title: Identification of novel small RNAs in tomato (Solanum lycopersicum).
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.
authors.affiliation: School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
authors.forename: Rachel L Rusholme
authors.initials: RL
authors.lastname: Pilcher
authors.forename: Simon
authors.initials: S
authors.lastname: Moxon
authors.forename: Nima
authors.initials: N
authors.lastname: Pakseresht
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
authors.forename: Kenneth
authors.initials: K
authors.lastname: Manning
authors.forename: Graham
authors.initials: G
authors.lastname: Seymour
authors.forename: Tamas
authors.initials: T
authors.lastname: Dalmay
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D015152:Blotting, Northern; D003001:Cloning, Molecular; D017124:Conserved Sequence; D020224:Expressed Sequence Tags; D018745:Genome, Plant / Q000235:genetics; D018551:Solanum lycopersicum / Q000235:genetics*; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation
chemical_list: D035683:MicroRNAs