Discovery of novel dsRNA viral sequences by in silico cloning and implications for viral diversity, host range and evolution

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Liu, Huiquan ^a,c   Fu, Yanping ^a   Xie, Jiatao ^a   Cheng, Jiasen ^a   Ghabrial, Said A ^b   Li, Guoqing ^a   Yi, Xianhong ^a   Jiang, Daohong ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF KENTUCKY   (United States)

^c NORTHWEST A F UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DOUBLE STRANDED RNA; VIRUS RNA;

ARTICLE; BIOINFORMATICS; CHRYSOVIRIDAE; COMPUTER MODEL; DNA LIBRARY; DNA SEQUENCE; ENDORNAVIRIDAE; EUKARYOTE; EXPRESSED SEQUENCE TAG; GENETIC DATABASE; GENETIC VARIABILITY; MICROBIAL DIVERSITY; MOLECULAR CLONING; MOLECULAR EVOLUTION; MYCOVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARTITIVIRIDAE; PHYLOGENY; PLANT PARTITIVIRUS; PLANT VIRUS; RNA SEQUENCE; TOTIVIRIDAE; VIRUS CELL INTERACTION; VIRUS STRAIN; VIRUS TRANSMISSION;

ANIMALS; BIODIVERSITY; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE LIBRARY; HOST-PATHOGEN INTERACTIONS; PHYLOGENY; RNA VIRUSES; RNA, DOUBLE-STRANDED;

CHRYSOVIRIDAE; DSRNA VIRUSES; EUKARYOTA; PARTITIVIRIDAE; TOTIVIRIDAE; UNCLASSIFIED DSRNA VIRUSES;

EID: 84864411545     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0042147     Document Type: Article

References (39)

1. Balijja A, Kvarnheden A, Turchetti T, ((2008)) A non-phenol-chloroform extraction of double-stranded RNA from plant and fungal tissues. J Virol Methods 152:: 32--37.
2. Froussard P, ((1992)) A random-PCR method (rPCR) to construct whole cDNA library from low amounts of RNA. Nucleic Acids Res 20:: 2900.
3. Delwart EL, ((2007)) Viral metagenomics. Rev Med Virol 17:: 115--131.
4. Edwards RA, Rohwer F, ((2005)) Viral metagenomics. Nat Rev Microbiol 3:: 504--510.
5. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, et al. ((2007)) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318:: 283--287.
6. Culley AI, Lang AS, Suttle CA, ((2006)) Metagenomic analysis of coastal RNA virus communities. Science 312:: 1795--1798.
7. Kim KH, Chang HW, Nam YD, Roh SW, Kim MS, et al. ((2008)) Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl Environ Microbiol 74:: 5975--5985.
8. Victoria JG, Kapoor A, Dupuis K, Schnurr DP, Delwart EL, ((2008)) Rapid identification of known and new RNA viruses from animal tissues. PLoS Pathog 4:: e1000163.
9. Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S, et al. ((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.
10. Vodovar N, Goic B, Blanc H, Saleh MC, ((2011)) In silico reconstruction of viral genomes from small RNAs improves virus-derived small interfering RNA profiling. J Virol 85:: 11016--11021.
11. Wu Q, Luo Y, Lu R, Lau N, Lai EC, et al. ((2010)) Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci U S A 107:: 1606--1611.
12. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, editors. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. New York: Elsevier.
13. Ghabrial SA, Suzuki N, ((2009)) Viruses of Plant Pathogenic Fungi. Annual Review of Phytopathology 47:: 353--384.
14. Blawid R, Stephan D, Maiss E (2008) Alphacryptovirus and Betacryptovirus. In: Encyclopedia of virology 3rd ed, vol 1. Mahy BWJ, Van Regenmortel MHV, editors. Oxford: Elsevier. 98-104.
15. Ghabrial SA, Ochoa WF, Baker TS, Nibert ML (2008) Partitiviruses: General Features. In: Encyclopedia of virology 3rd ed, vol 4. Mahy BWJ, Van Regenmortel MHV, editors. Oxford: Elsevier. 68-75.
16. Tavantzis S (2008) Partitiviruses of Fungi. In: Encyclopedia of virology 3rd ed, vol 4. Mahy BWJ, Van Regenmortel MHV, editors. Oxford: Elsevier. 63-68.
17. Ghabrial SA (2008) Chrysoviruses. In: Encyclopedia of virology 3rd ed, vol 1. Mahy BWJ, Van Regenmortel MHV, editors. Oxford: Elsevier. 503-513.
18. Fukuhara T, Moriyama H (2008) Endornavirus. In: Encyclopedia of virology 3rd ed, vol 2. Mahy BWJ, Van Regenmortel MHV, editors. Oxford: Elsevier. 109-116.
19. Martin RR, Zhou J, Tzanetakis IE, ((2011)) Blueberry latent virus: An amalgam of the Partitiviridae and Totiviridae. Virus Research 155:: 175--180.
20. Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Valverde RA, ((2010)) A novel monopartite dsRNA virus from rhododendron. Arch Virol 155:: 1859--1863.
21. Sabanadzovic S, Valverde RA, Brown JK, Martin RR, Tzanetakis IE, ((2009)) Southern tomato virus: The link between the families Totiviridae and Partitiviridae. Virus Research 140:: 130--137.
22. Chiba S, Salaipeth L, Lin YH, Sasaki A, Kanematsu S, et al. ((2009)) A Novel Bipartite Double-Stranded RNA Mycovirus from the White Root Rot Fungus Rosellinia necatrix: Molecular and Biological Characterization, Taxonomic Considerations, and Potential for Biological Control. Journal of Virology 83:: 12801--12812.
23. Lin YH, Chiba S, Tani A, Kondo H, Sasaki A, et al. ((2012)) A novel quadripartite dsRNA virus isolated from a phytopathogenic filamentous fungus, Rosellinia necatrix. Virology 426:: 42--50.
24. Ghabrial SA, ((1998)) Origin, adaptation and evolutionary pathways of fungal viruses. Virus Genes 16:: 119--131.
25. Villarreal LP (2005) Viruses and the evolution of life. Washington, DC: American Society for Microbiology.
26. Koonin EV, Wolf YI, Nagasaki K, Dolja VV, ((2008)) The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol 6:: 925--939.
27. Herrero N, Sanchez Marquez S, Zabalgogeazcoa I, ((2009)) Mycoviruses are common among different species of endophytic fungi of grasses. Arch Virol 154:: 327--330.
28. Salem NM, Golino DA, Falk BW, Rowhani A, ((2008)) Complete nucleotide sequences and genome characterization of a novel double-stranded RNA virus infecting Rosa multiflora. Arch Virol 153:: 455--462.
29. Liu H, Fu Y, Jiang D, Li G, Xie J, et al. ((2010)) Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. J Virol 84:: 11876--11887.
30. Chiba S, Kondo H, Tani A, Saisho D, Sakamoto W, et al. ((2011)) Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes. PLoS Pathog 7:: e1002146.
31. Poulos BT, Tang KF, Pantoja CR, Bonami JR, Lightner DV, ((2006)) Purification and characterization of infectious myonecrosis virus of penaeid shrimp. J Gen Virol 87:: 987--996.
32. Zhai Y, Attoui H, Mohd Jaafar F, Wang HQ, Cao YX, et al. ((2010)) Isolation and full-length sequence analysis of Armigeres subalbatus totivirus, the first totivirus isolate from mosquitoes representing a proposed novel genus (Artivirus) of the family Totiviridae. J Gen Virol 91:: 2836--2845.
33. Spear A, Sisterson MS, Yokomi R, Stenger DC, ((2010)) Plant-feeding insects harbor double-stranded RNA viruses encoding a novel proline-alanine rich protein and a polymerase distantly related to that of fungal viruses. Virology 404:: 304--311.
34. Haugland O, Mikalsen AB, Nilsen P, Lindmo K, Thu BJ, et al. ((2011)) Cardiomyopathy syndrome of atlantic salmon (Salmo salar L.) is caused by a double-stranded RNA virus of the Totiviridae family. J Virol 85:: 5275--5286.
35. Cox S, Mayo M, Jones AT, ((2000)) The occurrence of dsRNA species in apparently healthy and virus-infected Ribes cultivars, and evidence that one such species originates from a member of the virus family Totiviridae. European journal of plant pathology 106:: 353--364.
36. Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, et al. ((2005)) The tree of eukaryotes. Trends Ecol Evol 20:: 670--676.
37. Papadopoulos JS, Agarwala R, ((2007)) COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23:: 1073--1079.
38. Guindon S, Gascuel O, ((2003)) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:: 696--704.
39. Le SQ, Lartillot N, Gascuel O, ((2008)) Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci 363:: 3965--3976.