Skip to main content
SpringerLink
Log in

Molecular characterization of a distinct monopartite begomovirus associated with betasatellites and alphasatellites infecting Pisum sativum in Nepal

  • Published:
Virus Genes Aims and scope Submit manuscript

Abstract

Pea (Pisum sativum) plants exhibiting leaf distortion, yellowing, stunted growth and reduction in leaf size from Rampur, Nepal were shown to be infected by a begomovirus in association with betasatellites and alphasatellites. The begomovirus associated with the disease showed only low levels of nucleotide sequence identity (<91%) to previously characterized begomoviruses. This finding indicates that the pea samples were infected with an as yet undescribed begomovirus for which the name Pea leaf distortion virus (PLDV) is proposed. Two species of betasatellite were identified in association with PLDV. One group of sequences had high (>78%) nucleotide sequence identity to isolates of Ludwigia leaf distortion betasatellite (LuLDB), and the second group had less than 78% to all other betasatellite sequences. This showed PLDV to be associated with either LuLDB or a previously undescribed betasatellite for which the name Pea leaf distortion betasatellite is proposed. Two types of alphasatellites were identified in the PLDV-infected pea plants. The first type showed high levels of sequence identity to Ageratum yellow vein alphasatellite, and the second type showed high levels of identity to isolates of Sida yellow vein China alphasatellite. These are the first begomovirus, betasatellites and alphasatellites isolated from pea.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. J.K. Brown, C.M. Fauquet, R.W. Briddon, M. Zerbini, E. Moriones, J. Navas-Castillo, in Geminiviridae, ed. by A.M.Q. King, M.J. Adams, E.B. Carstens, E.J. Lefkowitz (Elsevier, Inc., London, 2011), pp. 351–373

    Google Scholar 

  2. M.R. Rojas, C. Hagen, W.J. Lucas, R.L. Gilbertson, Annu. Rev. Phytopathol. 43, 361–394 (2005)

    Article  CAS  PubMed  Google Scholar 

  3. L. Hanley-Bowdoin, E.R. Bejarano, D. Robertson, S. Mansoor, Nat. Rev. Microbiol. 11, 777–788 (2013)

    Article  CAS  PubMed  Google Scholar 

  4. R.W. Briddon, S. Ghabrial, N.S. Lin, P. Palukaitis, K.B.G. Scholthof, H.J. Vetten, in Virus Taxonomy—Ninth Report of the International Committee on Taxonomy of Viruses, ed. by A.M.Q. King, M.J. Adams, E.B. Carstens, E.J. Lefkowitz (Associated Press, Elsevier, Inc., London, 2012), pp. 1209–1219

    Google Scholar 

  5. S. Mansoor, S. Mukhtar, M. Hussain, I. Amin, Y. Zafar, K. Malik, P.G. Markham, Plant Dis. 84, 809 (2000)

    Article  Google Scholar 

  6. R.W. Briddon, S.E. Bull, I. Amin, S. Mansoor, I.D. Bedford, N. Rishi, S.S. Siwatch, M.Y. Zafar, A.M. Abdel-Salam, P.G. Markham, Virology 324, 462–474 (2004)

    Article  CAS  PubMed  Google Scholar 

  7. R.W. Briddon, J. Stanley, Virology 344, 198–210 (2006)

    Article  CAS  PubMed  Google Scholar 

  8. G. Lozano, H.P. Trenado, E. Fiallo-Olivé, D. Chirinos, F. Geraud-Pouey, R.W. Briddon, J. Navas-Castillo, Front. Microbiol. 7, 162 (2016)

    Article  PubMed  PubMed Central  Google Scholar 

  9. R.W. Briddon, S.E. Bull, I. Amin, A.M. Idris, S. Mansoor, I.D. Bedford, P. Dhawan, N. Rishi, S.S. Siwatch, A.M. Abdel-Salam, J.K. Brown, Y. Zafar, P.G. Markham, Virology 312, 106–121 (2003)

    Article  CAS  PubMed  Google Scholar 

  10. X. Cui, G. Li, D. Wang, D. Hu, X. Zhou, J. Virol. 79, 10764–10775 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. T. Kon, K. Kuwabara, S.H. Hidayat, M. Ikegami, Arch. Virol. 152, 1147–1157 (2007)

    Article  CAS  PubMed  Google Scholar 

  12. M. Saeed, S.A. Behjatnia, S. Mansoor, Y. Zafar, S. Hasnain, M.A. Rezaian, Mol. Plant Microbe Interact. 18, 7–14 (2005)

    Article  CAS  PubMed  Google Scholar 

  13. M. Saeed, Y. Zafar, J.W. Randles, M.A. Rezaian, J. Gen. Virol. 349(88), 2881–2889 (2007)

    Article  Google Scholar 

  14. J. Kumar, S.P. Singh, R. Tuli, J. Virol. 88, 7093–7104 (2014)

    Article  PubMed  PubMed Central  Google Scholar 

  15. A.M. Idris, M.S. Shahid, R.W. Briddon, A.J. Khan, J.K. Zhu, J.K. Brown, J. Gen. Virol. 92, 706–717 (2011)

    Article  CAS  PubMed  Google Scholar 

  16. M.S. Nawaz-ul-Rehman, N. Nahid, S. Mansoor, R.W. Briddon, C.M. Fauquet, Virology 405, 300–308 (2010)

    Article  CAS  PubMed  Google Scholar 

  17. S. Porebski, L.G. Bailey, B.R. Baum, Plant Mol. Biol. Rep. 15, 8–15 (1997)

    Article  CAS  Google Scholar 

  18. D. Haible, S. Kober, H. Jeske, J. Virol. Methods 135, 9–16 (2006)

    Article  CAS  PubMed  Google Scholar 

  19. R.W. Briddon, S.E. Bull, S. Mansoor, I. Amin, P.G. Markham, Mol. Biotechnol. 20, 315–318 (2002)

    Article  CAS  PubMed  Google Scholar 

  20. K. Tamura, G. Stecher, D. Peterson, A. Filipski, S. Kumar, Mol. Biol. Evol. 30, 2725–2729 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. B.M. Muhire, A. Varsani, D.P. Martin, PLoS ONE 9, e108277 (2014)

    Article  PubMed  PubMed Central  Google Scholar 

  22. R.D.M. Page, Comput. Appl. Biosci. 12, 357–358 (1996)

    CAS  PubMed  Google Scholar 

  23. D.P. Martin, B. Murrell, M. Golden, A. Khoosal, B. Muhire, Virus Evol. 1, 1–5 (2015)

    Article  Google Scholar 

  24. J.K. Brown, F.M. Zerbini, J. Navas-Castillo, E. Moriones, R. Ramos-Sobrinho, J.F. Silva, E. Fiallo-Olivé, R.W. Briddon, C. Hernández-Zepeda, A. Idris, V.G. Malathi, D.P. Martin, R. Rivera-Bustamante, S. Ueda, A. Varsani, Arch. Virol. 160, 1593–1619 (2015)

    Article  CAS  PubMed  Google Scholar 

  25. J. Stanley, D.M. Bisaro, R.W. Briddon, J.K. Brown, C.M. Fauquet, B.D. Harrison, E.P. Rybicki, D.C. Stenger, in Virus taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses, ed. by C.M. Fauquet, M.A. Mayo, J. Maniloff, U. Desselberger, L.A. Ball (Elsevier/Academic Press, London, 2005), pp. 301–326

    Google Scholar 

  26. R.W. Briddon, J.K. Brown, E. Moriones, J. Stanley, M. Zerbini, X. Zhou, C.M. Fauquet, Arch. Virol. 153, 763–781 (2008)

    Article  CAS  PubMed  Google Scholar 

  27. K. Saunders, J. Stanley, Virology 264, 142–152 (1999)

    Article  CAS  PubMed  Google Scholar 

  28. M.S. Shahid, S. Yoshida, G.B. Khatri-Chhetri, R.W. Briddon, K.T. Natsuaki, Virus Genes 46, 581–584 (2013)

    Article  CAS  PubMed  Google Scholar 

  29. K. Saunders, I.D. Bedford, J. Stanley, J. Gen. Virol. 83, 909–915 (2002)

    Article  Google Scholar 

  30. M.S. Shahid, M. Ikegami, K.T. Natsuaki, Australas. Plant Dis. 7, 85–89 (2012)

    Article  Google Scholar 

  31. M.S. Shahid, P.B. Pudashini, G.B. Khatri-Chhetri, M. Ikegami, K.T. Natsuaki, N. Dis. Rep. 25, 30 (2012)

    Article  Google Scholar 

  32. M. Tahir, I. Amin, S. Haider, S. Mansoor, R.W. Briddon, Viruses 7, 647–665 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. N. Nahid, I. Amin, S. Mansoor, E.P. Rybicki, E. van der Walt, R.W. Briddon, Arch. Virol. 153, 1441–1451 (2008)

    Article  CAS  PubMed  Google Scholar 

  34. M. Ilyas, J. Qazi, S. Mansoor, R.W. Briddon, J. Gen. Virol. 91, 2091–2101 (2010)

    Article  CAS  PubMed  Google Scholar 

  35. N.K. Gautam, M. Akram, J. Akhtar, Z. Khan, N.K. Dwiwedi, M. Latha, B. Ram, Phytopathol. Mediterr. 53, 428–437 (2014)

    Google Scholar 

  36. V.K. Satya, V.G. Malathi, R. Velazhahan, R. Rabindran, P. Jayamani, D. Alice, Acta Virol. 57, 405–414 (2013)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This research was partly supported by an Advanced Research Project of the Nodai Research Institute, Tokyo University of Agriculture, Japan. RWB was supported by the Higher Education Commission, Government of Pakistan, under the “Foreign Faculty Hiring Program”.

Authors’ contributions

MS Shahid designed and conducted the experiments, data analysis, and wrote the manuscript. BJ Pudashini and GB Khatri-Chhetri were involved in survey and sample collection. RW Briddon contributed to data analysis and writing the manuscript. KT Natsuaki supervised the sampling survey and reviewed the draft manuscript. All authors approved the final draft of the manuscript.

Author information

Authors and Affiliations

  1. Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, 123, Muscat, Oman

    M. S. Shahid

  2. Department of International Agricultural Development, Tokyo University of Agriculture, Tokyo, 156-8502, Japan

    B. J. Pudashini & K. T. Natsuaki

  3. Kisankalagi Unnat Biu-Bijan Karyakram Improved Seed for Farmers Program (KUBK-ISFP), District, Seed Coordinator, Janakinagar-3 Rupandehi, Butwal, Nepal

    B. J. Pudashini

  4. Department of Plant Pathology, Institute of Agriculture and Animal Science, Tribhuvan University, Chitwan, 44209, Nepal

    G. B. Khatri-Chhetri

  5. Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan

    R. W. Briddon

Authors
  1. M. S. Shahid
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. B. J. Pudashini
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. G. B. Khatri-Chhetri
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. R. W. Briddon
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. K. T. Natsuaki
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to M. S. Shahid.

Ethics declarations

Conflict of interest

Authors MS. Shahid, BJ. Pudashini, GB Khatri-Chhetri and RW Briddon declare that they have no conflict of interest. Author KT Natsuaki has received support from an Advanced Research Project of the Nodai Research Institute, Tokyo University of Agriculture, Japan.

Research involving human and animal rights

Finally, this research does not contain any studies with human/animal participants performed by any of the authors.

Additional information

Edited by Karel Petrzik.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (JPEG 1232 kb)

Supplementary material 2 (DOCX 26 kb)

Supplementary Fig. 1 Phylogenetic dendrograms based upon the complete nucleotide sequences of selected betasatellites (a) and alphasatellites (b). Vertical branches are arbitrary, horizontal branches are proportional to calculated mutation distance. Values at nodes indicate percentage boot strap values (1000 replicates). The betasatellite acronyms used are Chilli leaf curl betasatellite (ChLCB), Cotton leaf curl Multan betasatellite (CLCuMB), Corchorus yellow vein mosaic betasatellite (CoYVMB), Croton yellow vein mosaic betasatellite (CroYVMB), French bean leaf curl betasatellite (FbSLCB), Kenaf leaf curl betasatellite (KeLCuB), Ludwigia leaf distortion betasatellite (LuLDB), Papaya leaf curl betasatellite (PaLCuB), Sida yellow vein Vietnam betasatellite (SiYVVB), Tobacco leaf curl betasatellite (TbLCB), Tobacco leaf curl Vietnam betasatellite (TbLCVNB), Tomato leaf curl betasatellite (ToLCB) and Tomato leaf curl China betasatellite (ToLCCNB). Alphasatellite acronyms used are Ageratum yellow vein alphasatellite (AYVA), Cotton leaf curl Multan alphasatellite (CLCuMA), Guar leaf curl alphasatellite (GLCuA), Mesta yellow vein mosaic alphasatellite (MeYVMA), Okra leaf curl alphasatellite (OLCuA), Potato leaf curl alphasatellite (PotLCuA), Sida yellow vein China alphasatellite (SiYVCNA), Tobacco curly shoot alphasatellite (TbCSA), Tomato yellow leaf curl China alphasatellite (TYLCCNA). The trees were arbitrarily rooted on the sequence of Sida yellow vein China alphasatellite (SiYVCNA-[NP:R8:12]KC282643) (for the betasatellite phylogenetic tree) and Okra leaf curl betasatellite (OLCuB-[PK:09]AM432358) (for the alphasatellite phylogenetic tree) which are unrelated sequences of a similar size. The database accession numbers are indicated in each case. The sequences originating from P. sativum are indicated by white text on a black background in each case

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shahid, M.S., Pudashini, B.J., Khatri-Chhetri, G.B. et al. Molecular characterization of a distinct monopartite begomovirus associated with betasatellites and alphasatellites infecting Pisum sativum in Nepal. Virus Genes 53, 300–306 (2017). https://doi.org/10.1007/s11262-016-1424-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11262-016-1424-9

Keywords

Search

Navigation