Skip to main content
SpringerLink
Log in

Complete nucleotide sequence of a begomovirus associated with an alphasatellite and a betasatellite naturally infecting okra in Jordan

  • Annotated Sequence Record
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

The complete nucleotide sequences of a monopartite begomovirus and an associated alphasatellite and betasatellite isolated from naturally infected okra (Abelmoschus esculentus) plants originating from Jordan were determined. The sequences of the begomovirus, alphasatellite, and betasatellites were determined to be 2,764, 1,307, and 1,354 nucleotides in length, respectively. Sequence Demarcation Tool (SDT) and phylogenetic analysis revealed that the begomovirus isolate shared the highest (99.5-99.8%) nt sequence identity with isolates of cotton leaf curl Gezira virus (CLCuGeV), a begomovirus found to exclusively infect cotton in Africa, and recently, in Asia and the Middle East. The DNA sequences of the alphasatellite and betasatellite exhibited the highest nt sequence identity (98.7-98.9% and 92.2-95.3%, respectively) to cotton leaf curl Gezira alphasatellite and cotton leaf curl Gezira betasatellite, respectively. This is the first identification of an African begomovirus, associated with DNA satellites, infecting okra in Jordan.

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
Fig. 2

Similar content being viewed by others

References

  1. Abbas Q, Amin I, Mansoor S et al (2019) The Rep proteins encoded by alphasatellites restore expression of a transcriptionally silenced green fluorescent protein transgene in Nicotiana benthamiana. Virus Dis 30:101–105

    Article  Google Scholar 

  2. Al-Musa A, Anfoka G, Misbeh S et al (2008) Detection and molecular characterization of squash leaf curl virus (SLCV) in Jordan. J Phytopathol 156:311–316

    Article  CAS  Google Scholar 

  3. Al-Musa A, Anfoka G, Al-Abdulat A et al (2011) Watermelon chlorotic stunt virus (WmCSV): a serious disease threatening watermelon production in Jordan. Virus Genes 43:79–89

    Article  CAS  Google Scholar 

  4. Anfoka G, Abhary M, Haj Ahmad F et al (2008) Survey of tomato yellow leaf curl disease-associated viruses in the Eastern Mediterranean Basin. J Plant Pathol 90:311–320

    Google Scholar 

  5. Anfoka G, Al-Talb M, Haj-Ahmad F (2016) A new isolate of tomato yellow leaf curl Axarquia virus associated with tomato yellow leaf curl disease in Jordan. J Plant Pathol 98:145–149

    Google Scholar 

  6. Briddon RW, Bull SE, Mansoor S et al (2002) Universal primers for the PCR-mediated amplification of DNA β. Mol Biotechnol 20:315–318

    Article  CAS  Google Scholar 

  7. Briddon RW, Stanley J (2006) Sub-viral agents associated with plant-infecting single-stranded DNA viruses. Virology 344:198–210

    Article  CAS  Google Scholar 

  8. Briddon RW, Martin DP, Roumagnac P, Navas-Castillo J, Fiallo-Olivé E, Moriones E, Lett J-M, Zerbini FM, Varsani A (2018) Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites. Arch Virol 163:2587–2600

    Article  CAS  Google Scholar 

  9. Bull SE, Briddon RW, Markham PG (2003) Universal primers for the PCR-mediated amplification of DNA1: a satellite-like molecule associated with begomovirus-DNA b complexes. Mol Biotechnol 23:83–86

    Article  CAS  Google Scholar 

  10. Claverie S, Varsani A, Hoareau M et al (2020) Sorghum mastrevirus-associated alphasatellites: new geminialphasatellites associated with an African streak mastrevirus infecting wild Poaceae plants on Reunion Island. Arch Virol 165:1925–1928

    Article  CAS  Google Scholar 

  11. Cui X, Li G, Wang D et al (2005) A Begomovirus DNA β-encoded protein binds DNA, functions as a suppressor of RNA silencing, and targets the cell nucleus. J Virol 79:10764–10775

    Article  CAS  Google Scholar 

  12. Haj-Ahmad F, Odeh W, Anfoka G (2013) First report on the association of squash leaf curl virus and watermelon chlorotic stunt virus with tomato yellow leaf curl disease. Plant Dis 97:428

    Article  Google Scholar 

  13. Idris AM, Shahid MS, Briddon RW et al (2011) An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation. J Gen Virol 92:706–717

    Article  CAS  Google Scholar 

  14. Inoune-Nagata AK, Albuquerque LC, Roche WB, Nagata T (2004) A simple method for cloning the complete begomovirus genome using the bacteriophage ɸ29 DNA polymerase. J Virol Methods 116:209–211

    Article  Google Scholar 

  15. Lapidot M, Gelbart D, Gal-On A et al (2014) Frequent migration of introduced cucurbit-infecting begomoviruses among Middle Eastern countries. Virol J 11:181

    Article  Google Scholar 

  16. Martin DP, Murrell B, Golden M et al (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003

    Article  Google Scholar 

  17. Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9:e108277

    Article  Google Scholar 

  18. Navas-Castillo J, Fiallo-Olivé E, Sánchez-Campos S (2011) Emerging virus diseases transmitted by whiteflies. Annu Rev Phytopathol 49:219–248

    Article  CAS  Google Scholar 

  19. Nawaz-ul-Rehman MS, Nahid N, Mansoor S et al (2010) Post-transcriptional gene silencing suppressor activity of two non-pathogenic alphasatellites associated with a begomovirus. Virology 405:300–308

    Article  CAS  Google Scholar 

  20. Rojas MR, Macedo MA, Maliano MR et al (2018) World management of geminiviruses. Annu Rev Phytopathol 56:637–677

    Article  CAS  Google Scholar 

  21. Rosario K, Marr C, Varsani A et al (2016) Begomovirus-associated satellite DNA diversity captured through vector-enabled metagenomic (VEM) surveys using whiteflies (Aleyrodidae). Viruses 8:36

    Article  Google Scholar 

  22. Tahir MN, Amin I, Briddon RW, Mansoor S (2011) The merging of two dynasties—identification of an African cotton leaf curl disease-associated begomovirus with cotton in Pakistan. PLoS ONE 6:e20366

    Article  CAS  Google Scholar 

  23. Villegas C, Ramos-Sobrinho R, Jifon JL et al (2019) First report of cotton leaf curl Gezira virus and its associated alphasatellite and betasatellite from disease affected okra plants in the United States. Plant Dis 103:3291

    Article  Google Scholar 

  24. Wyatt SD, Brown JK (1996) Detection of subgroup III geminivirus isolates in leaf extracts by degenerate primers and polymerase chain reaction. Phytopathology 86:1288–1293

    Article  Google Scholar 

  25. Zerbini FM, Briddon RW, Idris A et al (2017) ICTV virus taxonomy profile: Geminiviridae. J Gen Virol 98:131–133

    Article  CAS  Google Scholar 

  26. Zhou XP (2013) Advances in understanding begomovirus satellites. Annu Rev Phytopathol 51:357–381

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We are thankful to the research assistants and farmers for their support in field surveys and sample collection. We also thank Dr. Joanna Gress for critically reviewing the English language of the manuscript.

Author information

Author notes

  1. Nida’M. Salem and Muhammad Shafiq Shahid contributed equally to this work.

Authors and Affiliations

  1. Department of Plant Protection, School of Agriculture, The University of Jordan, Amman, 11942, Jordan

    Nida’ M. Salem & Dina Hattab

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

    Muhammad Shafiq Shahid

  3. Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

    Ali Idris

  4. Royal Scientific Society, Amman, Jordan

    Amany Abdeen

Authors
  1. Nida’ M. Salem
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Muhammad Shafiq Shahid
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ali Idris
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Dina Hattab
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Amany Abdeen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nida’ M. Salem.

Ethics declarations

Conflict of interest

The authors declare there is no conflict of interest.

Ethical approval

This study does not include any experiments involving humans or animals by any of the authors.

Additional information

Handling Editor: Tim Skern.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Begomovirus sequences: GenBank Acc. No. MT316185-MT316187. Betasatellite sequences: GenBank Acc. No. MT316188-MT316190. Alphasatellite sequences: GenBank Acc. No. MT316191-MT316193.

Supplementary Information

Below is the link to the electronic supplementary material.

705_2021_5075_MOESM1_ESM.jpg

Supplementary Fig. S1 Genome-wide pairwise identity color matrix constructed with sequences of begomoviruses (or DNA A genomic components) (a), alphasatellites (b), and betasatellites (c) determined in this study and representatives of the different isolates of the virus and DNA satellites, calculated by SDT (v1.2) (DOC 35 KB)

705_2021_5075_MOESM2_ESM.doc

Supplementary Table S1 Features of monopartite begomoviruses, alphasatellites and betasatellites isolated from okra in Jordan (DOC 35 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Salem, N.M., Shahid, M.S., Idris, A. et al. Complete nucleotide sequence of a begomovirus associated with an alphasatellite and a betasatellite naturally infecting okra in Jordan. Arch Virol 166, 2033–2036 (2021). https://doi.org/10.1007/s00705-021-05075-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-021-05075-1

Search

Navigation