Archives of Virology

, Volume 157, Issue 9, pp 1825–1830 | Cite as

Complete genome sequence of switchgrass mosaic virus, a member of a proposed new species in the genus Marafivirus

  • Bright O. Agindotan
  • Michael E. Gray
  • Rosemarie W. Hammond
  • Carl A. Bradley
Annotated Sequence Record

Abstract

The complete genome sequence of a virus recently detected in switchgrass (Panicum virgatum) was determined and found to be closely related to that of maize rayado fino virus (MRFV), genus Marafivirus, family Tymoviridae. The genomic RNA is 6408 nucleotides long. It contains three predicted open reading frames (ORFs 1-3), encoding proteins of 227 kDa, 43.9 kDa, and 31.5 kDa, compared to two ORFs (1 and 2) for MRFV. The complete genome shares 76 % sequence identity with MRFV. The nucleotide sequence of ORF2 of this virus and the amino acid sequence of its encoded protein are 49 % and 77 % identical, respectively, to those of MRFV. The virus-encoded polyprotein and capsid protein aa sequences are 83 % and 74-80 % identical, respectively, to those of MRFV. Although closely related to MRFV, the amino acid sequence of its capsid protein (CP) forms a clade that is separate from that of MRFV. Based on the International Committee on Taxonomy of Viruses (ICTV) sequence-related criteria for delineation of species within the genus Marafivirus, the virus qualifies as a member of a new species, and the name Switchgrass mosaic virus (SwMV) is proposed.

References

  1. 1.
    Agindotan B, Perry KL (2007) Macroarray detection of plant RNA viruses using randomly primed and amplified complementary cDNAs from infected plants. Phytopathology 97:119–127PubMedCrossRefGoogle Scholar
  2. 2.
    Agindotan BO, Ahonsi MO, Domier LL, Gray ME, Bradley CA (2010) Application of sequence-independent amplification (SIA) for the identification of RNA viruses in bioenergy crops. J Virol Methods 169:119–128PubMedCrossRefGoogle Scholar
  3. 3.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410. doi:10.1006/jmbi.1990.9999. http://wwwmath.mit.edu/~lippert/18.417/papers/altschuletal1990.pdf Google Scholar
  4. 4.
    Bustamante PI, Hammond R, Ramirez P (1998) Evaluation of maize germplasm for resistance to maize rayado fino virus. Plant Dis 82:50–56CrossRefGoogle Scholar
  5. 5.
    Chicas M, Caviedes M, Hammond R, Madriz K, Albertazzi F, Villalobos HP, Ramirez P (2007) Partial characterization of maize rayado fino virus isolates from Ecuador: phylogenetic analysis supports a Central American origin of the virus. Virus Res 126:268–276PubMedCrossRefGoogle Scholar
  6. 6.
    Dien BS, Jung HG, Vogel KP, Casler MD, Lamb JFS, Iten L, Mitchell RB, Sarath G (2006) Chemical composition and response to dilute-acid pretreatment and enzymatic saccharification of alfalfa reed canarygrass and switchgrass. Biomass Bioenergy 30:880–891CrossRefGoogle Scholar
  7. 7.
    Ding S, Howe J, Keese P, MacKenzie A, Meek D, Osorio-Keese M, Skotnicki M, Srifah P, Torrenen M, Gibbs A (1990) The tymobox a sequence shared by most tymoviruses. Nucleic Acids Res 18:1181–1187PubMedCrossRefGoogle Scholar
  8. 8.
    Edwards MC, Weiland JJ (2011) Presence of a polyA tail at the 3’ end of maize rayado fino virus RNA. Arch Virol 156:331–334PubMedCrossRefGoogle Scholar
  9. 9.
    Edwards MC, Zhang ZJ, Weiland JJ (1997) Oat blue dwarf marafivirus resembles the tymoviruses in sequence genome organization and expression strategy. Virology 232:217–229PubMedCrossRefGoogle Scholar
  10. 10.
    Falk BW, Tsai JH (1986) The two capsid proteins of maize rayado fino virus contain common peptide sequences. Intervirology 25:111–116PubMedCrossRefGoogle Scholar
  11. 11.
    Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses. Elsevier/Academic Press, LondonGoogle Scholar
  12. 12.
    Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  13. 13.
    Gamez R (1973) Transmission of Rayado fino virus of maize (Zea mays) by Dalbulus maidis. Ann Appl Biol 73:285–292PubMedCrossRefGoogle Scholar
  14. 14.
    Gamez R (1977) Leafhopper-transmitted Maize rayado fino virus in Central America International maize virus disease colloquium and workshop proceedings pp 15–17Google Scholar
  15. 15.
    Hammond R, Hammond J (2009) Maize rayado fino virus capsid proteins assemble into virus-like particles in Escherichia coli. Virus Res 147:208–215PubMedCrossRefGoogle Scholar
  16. 16.
    Hammond WH, Hammond J (2010) Maize rayado fino virus proteins assemble into virus-like particles in Escherichia coli. Virus Res 147:208–215PubMedCrossRefGoogle Scholar
  17. 17.
    Hammond RW, Ramirez P (2001) Molecular characterization of the genome of Maize rayado fino virus the type member of the genus Marafivirus. Virology 282:338–347PubMedCrossRefGoogle Scholar
  18. 18.
    Hammond RW, Kogel R, Ramirez P (1997) Variability of geographically distinct isolates of maize rayado fino virus in Latin America. J Gen Virol 78:3153–3159PubMedGoogle Scholar
  19. 19.
    Haque M, Epplin FM, Taliaferro CM (2009) Nitrogen and harvest frequency effect on yield and cost for four perennial grasses. Agron J 101:1463–1469CrossRefGoogle Scholar
  20. 20.
    King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (2012) Virus Taxonomy. Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic, LondonGoogle Scholar
  21. 21.
    Lewandowski I, Scurlock JMO, Lindvall E, Christou M (2003) The development and current status of perennial rhizomatous grasses as energy crops in the US and Europe. Biomass Bioenergy 25:335–361CrossRefGoogle Scholar
  22. 22.
    Maccheroni W, Alegria MC, Greggio CC, Piazza JP, Kamla RF, Zacharias PRA, Bar-Joseph M, Kitajima EW, Assumpção LC et al (2005) Identification and genomic characterization of a new virus (Tymoviridae family) associated with citrus sudden death disease. J Virol 79:3028–3037PubMedCrossRefGoogle Scholar
  23. 23.
    Madriz-Ordenana K, Rojas-Montero R, Lundsgaard T, Ramirez P, Thordal-Christensen H, Collinge DB (2000) Mechanical transmission of maize rayado fino marafivirus (MRFV) to maize and barley by means of the vascular puncture technique. Plant Pathol 49:302–307CrossRefGoogle Scholar
  24. 24.
    Martelli GP, Sabanadzovic S, Sabanadzovic NAG, Edwards MC, Dreher T (2002) The family Tymoviridae. Arch Virol 147:1837–1846PubMedCrossRefGoogle Scholar
  25. 25.
    Nault LR, Madden LB (1985) Ecological strategies of Dalbulus leafhoppers. Ecol Entomol 10:57–63CrossRefGoogle Scholar
  26. 26.
    Nault LR, Gringery RE, Gordon DT (1980) Leafhopper transmission and host range of maize rayado fino virus. Phytopathology 70:709–712CrossRefGoogle Scholar
  27. 27.
    Oman PW (1948) Distribution of Baldulus maidis (DeLong and Wolcott). Proc Entomol Soc Wash 50(2):34Google Scholar
  28. 28.
    Sabanadzovic S, Abou Ghanem-Sabanadzovic N (2009) Identification and molecular characterization of a marafivirus in Rubus spp. Arch Virol 154:1729–1735PubMedCrossRefGoogle Scholar
  29. 29.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  30. 30.
    Segwagwe AT, Putnam ML, Druffel KL, Pappu HR, Eastwell KC (2008) Molecular characterization of a new tymovirus from Diascia ornamental plants. Arch Virol 153:1495–1503PubMedCrossRefGoogle Scholar
  31. 31.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis MEGA software version 40. Mol Biol Evol 24:1596–1599Google Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Bright O. Agindotan
    • 1
  • Michael E. Gray
    • 1
    • 2
  • Rosemarie W. Hammond
    • 3
  • Carl A. Bradley
    • 1
    • 2
  1. 1.Energy Biosciences InstituteUniversity of IllinoisUrbanaUSA
  2. 2.Department of Crop SciencesUniversity of IllinoisUrbanaUSA
  3. 3.United States Department of Agriculture USDA-ARSBeltsvilleUSA

Personalised recommendations