Evolutionary genomics of mycovirus-related dsRNA viruses reveals cross-family horizontal gene transfer and evolution of diverse viral lineages

BMC Evolutionary Biology

Volumn 12, Issue 1, 2012, Pages

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

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF KENTUCKY   (United States)

^c CHINA AGRICULTURAL UNIVERSITY   (China)

^d NORTHWEST A F UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTION; EVOLUTIONARY BIOLOGY; GENE TRANSFER; GENOME; GENOMICS; MACROECOLOGY; NEW SPECIES; PHYLOGENETICS; TAXONOMY; VIRUS;

CHRYSOVIRIDAE; DSRNA VIRUSES; MYCOVIRUS; ORTHOREOVIRUS; PARTITIVIRIDAE; PHYTOREOVIRUS; REOVIRIDAE; SCLEROTINIA SCLEROTIORUM; TOTIVIRIDAE;

DOUBLE STRANDED RNA;

AMINO ACID SEQUENCE; ARTICLE; ASCOMYCETES; CLASSIFICATION; GENETICS; HORIZONTAL GENE TRANSFER; ISOLATION AND PURIFICATION; MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; RNA VIRUS; SEQUENCE ANALYSIS; VIROLOGY; VIRUS GENOME;

AMINO ACID SEQUENCE; ASCOMYCOTA; CLONING, MOLECULAR; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA VIRUSES; RNA, DOUBLE-STRANDED; SEQUENCE ANALYSIS, RNA;

EID: 84862306931     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-12-91     Document Type: Article

References (50)

1. Viruses of plant pathogenic fungi. Ghabrial SA, Suzuki N, Annu Rev Phytopathol 2009 47 353 384 10.1146/annurev-phyto-080508-081932 19400634
2. Mycoviruses of filamentous fungi and their relevance to plant pathology. Pearson MN, Beever RE, Boine B, Arthur K, Mol Plant Pathol 2009 10 1 115 128 10.1111/j.1364-3703.2008.00503.x 19161358
3. A novel mycovirus that is related to the human pathogen hepatitis E virus and rubi-like viruses. Liu HQ, Fu YP, Jiang DH, Li GQ, Xie J, Peng YL, Yi XH, Ghabrial SA, J Virol 2009 83 4 1981 1991 10.1128/JVI.01897-08 19073734
4. A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Yu X, Li B, Fu YP, Jiang DH, Ghabrial SA, Li GQ, Peng YL, Xie JT, Cheng JS, Huang JB, et al. Proc Natl Acad Sci U S A 2010 107 18 8387 8392 10.1073/pnas.0913535107 20404139
5. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, (Eds): Virus taxonomy: Ninth Report of the International Committee on taxonomy of viruses New York: Elsevier 2011
6. Blueberry latent virus: an amalgam of the Partitiviridae and Totiviridae. Martin RR, Zhou J, Tzanetakis IE, Virus Res 2011 155 1 175 180 10.1016/j.virusres.2010.09.020 20888379
7. A novel monopartite dsRNA virus from rhododendron. Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Valverde RA, Arch Virol 2010 155 11 1859 1863 10.1007/s00705-010-0770-5 20721591
8. Southern tomato virus: the link between the families Totiviridae and Partitiviridae. Sabanadzovic S, Valverde RA, Brown JK, Martin RR, Tzanetakis IE, Virus Res 2009 140 1-2 130 137 19118586
9. 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. Chiba S, Salaipeth L, Lin YH, Sasaki A, Kanematsu S, Suzuki N, J Virol 2009 83 24 12801 12812 10.1128/JVI.01830-09 19828620
10. Rapid host adaptation by extensive recombination. van der Walt E, Rybicki EP, Varsani A, Polston JE, Billharz R, Donaldson L, Monjane AL, Martin DP, J Gen Virol 2009 90 Pt 3 734 746 19218220
11. Recombination every day: abundant recombination in a virus during a single multi-cellular host infection. Froissart R, Roze D, Uzest M, Galibert L, Blanc S, Michalakis Y, PLoS Biol 2005 3 3 89 10.1371/journal.pbio.0030089 15737066 (Pubitemid 40605289)
12. Generation of diversity in retroviruses. Katz RA, Skalka AM, Annu Rev Genet 1990 24 409 445 10.1146/annurev.ge.24.120190.002205 1708222 (Pubitemid 120011554)
13. A phylogenetic survey of recombination frequency in plant RNA viruses. Chare ER, Holmes EC, Arch Virol 2006 151 5 933 946 10.1007/s00705-005-0675-x 16292597
14. Evolutionary aspects of recombination in RNA viruses. Worobey M, Holmes EC, J Gen Virol 1999 80 Pt 10 2535 2543 10573145 (Pubitemid 29458613)
15. Recombination. Bujarski JJ, Encyclopedia of virology, Volume 4 Oxford: Elsevier, Mahy BWJ, Regenmortel MHV, 3 2008 374 382
16. A distinct group of hepacivirus/pestivirus-like internal ribosomal entry sites in members of diverse picornavirus genera: evidence for modular exchange of functional noncoding RNA elements by recombination. Hellen CU, de Breyne S, J Virol 2007 81 11 5850 5863 10.1128/JVI.02403-06 17392358 (Pubitemid 46847022)
17. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. Chare ER, Gould EA, Holmes EC, J Gen Virol 2003 84 Pt 10 2691 2703 13679603 (Pubitemid 37321311)
18. Phylogenetic evidence for homologous recombination within the family Birnaviridae. Hon CC, Lam TTY, Yip CW, Wong RTY, Shi M, Jiang JW, Zeng FY, Leung FCC, J Gen Virol 2008 89 3156 3164 10.1099/vir.0.2008/004101-0 19008406
19. Evidence of intragenic recombination in G1 rotavirus VP7 genes. Phan TG, Okitsu S, Maneekarn N, Ushijima H, J Virol 2007 81 18 10188 10194 10.1128/JVI.00337-07 17609273 (Pubitemid 350067721)
20. Evidence of rotavirus intragenic recombination between two sublineages of the same genotype. Parra GI, Bok K, Martinez M, Gomez JA, J Gen Virol 2004 85 1713 1716 10.1099/vir.0.79851-0 15166456 (Pubitemid 38807769)
21. Intragenic recombinations in rotaviruses. Suzuki Y, Gojobori T, Nakagomi O, FEBS Lett 1998 427 2 183 187 10.1016/S0014-5793(98)00415-3 9607308 (Pubitemid 28225054)
22. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Al Rwahnih M, Daubert S, Urbez-Torres JR, Cordero F, Rowhani A, Arch Virol 2011 156 3 397 403 10.1007/s00705-010-0869-8 21140178
23. Complete nucleotide sequence of double-stranded RNA viruses from Fusarium graminearum strain DK3. Yu J, Kwon SJ, Lee KM, Son M, Kim KH, Arch Virol 2009 154 11 1855 1858 10.1007/s00705-009-0507-5 19777156
24. Molecular characterisation of two novel double-stranded RNA elements from Phlebiopsis gigantea. Kozlakidis Z, Hacker CV, Bradley D, Jamal A, Phoon X, Webber J, Brasier CM, Buck KW, Coutts RH, Virus Genes 2009 39 1 132 136 10.1007/s11262-009-0364-z 19430898
25. Molecular characterization of Penicillium chrysogenum virus: reconsideration of the taxonomy of the genus Chrysovirus. Jiang D, Ghabrial SA, J Gen Virol 2004 85 Pt 7 2111 2121 15218197 (Pubitemid 39023291)
26. Programmed ribosomal frameshifting: much ado about knotting! Alam SL, Atkins JF, Gesteland RF, Proc Natl Acad Sci U S A 1999 96 25 14177 14179 10.1073/pnas.96.25.14177 10588670 (Pubitemid 30000615)
27. Programmed ribosomal frameshifting goes beyond viruses: organisms from all three kingdoms use frameshifting to regulate gene expression, perhaps signaling a paradigm shift. Dinman JD, Microbe Wash DC 2006 1 11 521 527 17541450
28. Cardiomyopathy syndrome of Atlantic Salmon (Salmo salar L.) is caused by a double-stranded RNA virus of the Totiviridae family. Haugland O, Mikalsen AB, Nilsen P, Lindmo K, Thu BJ, Eliassen TM, Roos N, Rode M, Evensen O, J Virol 2011 85 11 5275 5286 10.1128/JVI.02154-10 21411528
29. A novel double-stranded RNA virus detected in Primula malacoides is a plant-isolated partitivirus closely related to partitivirus infecting fungal species. Li L, Tian Q, Du Z, Duns GJ, Chen J, Arch Virol 2009 154 4 565 572 10.1007/s00705-009-0342-8 19267226
30. 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. Spear A, Sisterson MS, Yokomi R, Stenger DC, Virology 2010 404 2 304 311 10.1016/j.virol.2010.05.015 20541786
31. A viral double-stranded RNA up regulates the fungal virulence of Nectria radicicola. Ahn IP, Lee YH, Mol Plant Microbe Interact 2001 14 4 496 507 10.1094/MPMI.2001.14.4.496 11310737
32. Characterization of a novel bipartite double-stranded RNA mycovirus conferring hypovirulence in the phytopathogenic fungus Botrytis porri. Wu M, Jin F, Zhang J, Yang L, Jiang D, Li G, J Virol 2012 86 12 6605 6619 10.1128/JVI.00292-12 22496220
33. Intra- and interspecies virus transfer in Aspergilli via protoplast fusion. van Diepeningen AD, Debets AJ, Hoekstra RF, Fungal Genet Biol 1998 25 3 171 180 10.1006/fgbi.1998.1096 9917371 (Pubitemid 29097243)
34. A novel mycovirus associated with four double-stranded RNAs affects host fungal growth in Alternaria alternata. Aoki N, Moriyama H, Kodama M, Arie T, Teraoka T, Fukuhara T, Virus Res 2009 140 1-2 179 187 19118588
35. A novel quadripartite dsRNA virus isolated from a phytopathogenic filamentous fungus, Rosellinia necatrix. Lin YH, Chiba S, Tani A, Kondo H, Sasaki A, Kanematsu S, Suzuki N, Virology 2012 426 1 42 50 10.1016/j.virol.2012. 01.013 22321722
36. Molecular characterization of the largest mycoviral-like double-stranded RNAs associated with Amasya cherry disease, a disease of presumed fungal aetiology. Kozlakidis Z, Covelli L, Di Serio F, Citir A, Acikgoz S, Hernandez C, Ragozzino A, Flores R, Coutts RH, J Gen Virol 2006 87 Pt 10 3113 3117 16963771 (Pubitemid 44463921)
37. Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses. Ahlquist P, Nat Rev Microbiol 2006 4 5 371 382 10.1038/nrmicro1389 16582931 (Pubitemid 43771855)
38. Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Koonin EV, Dolja VV, Crit Rev Biochem Mol Biol 1993 28 5 375 430 10.3109/10409239309078440 8269709 (Pubitemid 23294324)
39. Evolution of double-stranded RNA viruses: a case for polyphyletic origin from different groups of positive-stranded RNA viruses. Koonin EV, Semin Virol 1992 3 327 339
40. The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Koonin EV, Wolf YI, Nagasaki K, Dolja VV, Nat Rev Microbiol 2008 6 12 925 939 10.1038/nrmicro2030 18997823
41. Nucleotide sequences of four RNA segments of a reovirus isolated from the mud crab Scylla serrata provide evidence that this virus belongs to a new genus in the family Reoviridae. Chen J, Xiong J, Yang J, Mao Z, Chen X, Arch Virol 2011 156 3 523 528 10.1007/s00705-010-0852-4 21153426
42. The dsRNA viruses. Mertens P, Virus Res 2004 101 1 3 13 10.1016/j.virusres.2003.12.002 15010213 (Pubitemid 38317105)
43. Extraction of double-stranded RNA from plant tissues without the use of organic solvents. DePaulo J, Powell C, Plant Dis 1995 79 3 246 248 10.1094/PD-79-0246
44. Cherry chlorotic rusty spot and Amasya cherry diseases are associated with a complex pattern of mycoviral-like double-stranded RNAs. I. Characterization of a new species in the genus Chrysovirus. Covelli L, Coutts RH, Di Serio F, Citir A, Acikgoz S, Hernandez C, Ragozzino A, Flores R, J Gen Virol 2004 85 Pt 11 3389 3397 15483256 (Pubitemid 39445459)
45. KnotSeeker: heuristic pseudoknot detection in long RNA sequences. Sperschneider J, Datta A, RNA 2008 14 4 630 640 10.1261/rna.968808 18314500 (Pubitemid 351480875)
46. VARNA: interactive drawing and editing of the RNA secondary structure. Darty K, Denise A, Ponty Y, Bioinformatics 2009 25 15 1974 1975 10.1093/bioinformatics/btp250 19398448
47. MrBayes 3: Bayesian phylogenetic inference under mixed models. Ronquist F, Huelsenbeck JP, Bioinformatics 2003 19 12 1572 1574 10.1093/bioinformatics/ btg180 12912839 (Pubitemid 37038874)
48. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O, Syst Biol 2010 59 3 307 321 10.1093/sysbio/syq010 20525638
49. ProtTest: selection of best-fit models of protein evolution. Abascal F, Zardoya R, Posada D, Bioinformatics 2005 21 9 2104 2105 10.1093/bioinformatics/ bti263 15647292 (Pubitemid 40668057)
50. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Schmidt HA, Strimmer K, Vingron M, von Haeseler A, Bioinformatics 2002 18 3 502 504 10.1093/bioinformatics/18.3.502 11934758 (Pubitemid 34284960)