Identification and molecular characterization of a single-stranded circular DNA virus with similarities to Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1

Archives of Virology

Volumn 159, Issue 6, 2014, Pages 1527-1531

  Du, Zhenguo ^a,b   Tang, Yafei ^a   Zhang, Songbai ^c   She, Xiaoman ^a   Lan, Guobing ^a   Varsani, Arvind ^d,e   He, Zifu ^a,b  

^a INSTITUTE OF ANIMAL SCIENCE   (China)

^b Guangdong Provincial Key Laboratory of High Technology for Plant Protection   (China)

^c YANGTZE UNIVERSITY   (China)

^d UNIVERSITY OF CAPE TOWN   (South Africa)

^e UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

DNA VIRUSES; GEMINIVIRIDAE; HYPERICUM; HYPERICUM JAPONICUM; MIRIDAE; SCLEROTINIA SCLEROTIORUM;

CIRCULAR DNA; VIRUS DNA;

ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; DNA SEQUENCE; DNA VIRUS; GENETICS; HYPERICUM; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PROTEIN MOTIF; SEQUENCE HOMOLOGY; VIET NAM; VIROLOGY;

AMINO ACID MOTIFS; CLUSTER ANALYSIS; DNA VIRUSES; DNA, CIRCULAR; DNA, VIRAL; HYPERICUM; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; VIETNAM;

EID: 84901975965     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-013-1890-5     Document Type: Article

References (27)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Dayaram A, Opong A, Jaschke A, Hadfield J, Baschiera M, Dobson RC, Offei SK, Shepherd DN, Martin DP, Varsani A (2012) Molecular characterisation of a novel cassava associated circular ssDNA virus. Virus Res 166: 130-135.
3. Delwart E, Li L (2012) Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes. Virus Res 164: 114-121.
4. Desbiez C, David C, Mettouchi A, Laufs J, Gronenborn B (1995) Rep protein of tomato yellow leaf curl geminivirus has an ATPase activity required for viral DNA replication. Proc Natl Acad Sci USA 92: 5640-5644.
5. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
6. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3. 0. Syst Biol 59: 307-321.
7. Hafner GJ, Stafford MR, Wolter LC, Harding RM, Dale JL (1997) Nicking and joining activity of banana bunchy top virus replication protein in vitro. J Gen Virol 78(Pt 7): 1795-1799.
8. Haible D, Kober S, Jeske H (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135: 9-16.
9. Harrison BD, Liu YL, Khalid S, Hameed S, OtimNape GW, Robinson DJ (1997) Detection and relationships of cotton leaf curl virus and allied whitefly-transmitted geminiviruses occurring in Pakistan. Annu Appl Biol 130: 61-75.
10. Kraberger S, Stainton D, Dayaram A, Zawar-Reza P, Gomez C, Harding JS, Varsani A (2013) Discovery of Sclerotinia sclerotiorum hypovirulence-associated virus-1 in Urban River sediments of Heathcote and Styx Rivers in Christchurch city, New Zealand. Genome Announcements 1: e00513-e00559.
11. Laufs J, Schumacher S, Geisler N, Jupin I, Gronenborn B (1995) Identification of the nicking tyrosine of geminivirus Rep protein. FEBS Lett 377: 258-262.
12. Laufs J, Traut W, Heyraud F, Matzeit V, Rogers SG, Schell J, Gronenborn B (1995) In vitro cleavage and joining at the viral origin of replication by the replication initiator protein of tomato yellow leaf curl virus. Proc Natl Acad Sci USA 92: 3879-3883.
13. Merits A, Fedorkin ON, Guo D, Kalinina NO, Morozov SY (2000) Activities associated with the putative replication initiation protein of coconut foliar decay virus, a tentative member of the genus Nanovirus. J Gen Virol 81: 3099-3106.
14. Muhire B, Martin DP, Brown JK, Navas-Castillo J, Moriones E, Zerbini FM, Rivera-Bustamante R, Malathi VG, Briddon RW, Varsani A (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158: 1411-1424.
15. Nash TE, Dallas MB, Reyes MI, Buhrman GK, Ascencio-Ibanez JT, Hanley-Bowdoin L (2011) Functional analysis of a novel motif conserved across geminivirus Rep proteins. J Virol 85: 1182-1192.
16. Ng TF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan Y, Rohwer F, Breitbart M (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PloS One 6: e20579.
17. Ng TFF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, Oderinde BS, Wommack KE, Delwart E (2012) High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. J Virol 86 (22): 12161-12175.
18. Rosario K, Dayaram A, Marinov M, Ware J, Kraberger S, Stainton D, Breitbart M, Varsani A (2012) Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta). J Gen Virol 93: 2668-2681.
19. Rosario K, Duffy S, Breitbart M (2012) A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch Virol 157: 1851-1871.
20. Steinfeldt T, Finsterbusch T, Mankertz A (2006) Demonstration of nicking/joining activity at the origin of DNA replication associated with the Rep and Rep' proteins of porcine circovirus type 1. J Virol 80: 6225-6234.
21. Steinfeldt T, Finsterbusch T, Mankertz A (2007) Functional analysis of cis- and trans-acting replication factors of porcine circovirus type 1. J Virol 81: 5696-5704.
22. Timchenko T, de Kouchkovsky F, Katul L, David C, Vetten HJ, Gronenborn B (1999) A single rep protein initiates replication of multiple genome components of faba bean necrotic yellows virus, a single-stranded DNA virus of plants. J Virol 73: 10173-10182.
23. van den Brand JM, van Leeuwen M, Schapendonk CM, Simon JH, Haagmans BL, Osterhaus AD, Smits SL (2012) Metagenomic analysis of the viral flora of pine marten and European badger feces. J Virol 86: 2360-2365.
24. Vega-Rocha S, Gronenborn B, Gronenborn AM, Campos-Olivas R (2007) Solution structure of the endonuclease domain from the master replication initiator protein of the nanovirus faba bean necrotic yellows virus and comparison with the corresponding geminivirus and circovirus structures. Biochemistry 46: 6201-6212.
25. Wright EA, Heckel T, Groenendijk J, Davies JW, Boulton MI (1997) Splicing features in maize streak virus virion- and complementary-sense gene expression. Plant J Cell Mol Biol 12: 1285-1297.
26. Yu X, Li B, Fu Y, Jiang D, Ghabrial SA, Li G, Peng Y, Xie J, Cheng J, Huang J, Yi X (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc Natl Acad Sci USA 107: 8387-8392.
27. Yu X, Li B, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, Yi X, Jiang D (2013) Extracellular transmission of a DNA mycovirus and its use as a natural fungicide. Proc Natl Acad Sci USA 110: 1452-1457.