Identification of novel short RNAs in tomato (Solanum lycopersicum)

Rusholme Pilcher, Rachel, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Pakseresht, Nima, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Manning, Kenneth, Seymour, Graham and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2007) Identification of novel short RNAs in tomato (Solanum lycopersicum). Planta, 226 (3). pp. 709-717. ISSN 0032-0935

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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.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Computing Sciences Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology > Computational biology of RNA (former - to 2018) Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Groups > Plant Sciences Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre
Depositing User:	Vishal Gautam
Date Deposited:	19 May 2011 07:40
Last Modified:	16 Jun 2023 00:04
URI:	https://ueaeprints.uea.ac.uk/id/eprint/22241
DOI:	10.1007/s00425-007-0518-y

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