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Characterisation of a subgroup IB isolate of Cucumber mosaic virus from Xanthosoma sp. in sub-Saharan Africa


Three tannia (Xanthosoma sp.) plants showing mosaic, mottling and vein chlorosis symptoms were observed in Buikwe district, Uganda. Next generation sequencing (NGS) of RNA extracted from the three plants revealed the presence of Cucumber mosaic virus (CMV). The complete genome sequence of this isolate, designated CMV-Xa, was assembled and sequence analyses based on the three genomic RNAs revealed that CMV–Xa belongs to subgroup IB. This is the first report of CMV infecting Xanthosoma sp. and also the first CMV isolate from subgroup IB detected from sub-Saharan Africa.

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  1. Akwee E, Netondo G, Kataka A, Palapala A (2015) A critical review of the role of taro Colocasia esculenta L. (Schott) to food security: a comparative analysis of Kenya and Pacific Island taro germplasm. Scientia Agri 9:101–108

    CAS  Google Scholar 

  2. Bujarski J, Figlerowicz M, Gallitelli D, Roossinck J, Scott W (2012) Bromoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy, ninth report of the international committee on taxonomy of viruses. Elsevier, Amsterdam, pp 965–976

    Google Scholar 

  3. Chen Y, Chen J, Zhang H, Tang X, Du Z (2007) Molecular evidence and sequence analysis of a natural reassortant between cucumber mosaic virus subgroup IA and II strains. Virus Genes 35:405–413

    Article  CAS  PubMed  Google Scholar 

  4. Cox P, Peterson A, Biggs J (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinf 11:485

    Article  Google Scholar 

  5. Ding W, Anderson J, Haase R, Symons H (1994) New overlapping gene encoded by the cucumber mosaic virus genome. Virology 198:593–601

    Article  CAS  PubMed  Google Scholar 

  6. Eiras M, Boari J, Colariccio A, Chaves R, Briones S, Figueira R, Harakava R (2004) Characterization of isolates of the Cucumovirus cucumber mosaic virus present in Brazil. J Plant Pathol 86:61–69

    CAS  Google Scholar 

  7. Gallitelli D (2000) The ecology of cucumber mosaic virus and sustainable agriculture. Virus Res 71:9–21

    Article  CAS  PubMed  Google Scholar 

  8. Grabherr G, Haas J, Yassour M, Levin Z, Thompson A, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohe N, Gnirke A, Rhind N, di Palma F, Birren W, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Ha C, Coombs S, Revill P, Harding M, Vu M, Dale L (2008) Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses. Arch Virol 153:25–36

    Article  CAS  PubMed  Google Scholar 

  10. Jacquemond M (2012) Cucumber mosaic virus. In: Maramorosch M, Shatkin AJ, murphy FA, (eds). Adv Virus Res 84:439–504

    Article  PubMed  Google Scholar 

  11. Lin X, Rubio L, Smythe B, Falk W (2004) Molecular population genetics of cucumber mosaic virus in California: evidence for founder effects and reassortment. J Virol 78:6666–6675

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Liu Y, Yu L, Lan F, Zhang L, Hou S, Li D, Li D, Zhang M, Shi K (2009) Molecular variability of five cucumber mosaic virus isolates from China. Acta Virol 53:89–97

    Article  CAS  PubMed  Google Scholar 

  13. Miura S, Beriam O, Rivas B (2013) Detection of cucumber mosaic virus in commercial Anthurium crops and genotypes evaluation. Hortic Bras 31:322–327

    Article  Google Scholar 

  14. Nouri S, Arevalo R, Falk B, Groves R (2014) Genetic structure and molecular variability of cucumber mosaic virus isolates in the United States. PLoS One 9:e96582

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Roossinck J (2002) Evolutionary history of cucumber mosaic virus deduced by phylogenetic analyses. J Virol 76:3382–3387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Roossinck J, Zhang L, Hellwald H (1999) Rearrangements in the 5′ nontranslated region and phylogenetic analyses of cucumber mosaic virus RNA 3 indicate radial evolution of three subgroups. J Virol 73:6752–6758

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Sclavounos P, Voloudakis E, Arabatzis C, Kyriakopoulou E (2006) A severe Hellenic CMV tomato isolate: symptom variability in tobacco, characterization and discrimination of variants. Eur J Plant Pathol 115:163–172

    Article  Google Scholar 

  18. Tepfer M, Girardot G, Fénéant L, Tamarzizt B, Verdin E, Moury B, Jacquemond M (2016) A genetically novel, narrow-host-range isolate of cucumber mosaic virus (CMV) from rosemary. Arch Virol 161:2013–2017

    Article  CAS  PubMed  Google Scholar 

  19. Valderrama-Cháirez L, Cruz-Hernández A, Paredes-López O (2002) Isolation of functional RNA from cactus fruit. Plant Mol Biol Report 20:279–286

    Article  Google Scholar 

  20. Wang F, Wang P, Wang P, Hong N (2014) First report of cucumber mosaic virus in taro plants in China. Plant Dis 98:574–574

    Article  CAS  PubMed  Google Scholar 

  21. Yamamoto H, Fuji S (2008) Rapid determination of the nucleotide sequences of potyviral coat protein genes using semi-nested RT-PCR with universal primers. J Gen Plant Pathol 74:97–100

    Article  CAS  Google Scholar 

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This project was funded by the Biosciences eastern and central Africa – International Livestock Research Institute (BecA-ILRI) Hub through the African Biosciences Challenge Fund (ABCF). DK is the recipient of an Australia Awards Scholarship.

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Correspondence to Robert M. Harding.

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Authors declare that they have no conflict of interest.

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Kidanemariam, D.B., Sukal, A.C., Abraham, A.D. et al. Characterisation of a subgroup IB isolate of Cucumber mosaic virus from Xanthosoma sp. in sub-Saharan Africa. Australasian Plant Pathol. 48, 457–460 (2019).

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  • Cucumovirus
  • Tannia
  • Aracaeae