Complete nucleotide sequence of a new strain of grapevine leafroll-associated virus 3 in South Africa

Archives of Virology

Volumn 157, Issue 9, 2012, Pages 1815-1819

  Bester, R ^a   Maree, H J ^a,b   Burger, J T ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b ARC INFRUITEC NIETVOORBIJ   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

ARTICLE; CLASSIFICATION; CLOSTEROVIRIDAE; CLUSTER ANALYSIS; DNA SEQUENCE; GENE ORDER; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PLANT DISEASE; SOUTH AFRICA; SYNTENY; VIROLOGY; VIRUS GENOME; VITIS;

CLOSTEROVIRIDAE; CLUSTER ANALYSIS; GENE ORDER; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; PLANT DISEASES; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SOUTH AFRICA; SYNTENY; VITIS;

GRAPEVINE LEAFROLL-ASSOCIATED VIRUS 3;

EID: 84865705970     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-012-1333-8     Document Type: Article

References (17)

1. Pietersen G (2004) Spread of grapevine leafroll disease in South Africa-a difficult, but not insurmountable problem. Wynboer-a technical guide for wine producers. June 2004. http://www. wynboer. co. za/recentarticles/articles. php3. Accessed 17 Jan 2012.
2. Martelli GP, Agranovsky AA, Bar-Joseph M, Boscia D, Candresse T, Coutts RHA, Dolja VV, Falk BW, Gonsalves D, Jelkmann W, Karasev AV, Minafra A, Namba S, Vetten HJ, Wisler GC, Yoshikawa N (2002) The family Closteroviridae revised. Arch Virol 147(10): 2039-2044.
3. Jooste AEC, Maree HJ, Bellstedt DU, Goszczynski DE, Pietersen G, Burger JT (2010) Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5′UTR. Arch Virol 155: 1997-2006.
4. Maree HJ, Freeborough M-J, Burger JT (2008) Complete nucleotide sequence of a South African isolate of grapevine leafroll-associated virus 3 reveals a 5′UTR of 737 nucleotides. Arch Virol 153: 755-757.
5. Coetzee B, Freeborough M-J, Maree HJ, Celton J, Rees DJG, Burger JT (2010) Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 400(2): 157-163.
6. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5): 821-829.
7. Osman F, Leutenegger C, Golino D, Rowhani A (2007) Real-time RT-PCR (TaqMan®) assays for the detection of grapevine leafroll associated viruses 1-5 and 9. J Virol Methods 141(1): 22-29.
8. White EJ, Venter M, Hiten NF, Burger JT (2008) Modified Cetyltrimethylammonium bromide method improves robustness and versatility: the benchmark for plant RNA extraction. Biotechnol J 3(11): 1424-1428.
9. Valverde RA, Nameth ST, Jordan RL (1990) Analysis of double-stranded-RNA for plant-virus diagnosis. Plant Dis 74(3): 255-258.
10. Meng B, Li C, Goszczynski DE, Gonsalves D (2005) Genome sequences and structures of two biologically distinct strains of Grapevine leafroll-associated virus 2 and sequence analysis. Virus Genes 31: 31-41.
11. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
12. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
13. Gouveia P, Santos MT, Eiras-Dias JE, Nolasco G (2010) Five phylogenetic groups identified in the coat protein gene of grapevine leafroll-associated virus 3 obtained from Portuguese grapevine varieties. Arch Virol 156(3): 413-420.
14. Sharma AM, Wang J, Duffy S, Zhang S, Wong MK, Rashed A, Cooper ML, Daane KM, Almeida RPP (2011) Occurence of grapevine leafroll-associated virus complex in Napa valley. PLoS ONE 6(10): e26227. doi: 10. 1371/journal. pone. 0026227.
15. Ling KS, Zhu HY, Gonsalves D (2004) Complete nucleotide sequence and genome organization of grapevine leafroll-associated virus 3, type member of the genus Ampelovirus. J Gen Virol 85: 2099-2102.
16. Ling KS, Zhu HY, Drong RF, Slightom JL, Gonsalves D (1998) Nucleotide sequence of the 39-terminal two-thirds of the grapevine leafroll-associated virus-3 genome reveals a typical monopartite closterovirus. J Gen Virol 79: 1299-1307.
17. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M (2008) CDD: specific functional annotation with the conserved domain database. Nucleic Acids Res 37: 205-210.