title: Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening.
abstract: In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato fruit and leaf. Several conserved miRNAs showed tissue-specific expression, which, combined with target gene validation results, suggests that miRNAs may play a role in fleshy fruit development. We also identified four new nonconserved miRNAs. One of the validated targets of a novel miRNA is a member of the CTR family involved in fruit ripening. However, 62 predicted targets showing near perfect complementarity to potential new miRNAs did not validate experimentally. This suggests that target prediction of plant short RNAs could have a high false-positive rate and must therefore be validated experimentally. We also found short RNAs from a Solanaceae-specific foldback transposon, which showed a miRNA/miRNA*-like distribution, suggesting that this element may function as a miRNA gene progenitor. The other Solanaceae-specific class of short RNA was derived from an endogenous pararetrovirus sequence inserted into the tomato chromosomes. This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation.
authors.affiliation: School of Computing, University of East Anglia, Norwich NR4 7TJ, United Kingdom.
authors.forename: Simon
authors.initials: S
authors.lastname: Moxon
authors.forename: Runchun
authors.initials: R
authors.lastname: Jing
authors.forename: Gyorgy
authors.initials: G
authors.lastname: Szittya
authors.forename: Frank
authors.initials: F
authors.lastname: Schwach
authors.forename: Rachel L
authors.initials: RL
authors.lastname: Rusholme Pilcher
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
authors.forename: Tamas
authors.initials: T
authors.lastname: Dalmay
mesh_terms: D001483:Base Sequence; D015152:Blotting, Northern; D019295:Computational Biology; D017124:Conserved Sequence; D004251:DNA Transposable Elements; D005638:Fruit / Q000235:genetics* / Q000378:metabolism; D018628:Gene Dosage; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D018551:Solanum lycopersicum / Q000235:genetics* / Q000378:metabolism; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism; D008969:Molecular Sequence Data; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism; D019657:Solanaceae / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs; D018749:RNA, Plant