, Hong J, Zhou X, 2011. Characterization of Maize chlorotic mottle virus associated with maize lethal necrosis disease in China. Journal of Phytopathology 159, 191-3.
25. Zhang Y, Zhao W, Li M, Chen H, Zhu S, Fan Z, 2011. Real-time TaqMan RT-PCR for detection of Maize chlorotic mottle virus in maize seeds. Journal of Virological Methods 171, 292-4.