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Identification of novel small RNAs in tomato (Solanum lycopersicum)

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Abstract

To date, the majority of plant small RNAs (sRNA) have been identified in rice, poplar and Arabidopsis. To identify novel tomato sRNAs potentially involved in tomato specific processes such as fruit development and/or ripening, we cloned 4,018 sRNAs from tomato fruit tissue at the mature green stage. From this pool of sRNAs, we detected tomato homologues of nine known miRNAs, including miR482; a poplar miRNA not conserved in Arabidopsis or rice. We identified three novel putative miRNAs with flanking sequence that could be folded into a stem-loop precursor structure and which accumulated as 19-24nt RNA. One of these putative miRNAs (Put-miRNA3) exhibited significantly higher expression in fruit compared with leaf tissues, indicating a specific role in fruit development processes. We also identified nine sRNAs that accumulated as 19–24nt RNA species in tomato but genome sequence was not available for these loci. None of the nine sRNAs or three putative miRNAs possessed a homologue in Arabidopsis that had a precursor with a predicted stem-loop structure or that accumulated as a sRNA species, suggesting that the 12 sRNAs we have identified in tomato may have a species specific role in this model fruit species.

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Abbreviations

AGO:

ARGONAaUT

BAC:

Bacterial artificial chromosome

DAP:

Days after pollination

DCL:

DICER LIKE

dsRNA:

Double stranded RNA

EST:

Expressed sequence tag

nat-siRNAs:

Natural antisense siRNAs

nt:

Nucleotide

MFE:

Minimum free energy

MiRNA:

microRNA

put-miRNA:

Putative microRNA

RISC:

RNA induced silencing complex

RDR:

RNA dependent RNA polymerase

rRNA:

Ribosomal RNA

siRNA:

Small interfering RNA

sRNA:

Small RNA

tRNA:

Transfer RNA

ta-siRNA:

Trans-acting small interfering RNA

TSD:

Tomato sequence database

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Acknowledgments

We thank Peter Walley (Warwick-HRI, UK) for providing RNA extracted from pericarp of Ailsa Craig tomato fruits. This work was funded by the BBSRC (BB/E006981/1 and BB/E004091/1).

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Authors and Affiliations

  1. School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK

    Rachel L. Rusholme Pilcher & Tamas Dalmay

  2. School of Computing, University of East Anglia, Norwich, NR4 7TJ, UK

    Simon Moxon, Nima Pakseresht & Vincent Moulton

  3. Warwick Horticulture Research International, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK

    Kenneth Manning

  4. School of Biosciences, Division of Plant Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK

    Graham Seymour

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  1. Rachel L. Rusholme Pilcher
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Correspondence to Tamas Dalmay.

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Pilcher, R.L.R., Moxon, S., Pakseresht, N. et al. Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta 226, 709–717 (2007). https://doi.org/10.1007/s00425-007-0518-y

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  • DOI: https://doi.org/10.1007/s00425-007-0518-y

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