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Unveiling the complete genome sequence of clerodendrum chlorotic spot virus, a putative dichorhavirus infecting ornamental plants

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Abstract

The genus Dichorhavirus includes plant-infecting rhabdoviruses with bisegmented genomes that are horizontally transmitted by false spider mites of the genus Brevipalpus. The complete genome sequences of three isolates of the putative dichorhavirus clerodendrum chlorotic spot virus were determined using next-generation sequencing (Illumina) and traditional RT-PCR. Their genome organization, sequence similarity and phylogenetic relationship to other viruses, and transmissibility by Brevipalpus yothersi mites support the assignment of these viruses to a new species of dichorhavirus, as suggested previously. New data are discussed stressing the reliability of the current rules for species demarcation and taxonomic status criteria within the genus Dichorhavirus.

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Acknowledgements

The authors thank Dr. G. Otero-Colina (Colegio de Postgraduados, Texcoco, Mexico) for kindly providing the OFV-citrus cDNA control used in this study.

Funding

This work was partially supported by FAPESP (2014/08458-9, 2016/01960-6 and 2013/25713-0).

Author information

Authors and Affiliations

  1. Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo, SP, 04014-002, Brazil

    Pedro Luis Ramos-González, Camila Chabi-Jesus, Alexander Banguela-Castillo, Mariane da Costa Rodrigues, Ricardo Harakava & Juliana Freitas-Astúa

  2. Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil

    Camila Chabi-Jesus, Aline Daniele Tassi & Elliot Watanabe Kitajima

  3. Universidade Anhembi Morumbi/UAM, São Paulo, SP, 03164-000, Brazil

    Mariane da Costa Rodrigues

  4. Embrapa Mandioca e Fruticultura, Cruz das Almas, BA, 44380-000, Brazil

    Juliana Freitas-Astúa

Authors
  1. Pedro Luis Ramos-González
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  2. Camila Chabi-Jesus
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  3. Alexander Banguela-Castillo
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  4. Aline Daniele Tassi
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  5. Mariane da Costa Rodrigues
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  6. Elliot Watanabe Kitajima
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  7. Ricardo Harakava
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  8. Juliana Freitas-Astúa
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Corresponding author

Correspondence to Juliana Freitas-Astúa.

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The authors declare 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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Handling Editor: Stephen John Wylie.

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Supplementary Figure 1

1% agarose gel electrophoresis of RT-PCR products for detection of dichorhaviruses. Each RNA sample was analyzed with seven primer pairs for the detection of known dichorhaviruses as follows: OFV (N gene), OFV and OFV-citrus (degenerate primer pair for the detection of L gene), CiLV-N (N gene), CiCSV (G gene), CoRSV (N and L genes) and ClCSV (L gene). MW, molecular weight marker, 1kb DNA Ladder (Promega, Madison, WI, USA). Lane 1, reverse transcription blank; 2, PCR blank; 3 and 4, leaf asymptomatic areas from ClCSV-infected Clerodendrum sp. plants collected in Piracicaba and São Paulo, respectively; 5, leaf asymptomatic area from a ClCSV-infected Hibiscus rosa-sinensis plant collected in Santa Barbara d’Oeste; 6 and 7, leaf chlorotic area from Clerodendrum sp. plants collected in Piracicaba and São Paulo, respectively; 8, leaf chlorotic area from an H. rosa-sinensis plant collected in Santa Barbara d’Oeste; 9, OFV-infected orchid plant from Piracicaba, SP; 10, OFV-citrus-infected citrus tree, Mexico; 11, CiLV-N-infected citrus tree, Ibiúna, SP; 12, CiCSV-infected citrus tree, Teresina, PI; 13 and 14, CoRSV-infected coffee plant, Limeira, SP; 15, ClCSV-infected Clerodendrum plant 2, Piracicaba, SP (positive control) (DOCX 552 kb)

Supplementary Table 1

Library composition, viral genome coverage, and generated contigs corresponding to the genome of clerodendrum chlorotic spot virus isolates SBO1 and Prb1 obtained by next-generation sequencing from infected Hibiscus rosa-sinensis and Clerodendrum sp. plants (DOCX 16 kb)

Supplementary Table 2

List of primers for the secondary sequencing and RACE (rapid amplification of cDNA ends) of the genome of clerodendrum chlorotic spot virus (ClCSV_Prb1 isolate) (DOCX 43 kb)

Supplementary material 4 (TXT 14 kb)

Supplementary material 5 (TXT 12 kb)

Supplementary material 6 (TXT 14 kb)

Supplementary material 7 (TXT 12 kb)

Supplementary material 8 (TXT 13 kb)

Supplementary material 9 (TXT 11 kb)

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Ramos-González, P.L., Chabi-Jesus, C., Banguela-Castillo, A. et al. Unveiling the complete genome sequence of clerodendrum chlorotic spot virus, a putative dichorhavirus infecting ornamental plants. Arch Virol 163, 2519–2524 (2018). https://doi.org/10.1007/s00705-018-3857-z

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