Deep-sequencing analysis of double-stranded RNA extracted from a mosaic-diseased pigeonpea plant (Cajanus cajan L., family Fabaceae) revealed the complete sequence of six emaravirus-like negative-sense RNA segments of 7009, 2229, 1335, 1491, 1833 and 1194 nucleotides in size. In the order from RNA1 to RNA6, these genomic RNAs contained ORFs coding for the RNA-dependent RNA polymerase (RdRp, p1 of 266 kDa), the glycoprotein precursor (GP, p2 of 74.5 kDa), the nucleocapsid (NC, p3 of 34.9 kDa), and the putative movement protein (MP, p4 of 40.7 kDa), while p5 (55 kDa) and p6 (27 kDa) had unknown functions. All RNA segments showed distant relationships to viruses of the genus Emaravirus, and in particular to pigeonpea sterility mosaic virus (PPSMV), with which they shared nucleotide sequence identity ranging from 48.5 % (RNA3) to 62.5 % (RNA1). In phylogenetic trees constructed from the sequences of the proteins encoded by RNA1, RNA2 and RNA3 (p1, p2 and p3), this new viral entity showed a consistent grouping with fig mosaic virus (FMV) and rose rosette virus (RRV), which formed a cluster of their own, clearly distinct from PPSMV-1. In experimental greenhouse trials, this novel virus was successfully transmitted to pigeonpea and French bean seedlings by the eriophyid mite Aceria cajani. Preliminary surveys conducted in the Hyderabad region (India) showed that the virus in question is widespread in pigeonpea plants affected by sterility mosaic disease (86.4 %) but is absent in symptomless plants. Based on molecular, biological and epidemiological features, this novel virus is the second emaravirus infecting pigeonpea, for which the provisional name pigeonpea sterility mosaic virus 2 (PPSMV-2) is proposed.
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Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389–3402
Bradfute OR, Whitmoyer RE, Nault RL (1970) Ultrastructure of plant leaf tissue infected with mite-borne viral-like particles. Proc Electron Microsc Soc Am 258:178–179
Bruenn JA (2003) A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases. Nucl Acids Res 31:1821–1829
Coutts RHA, Livieratos IC (2003) A rapid method for sequencing the 5′- and 3′-termini of double-stranded RNA viral templates using RLM-RACE. J Phytopathol 151:525–527
Dodds JA (1993) DsRNA in diagnosis. In: Matthews REF (ed) Diagnosis of plant virus diseases. CRC Press, Boca Raton, pp 273–294
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32:1792–1797
Elbeaino T, Digiaro M, Alabdullah A, De Stradis A, Minafra A, Mielke N, Castellano MA, Martelli GP (2009) A multipartite single-stranded negative-sense RNA virus is the putative agent of fig mosaic disease. J Gen Virol 90:1281–1288
Elbeaino T, Digiaro M, Martelli GP (2009) Complete nucleotide sequence of four RNA segments of Fig mosaic virus. Arch Virol 154:1719–1727
Elbeaino T, Digiaro M, Uppala M, Sudini H (2014) Deep sequencing of Pigeonpea sterility mosaic virus discloses five RNA segments related to emaraviruses. Virus Res 188:27–31
Emanuelsson O, Nielsen H, Brunak S, Von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300:1005–1016
Emanuelsson O, Brunak S, Von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP, and related tools. Nat Protoc 2:953–971
Foissac X, Svanella-Dumas L, Dulucq MJ, Candresse T, Gentit P (2001) Polyvalent detection of fruit tree tricho, capillo and foveavirus by nested RT-PCR using degenerated and inosine containing primers (DOP RT-PCR). Acta Hort 550:37–44
Hassan M, Sabanadzovic S, Keller KE, Martin RR, Tzanetakis IE (2012) A putative new emaravirus associated with blackberry yellow vein disease. In: Proceedings of the 22nd international conference on virus and other transmissible diseases of fruit crops (ICVF). Petria 22:354–358
Ishikawa K, Maejima K, Komatsu K, Netsu O, Keima T, Shiraishi T, Okano Y, Hashimoto M, Yamaji Y, Namba S (2013) Fig mosaic emaravirus p4 protein is involved in cell-to-cell movement. J Gen Virol 94:682–686
Jensen SG, Lane LC, Seifers DL (1996) A new disease of maize and wheat in the High Plains. Plant Dis 80:1387–1390
Jones AT, Kumar PL, Saxena KB, Kulkarni NK, Muniyappa V, Waliyar F (2004) Sterility mosaic disease: the ‘green plague’ of pigeonpea. Plant Dis 88:436–445
Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282
Kannaiyan J, Nene YL, Reddy MV, Ryan JG, Raju TN (1984) Prevalence of pigeonpea disease and associated crop losses in Asia, Africa and the Americas. Trop Pest Manag 30:62–71
Kulkarni NK, Kumar PL, Muniyappa V, Jones AT, Reddy DVR (2002) Transmission of Pigeon pea sterility mosaic virus by the eriophyid mite, Aceria cajani (Acari: Arthropoda). Plant Dis 86:1297–1302
Kumar PL, Duncan GC, Roberts IM, Jones AT, Reddy DVR (2002) Cytopathology of Pigeonpea sterility mosaic virus in pigeonpea and Nicotiana benthamiana: similarities with those of eriophyid mite-borne agents of undefined aetiology. Ann Appl Biol 140:87–96
Kumar PL, Jones AT, Reddy DVR (2003) A novel mite-transmitted virus with a divided RNA genome closely associated with pigeonpea sterility mosaic disease. Phytopathology 93:71–81
Kumar PL, Jones AT, Waliyar F (2004) Biology, etiology and management of pigeonpea sterility mosaic disease. Annu Rev Plant Pathol 3:1–24
Kumar PL, Latha TKS, Kulkarni NK, Raghavendra N, Saxena KB, Waliyar F, Rangaswamy KT, Muniyappa V, Doriswamy S, Jones AT (2005) Broad-Based resistance to Pigeonpea sterility mosaic disease in wild relatives of pigeonpea (Cajanus: Phaseolae). Ann Appl Biol 146:371–379
Laney AG, Gergerich RC, Tzanetakis IE (2010) Redbud yellow ringspot disease: 30 years of research. Phytopathology 100:S201
Laney AG, Gergerich RC, Keller KE, Martin RR, Tzanetakis IE (2011a) In: GenBank database. Accession no. JF795479–JF795482
Laney AG, Keller KE, Martin RR, Tzanetakis IE (2011) A discovery 70 years in the making: characterization of the Rose rosette virus. J Gen Virol 92:1727–1732
Marck C (1988) DNA Strider: a “C” programme for the fast analysis of DNA and protein sequences on the Apple Macintosh family computers. Nucl Acids Res 16:1829–1836
Martelli GP, Castellano MA, Lafortezza R (1993) An ultrastructural study of fig mosaic. Phytopathol Medit 32:33–43
Matsuda S, Vert JP, Saigo H, Ueda N, Toh H, Akutsu T (2005) A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci 14:2804–2813
McGavin WJ, Mitchell C, Cock PJA, Wright KM, MacFarlane SA (2012) Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA. J Gen Virol 93:430–437
Mielke N, Muehlbach HP (2007) A novel, multipartite, negative-strand RNA virus is associated with the ringspot disease of European mountain ash (Sorbus aucuparia L.). J Gen Virol 88:1337–1346
Mielke-Ehret N, Muehlbach HP (2012) Emaravirus: a novel genus of multipartite, negative strand RNA plant viruses. Viruses 4:1515–1536
Muehlbach HP, Mielke-Ehret N (2011) Genus Emaravirus. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz E (eds) Virus taxonomy. Ninth report of the international committee on the taxonomy of viruses. Elsevier-Academic Press, Amsterdam, pp 767–769
Nene YL, Kannaiyan J, Haware MP, Reddy MV (1981) Pigeonpea diseases: resistance-screening techniques. Information Bulletin No. 9. International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India, pp 1–14
Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444–2448
Singh AK, Agrawal KC, Rathi YPS (1999) Sterility mosaic of pigeonpea: a challenge of 20th Century. Indian J Virol 15:85–92
Skare JM, Wijkamp I, Rezende JAM, Kitajima EW, Park JW, Desvoyes B, Rush CM, Michels G, Scholthof KBG, Scholthof HB (2006) A new eriophyid mite-borne membrane-enveloped virus-like complex isolated from plants. Virology 347:343–353
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Tatineni S, McMechan AJ, Wosula EN, Wegulo SN, Graybosch RA, French R, Heinb GL (2014) An eriophyid mite-transmitted plant virus contains eight genomic RNA segments with unusual heterogeneity in the nucleocapsid protein. J Virol 88:11834–11845
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 24:4876–4882
Yu C, Karlin DG, Lu Y, Wright K, Chen J, MacFarlane S (2013) Experimental and bioinformatic evidence that Raspberry leaf blotch emaravirus p4 is a movement protein of the 30K superfamily. J Gen Virol 94:2117–2128
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
The authors are grateful to Prof. G. P Martelli for his critical reading of the manuscript.
Conflict of interest
The authors declare that they have no conflict of interest.
In order from RNA1 to RNA6, accession numbers are: HF912243-HF912246, HG939489, HG939490.
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Elbeaino, T., Digiaro, M., Uppala, M. et al. Deep sequencing of dsRNAs recovered from mosaic-diseased pigeonpea reveals the presence of a novel emaravirus: pigeonpea sterility mosaic virus 2. Arch Virol 160, 2019–2029 (2015). https://doi.org/10.1007/s00705-015-2479-y
- Nucleocapsid Protein
- Glycoprotein Precursor
- Sterility Mosaic Disease
- Eriophyid Mite
- Pigeonpea Plant