title: Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns.
abstract: Plants feature a particularly diverse population of short (s)RNAs, the central component of all RNA silencing pathways. Next generation sequencing techniques enable deeper insights into this complex and highly conserved mechanism and allow identification and quantification of sRNAs. We employed deep sequencing to monitor the sRNAome of developing tomato fruits covering the period between closed flowers and ripened fruits by profiling sRNAs at 10 time-points. It is known that microRNAs (miRNAs) play an important role in development but very little information is available about the majority of sRNAs that are not miRNAs. Here we show distinctive patterns of sRNA expression that often coincide with stages of the developmental process such as flowering, early and late fruit maturation. Moreover, thousands of non-miRNA sRNAs are differentially expressed during fruit development and ripening. Some of these differentially expressed sRNAs derived from transposons but many derive from protein coding genes or regions that show homology to protein coding genes, several of which are known to play a role in flower and fruit development. These findings raise the possibility of a regulative role of these sRNAs during fruit onset and maturation in a crop species. We also identified six new miRNAs and experimentally validated two target mRNAs. These two mRNAs are targeted by the same miRNA but do not belong to the same gene family, which is rare for plant miRNAs. Expression pattern and putative function of these targets indicate a possible role in glutamate accumulation, which contributes to establishing the taste of the fruit.
authors: School of Computing Sciences, University of East Anglia, Norwich, UK.
authors: Irina
authors: I
authors: Mohorianu
authors: Frank
authors: F
authors: Schwach
authors: Runchun
authors: R
authors: Jing
authors: Sara
authors: S
authors: Lopez-Gomollon
authors: Simon
authors: S
authors: Moxon
authors: Gyorgy
authors: G
authors: Szittya
authors: Karim
authors: K
authors: Sorefan
authors: Vincent
authors: V
authors: Moulton
authors: Tamas
authors: T
authors: Dalmay
mesh_terms: D016000:Cluster Analysis; D035264:Flowers / Q000235:genetics / Q000254:growth & development; D005638:Fruit / Q000235:genetics / Q000254:growth & development*; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant