Nanopore sequencing of a novel bipartite New World begomovirus infecting cowpea

  • Fernanda Y. B. Naito
  • Fernando L. MeloEmail author
  • Maria Esther N. Fonseca
  • Carlos A. F. Santos
  • Carolina R. Chanes
  • Bergmann M. Ribeiro
  • Robert L. Gilbertson
  • Leonardo S. Boiteux
  • Rita de Cássia Pereira-Carvalho
Annotated Sequence Record


A new bipartite begomovirus (family Geminiviridae) was detected on cowpea (Vigna unguiculata) plants exhibiting bright golden mosaic symptoms on leaves under field conditions in Brazil. Complete consensus sequences of DNA-A and DNA-B components of an isolate of the virus (PE–088) were obtained by nanopore sequencing and confirmed by Sanger sequencing. The genome components presented the typical genomic organization of New World (NW) begomoviruses. Pairwise sequence comparisons revealed low levels of identity with other begomovirus species previously reported infecting cowpea around the world. Phylogenetic analysis using complete sequences of DNA-A components revealed that the closest relatives of PE–088 (85-87% nucleotide sequence identities) were three legume-infecting begomoviruses from Brazil: bean golden mosaic virus, macroptilium common mosaic virus and macroptilium yellow vein virus. According to the current classification criteria, PE–088 represents a new species in the genus Begomovirus, tentatively named as cowpea bright yellow mosaic virus (CoBYMV).



This research had financial support from grants from Embrapa, CAPES, CNPq and FAPDF (Grant nos. 407908/2013-7, 312646/2018-6). FLM, CAFS, BMR and LSB are CNPq fellows.

Compliance with ethical standards

Conflict of interest

The authors declare that no conflict of interest exists.

Ethical approval

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

Supplementary material

705_2019_4254_MOESM1_ESM.docx (2.6 mb)
Supplementary material 1 (DOCX 2681 kb)


  1. 1.
    Rojas MR, Macedo MA, Maliano MR, Soto-Aguilar M, Souza JO, Briddon RW, Kenyon L, Rivera RB, Zerbini FM, Adkins S, Legg JP (2018) World management of geminiviruses. Annu Rev Phytopathol 56:637–677CrossRefGoogle Scholar
  2. 2.
    Navas-Castillo J, Fiallo-Olivé E, Sánchez-Campos S (2011) Emerging virus diseases transmitted by whiteflies. Annu Rev Phytopathol 8(49):219–248CrossRefGoogle Scholar
  3. 3.
    Santos CAF, Boiteux LS (2013) Breeding biofortified cowpea lines for semi-arid tropical areas by combining higher seed protein and mineral levels. Genet Mol Res 12:6782–6789CrossRefGoogle Scholar
  4. 4.
    Inoue-Nagata AK, Albuquerque LC, Rocha WB, Nagata T (2004) A simple method for cloning the complete begomovirus genome using the bacteriophage φ29 DNA polymerase. J Virol Methods 116:209–211CrossRefGoogle Scholar
  5. 5.
    Rojas MR, Gilbertson RL, Russel DR, Maxwell DP (1993) Use of degenerate primers in the polymerase chain reaction to detect whitefly-transmitted geminiviruses. Plant Dis 77:334–340CrossRefGoogle Scholar
  6. 6.
    Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736CrossRefGoogle Scholar
  7. 7.
    Loman NJ, Quick J, Simpson JT (2015) A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 12:733–735CrossRefGoogle Scholar
  8. 8.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefGoogle Scholar
  9. 9.
    Kearse M, Moir R, Wilson W, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649CrossRefGoogle Scholar
  10. 10.
    Gregorio-Jorge J, Bernal-Alcocer A, Bañuelos-Hernández B, Alpuche-Solís AG, Hernández-Zepeda C, Moreno-Valenzuela O, Frías-Treviño G, Argüello-Astorga GR (2010) Analysis of a new strain of Euphorbia mosaic virus with distinct replication specificity unveils a lineage of begomoviruses with short Rep sequences in the DNA-B intergenic region. Virol J 7:275CrossRefGoogle Scholar
  11. 11.
    Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066CrossRefGoogle Scholar
  12. 12.
    Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650CrossRefGoogle Scholar
  13. 13.
    Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9:e108277CrossRefGoogle Scholar
  14. 14.
    He Z, Zhang H, Gao S, Lercher MJ, Chen WH, Hu S (2016) Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res 44:W236–W241CrossRefGoogle Scholar
  15. 15.
    Chalupowicz L, Dombrovsky A, Gaba V, Luria N, Reuven M, Beerman A, Lachman O, Dror O, Nissan G, Manulis-Sasson S (2018) Diagnosis of plant diseases using the nanopore sequencing platform. Plant Pathol. Google Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  • Fernanda Y. B. Naito
    • 1
  • Fernando L. Melo
    • 1
    Email author
  • Maria Esther N. Fonseca
    • 2
  • Carlos A. F. Santos
    • 3
  • Carolina R. Chanes
    • 4
  • Bergmann M. Ribeiro
    • 1
  • Robert L. Gilbertson
    • 5
  • Leonardo S. Boiteux
    • 1
    • 2
  • Rita de Cássia Pereira-Carvalho
    • 1
  1. 1.University of BrasíliaBrasíliaBrazil
  2. 2.Embrapa VegetablesBrasíliaBrazil
  3. 3.Embrapa Semi-Arid RegionPetrolinaBrazil
  4. 4.Catholic University of BrasíliaBrasíliaBrazil
  5. 5.University of CaliforniaDavisUSA

Personalised recommendations