The potyviruses of Australia

Archives of Virology

Volumn 153, Issue 8, 2008, Pages 1411-1420

  Gibbs, A J ^a,b   MacKenzie, A M ^a,c   Wei, K J ^a   Gibbs, M J ^a,b  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b Black Mountain Laboratories ^*  (Australia)

^c CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA;

AUSTRALIA; CHEMISTRY; CLASSIFICATION; CROP; GENETICS; ISOLATION AND PURIFICATION; PHYLOGENY; PLANT DISEASE; POTYVIRUS; SEQUENCE ALIGNMENT; SHORT SURVEY; VIROLOGY; VIRUS CAPSID; VIRUS GENOME;

AUSTRALIA; CAPSID; CROPS, AGRICULTURAL; DNA, VIRAL; GENOME, VIRAL; PHYLOGENY; PLANT DISEASES; POTYVIRUS; SEQUENCE ALIGNMENT;

BEAN COMMON MOSAIC VIRUS; POTYVIRUS;

EID: 47549099787     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-008-0134-6     Document Type: Short Survey

References (37)

1. Brunt AA, Crabtree K, Dallwitz M, Gibbs A, Watson L (1996) Viruses of plants. C. A. B. International, UK
2. Buchen-Osmond C, Crabtree K, Gibbs A, McLean G (1988) Viruses of plants in Australia. Australian National University, Canberra
3. Carver M, Gross GF, Woodward TE (1991) Hemiptera (bugs, leafhoppers, cicadas, aphids, scale insects, etc). In: Naumann ID (ed) The insects of Australia, vol 1. Melbourne University Press, Melbourne
4. Chen J, Chen J, Adams MJ (2001) A universal PCR primer to detect members of the Potyviridae and its use to examine the taxonomic status of several members of the family. Arch Virol 146:757-766
5. Clemens WA, Richardson AJ, Baverstock PR (1989) Biogeography and phylogeny of the Metatheria. In: Walton DW, Richardson BJ (eds) Fauna of Australia vol IB Mammalia. Australian Government Publishing Service, Canberra, pp 527-548
6. Crisp MD (2001) Historical biogeography and patterns of diversity in plants, algae and fungi: introduction. J Biogeogr 28:153
7. Dwyer GI, Gibbs 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 Dis 91:164-170
8. Eastop V (1966) A taxonomic study of Australian Aphidoidea (Homoptera). Aust J Zool 14:399-592
9. Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy: classification and nomenclature of viruses. 8th report of the international committee on the taxonomy of viruses. Elsevier-Academic Press, New York
10. Fourment M, Gibbs MJ (2006) PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change. BMC Evol Biol 6:1
11. Gibbs A, Guy P (1978) How long have there been plant viruses in Australia? Aust Plant Pathol 8:41-42
12. Gibbs AJ, Mackenzie AM, Gibbs MJ (2003) The 'potyvirid primers' will probably provide phylogenetically informative DNA fragments from all species of Potyviridae. J Virol Methods 112:41-44
13. Gibbs AJ, Ohshima K, Phillips MJ, Gibbs MJ (2008) The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. PLoS ONE (in press)
14. Gibbs MJ, Wayper P, Fourment ML, Wood JT, Ohshima K, Armstrong JS, Gibbs AJ (2006) The variable codons of H3 influenza A virus haemagglutinin genes. Arch Virol 52:11-24
15. Guindon S, Gascuel O (2003) PhyML-a simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704
16. Hancock JM (1995) The contribution of slippage-like processes to genome evolution. J Mol Evol 41:1038-1047
17. Hasegawa M, Kishino H, Yano T-A (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
18. Holmes FO (1951) Indications of a new world origin of tobacco mosaic virus. Phytopathology 41:341-349
19. Jeanmougin F, Thompson JD, Gibson TJ, Gouy M, Higgins DG (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23:403-405
20. Jones DR, Baker RHA (2007) Introductions of non-native plant pathogens into Great Britain, 1970-2004. Plant Pathol 56:891-910
21. Jones RAC, Coutts BA, Mackie AE, Dwyer GI (2005) Seed transmission of wheat streak mosaic virus shown unequivocally in wheat. Plant Dis 89:1048-1050
22. Kiratyi-Angul S, Gibbs A (1992) Group-specific antiserum detects potyviruses in several wild plant species in S.E. Australia. Aust Plant Pathol 21:118-119
23. Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20:86-93
24. Martin DP, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260-262
25. McLean GD, Price LK (1984) Virus, viroid, mycoplasma and rickettsial diseases of plants in Western Australia. Technical Bulletin. Department of Agriculture, Western Australia, Perth, vol 68, p 22
26. Murray RGE, Stackebrandt E (1995) Taxonomic Note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int J Syst Bacteriol 45:186-187
27. Robaglia C, Durand-Tardif M, Tronchet M, Boudazin G, Astier-Manifacier S, Casse-Delbart F (1989) Nucleotide sequence of potato virus Y (N Strain) genomic RNA. J Gen Virol 70:935-947
28. Sampson PJ, Walker J (1982) An annotated list of plant diseases in Tasmania. Department of Agriculture, Tasmania, p 121
29. Shukla DD, Ward CW, Brunt AA (1994) The potyviridae. CAB International, Wallingford
30. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ, Nesme X, Possello-Mora R, Swings J, Trüper HG, Vauterin L, Ward A, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043-1047
31. Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Sunderland
32. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882
33. Ward CW, Weiller G, Shukla DD, Gibbs AJ (1995) Molecular systematics of the potyviridae, the largest plant virus family. In: Gibbs AJ, Calisher CH, Garcia-Arenal H (eds) Molecular basis of virus evolution. Cambridge University Press, Cambridge, pp 477-500
34. Webster CG, Coutts BA, Jones RAC, Jones MGK, Wylie SJ (2007) Virus impact at the ancient ecosystem-recent agroecosystem interface: studies on three legume-infecting potyviruses in the Southwest Australian floristic region. Plant Pathol 56(5):729-742
35. Weiller GF (1998) Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15:326-335
36. White NH (1973) The geographic isolation of Australia in relation to plant viruses. Aust Plant Path Soc Newsl 2:32-33
37. Zheng L, Wayper PJ, Gibbs AJ, Fourment M, Rodoni BC, Gibbs MJ (2008) Accumulating variation at conserved sites in potyvirus genomes is driven by species discovery and affects degenerate primer design. PLoS ONE 3:e1586