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Citrus tristeza virus infection induces the accumulation of viral small RNAs (21–24-nt) mapping preferentially at the 3′-terminal region of the genomic RNA and affects the host small RNA profile

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Abstract

To get an insight into the host RNA silencing defense induced by Citrus tristeza virus (CTV) and into the counter defensive reaction mediated by its three silencing suppressors (p25, p20 and p23), we have examined by deep sequencing (Solexa-Illumina) the small RNAs (sRNAs) in three virus-host combinations. Our data show that CTV sRNAs: (i) represent more than 50% of the total sRNAs in Mexican lime and sweet orange (where CTV reaches relatively high titers), but only 3.5% in sour orange (where the CTV titer is significantly lower), (ii) are predominantly of 21–22-nt, with a biased distribution of their 5′ nucleotide and with those of (+) polarity accumulating in a moderate excess, and (iii) derive from essentially all the CTV genome (ca. 20 kb), as revealed by its complete reconstruction from viral sRNA contigs, but adopt an asymmetric distribution with a prominent hotspot covering approximately the 3′-terminal 2,500 nt. These results suggest that the citrus homologues of Dicer-like (DCL) 4 and 2 most likely mediate the genesis of the 21 and 22 nt CTV sRNAs, respectively, and show that both ribonucleases act not only on the genomic RNA but also on the 3′ co-terminal subgenomic RNAs and, particularly, on their double-stranded forms. The plant sRNA profile, very similar and dominated by the 24-nt sRNAs in the three mock-inoculated controls, was minimally affected by CTV infection in sour orange, but exhibited a significant reduction of the 24-nt sRNAs in Mexican lime and sweet orange. We have also identified novel citrus miRNAs and determined how CTV influences their accumulation.

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Acknowledgments

This research was supported by a grant (Prometeo/2008/121) from the Generalitat Valenciana, Spain, and by an aid (PAID-02-10/2180) from the Program for Research and Development of the Universidad Politécnica de Valencia. We are grateful to Jaime Piquer and Pablo Lemos for technical support in the greenhouse and with the illustrations, respectively.

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Authors and Affiliations

  1. Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos, 46022, Valencia, Spain

    Susana Ruiz-Ruiz & Ricardo Flores

  2. Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Via Amendola 165/A, 70126, Bari, Italy

    Beatriz Navarro & Francesco Di Serio

  3. Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Via Amendola 122/D, 70126, Bari, Italy

    Andreas Gisel

  4. Instituto Valenciano de Investigaciones Agrarias, 46113, Moncada, Valencia, Spain

    Susana Ruiz-Ruiz, Leandro Peña, Luis Navarro & Pedro Moreno

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  1. Susana Ruiz-Ruiz
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  2. Beatriz Navarro
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  3. Andreas Gisel
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  4. Leandro Peña
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  5. Luis Navarro
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  6. Pedro Moreno
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  7. Francesco Di Serio
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  8. Ricardo Flores
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Correspondence to Ricardo Flores.

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The first two authors have contributed equally to this work.

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Ruiz-Ruiz, S., Navarro, B., Gisel, A. et al. Citrus tristeza virus infection induces the accumulation of viral small RNAs (21–24-nt) mapping preferentially at the 3′-terminal region of the genomic RNA and affects the host small RNA profile. Plant Mol Biol 75, 607–619 (2011). https://doi.org/10.1007/s11103-011-9754-4

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