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Complete genome sequence of a new bipartite begomovirus infecting cotton in the Republic of Benin in West Africa

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Abstract

Here, we report the complete genome sequence of a novel bipartite begomovirus isolated from cotton plants (Gossypium raimondii, Malvaceae) exhibiting light yellow mosaic symptoms. The genome sequence was determined by Illumina DNA sequencing and confirmed by Sanger sequencing of RCA-enriched, cloned circular genomic components. The DNA-A and DNA-B components were each ~2.7 kb in size, and their genome arrangement was characteristic of other Old World bipartite begomoviruses. While the DNA-A component was most closely related to tobacco leaf curl Comoros virus (TbLCKMV) at 80 %, the DNA-B component had as its closet relative soybean chlorotic blotch virus (SbCBV) at 66 %. This previously undescribed begomovirus is herein named “cotton yellow mosaic virus” (CYMV).

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References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  2. Brown JK (1992) Virus diseases of cotton. In: Hillocks RJ (ed) Cotton diseases. Commonwealth Agricultural Bureaux International, Oxon, pp 275–330

    Google Scholar 

  3. Brown JK, Zerbini FM, Navas-Castillo J, Moriones E, Ramos-Sobrinho R, Silva JCF, Fiallo-Olive E, Briddon RW, Hernandez-Zepeda C, Idris A, Malathi VG, Martin DP, Rivera-Bustamante R, Ueda S, Varsani A (2015) Revision of begomovirus taxonomy based on pairwise sequence comparisons. Arch Virol 160:1593–1619

    Article  CAS  PubMed  Google Scholar 

  4. FAO (2015) Food and Agriculture Organization of the United Nations. On-line and Multilingual Database. http://faostat.fao.org/

  5. Fiallo-Olive E, Zerbini FM, Navas-Castillo J (2015) Complete nucleotide sequences of two new begomoviruses infecting the wild malvaceous plant Melochia sp. in Brazil. Arch Virol. doi:10.1007/s00705-015-2619-4

    Google Scholar 

  6. Hanley-Bowdoin L, Settlage SB, Orozco BM, Nagar S, Robertson D (1999) Geminiviruses: models of plant DNA replication, transcription, and cell cycle regulation. Crit Rev Plant Sci 18:71–106

    Article  CAS  Google Scholar 

  7. Idris AM, Briddon RW, Bull SE, Brown JK (2005) Cotton leaf curl Gezira virus-satellite DNAs represent a divergent, geographically isolated Nile Basin lineage: predictive identification of a satDNA REP-binding motif. Virus Res 109:19–32

    Article  CAS  PubMed  Google Scholar 

  8. Idris A, Al-Saleh M, Piatek MJ, Al-Shahwan I, Ali S, Brown JK (2014) Viral metagenomics: analysis of begomoviruses by Illumina High-Throughput sequencing. Viruses 6:1219–1236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Mansoor S, Khan SH, Bashir A, Saeed M, Zafar Y, Malik KA, Briddon RW, Stanley J, Markham PG (1999) Identification of a novel circular single-stranded DNA associated with cotton leaf curl disease in Pakistan. Virology 259:190–199

    Article  CAS  PubMed  Google Scholar 

  10. Muhire B, Martin DP, Brown JK, Navas-Castillo Moriones JE, Zerbini FM, Rivera-Bustamante R, Malathi VG, Briddon RW, Varsani A (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158:1411–1424

    Article  CAS  PubMed  Google Scholar 

  11. Nawaz-ul-Rehman MS, Briddon RW, Fauquet CM (2012) A melting pot of old world begomoviruses and their satellites infecting a collection of gossypium species in pakistan. PLoS One 7(8):e40050. doi:10.1371/journal.pone.0040050

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ng TFF, Duffy S, Polston JE, Bixby E, Vallad GE, Breitbart M (2011) Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies. PLoS One 6(4):e19050. doi:10.1371/journal.pone.0019050

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Pita JS, Fondong VN, Sangare A, Otim-Nape GW, Ogwal S, Fauquet CM (2001) Recombination, pseudorecombination and synergism of geminivurses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. J Gen Virol 82:655–665

    Article  CAS  PubMed  Google Scholar 

  14. Roossinck MJ (2012) Plant virus metagenomics: biodiversity and ecology. Annu Rev Genet 46:359–369

    Article  CAS  PubMed  Google Scholar 

  15. Sanderfoot AA, Ingham DJ, Lazarowitz SG (1996) A viral movement protein as a nuclear shuttle. Plant Physiol 110:23

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Sattar MN, Kvarnheden A, Saeed M, Briddon RW (2013) Cotton leaf curl disease-an emerging threat to cotton production worldwide. J Gen Virol 10:695–710

    Article  Google Scholar 

  17. (2012) SeqMan Ngen, version 3. DNASTAR Inc., Madison

  18. Shepherd DN, Martin DP, Lefeuvre P, Monjane AL, Owor BE, Rybicki EP, Varsani A (2008) A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. J Virol Methods 149:97–102

    Article  CAS  PubMed  Google Scholar 

  19. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101:11030–11035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. (2011) United Nations conference on trade and development—commodities at a glance: special issue on cotton in Africa (no. 2 June 2011) (UNCTAD/SUC/2011/2(b))

  22. Wendel JF, Brubaker C, Alvarez I, Cronn R, Stewart JM (2009) Evolution and natural history of the cotton genus, Genet Genom Cotton. Springer, New York, pp 1–20

  23. Wyant P, Strohmeier S, Fischer A, Schafer B, Briddon RW, Krenz B, Jeske H (2015) Light-dependent segregation of begomoviruses in Asystasia gangetica leaves. Virus Res 195:225–235

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Walter N. Leke.

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This research was partly funded by National Science Foundation (NSF) award # IOS-1212576.

Walter N. Leke was supported by the Fulbright Foundation and declares that he has no conflict of interest. Judith K. Brown, Vincent N. Fondong, Behnam Khatabi, and Djana B. Mignouna declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Leke, W.N., Khatabi, B., Mignouna, D.B. et al. Complete genome sequence of a new bipartite begomovirus infecting cotton in the Republic of Benin in West Africa. Arch Virol 161, 2329–2333 (2016). https://doi.org/10.1007/s00705-016-2894-8

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  • DOI: https://doi.org/10.1007/s00705-016-2894-8

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