Abstract
This study reports the first complete genome sequence of Piper yellow mottle virus (PYMoV, KC808712) identified in black pepper. The genome is 7,622 nucleotides long, possessing four open reading frames (ORFs). ORF1, ORF2 and ORF4 of PYMoV are reported as hypothetical proteins of unknown function with a predicted molecular mass of 15.7, 17.1 and 17.9 kDa, respectively. ORF3 of PYMoV encodes a polyprotein of 218.6 kDa and consists of a viral movement protein (MP), trimeric dUTPase, zinc finger, retropepsin, RT-LTR, and RNAse H. Detailed PYMoV genome analysis confirmed that it is a member of the family Caulimoviridae, genus Badnavirus. Fragments of two additional novel sequences resembling those found in members of the family Caulimoviridae were also identified in the black pepper sample, and the viruses from which they were derived were tentatively named Piper DNA virus 1 and 2.
Similar content being viewed by others
References
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2010) GenBank. Nucleic Acids Res 38:D46–D51
Bhat AI, Siljo A, Devasahayam S (2012) Occurrence of symptomless source of Piper yellow mottle virus in black pepper (Piper nigrum L.) varieties and a wild Piper species. Arch Phytopathol Plant Protect 45:1000–1009
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinform 10:421
De Silva DPP, Jones P, Shaw MW (2002) Identification and transmission of Piper yellow mottle virus and Cucumber mosaic virus infecting black pepper (Piper nigrum) in Sri Lanka. Plant Pathol 51:537–545
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38:D211–D222
Hagen LS, Jacquemond M, Lepingle A, Lot H, Tepfer M (1993) Nucleotide sequence and genomic organization of cacao swollen shoot virus. Virology 196:619–628
Hareesh PS, Bhat AI (2008) Detection and partial nucleotide sequence analysis of Piper yellow mottle virus infecting black pepper in India. Indian J Virol 19:160–167
King E, Lefkowitz E, Adams M, Carstens E (2011) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier, London
Lockhart BEL, Kiratiya-Angul K, Jones P, Eng L, Silva PD, Olszewski NE, Lockhart N, Deema N, Sangalang J (1997) Identification of Piper yellow mottle virus, a mealybug-transmitted badnavirus infecting Piper spp. in Southeast Asia. Eur J Plant Pathol 103:303–311
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 39:D225–D229
Medberry SL, Lockhart BE, Olszewski NE (1990) Properties of Commelina yellow mottle virus’s complete DNA sequence, genomic discontinuities and transcript suggest that it is a pararetrovirus. Nucleic Acids Res 18:5505–5513
Ravindran PN (2000) Black pepper (Piper nigrum L) Hardwood Academic Publishers, The Netherlands
Seal S, Muller E (2007) Molecular analysis of a full-length sequence of a new yam badnavirus from Dioscorea sansibarensis. Arch Virol 152:819–825
Sether DM, Melzer MJ, Borth WB, Hu JS (2012) Pineapple bacilliform CO virus: Diversity, Detection, Distribution, and Transmission. Plant Dis 96:1798–1804
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Acknowledgments
This project was funded by EU-QBOL and Defra.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Hany, U., Adams, I.P., Glover, R. et al. The complete genome sequence of Piper yellow mottle virus (PYMoV). Arch Virol 159, 385–388 (2014). https://doi.org/10.1007/s00705-013-1824-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-013-1824-2