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Recently,long non-coding RNA(lncRNA)has been shown to play critical regulatory roles in model plants,such as Arabidopsis,rice,and maize.However,the presence of lncRNAs and how they function in fleshy fruit ripening are still largely unknown because fleshy fruit ripening is not present in the above model plants.Tomato is the model system for fruit ripening studies due to its dramatic ripening process.To investigate further the role of lncRNAs in fruit ripening,it is necessary and urgent to discover and identify novel lncRNAs and understand the function of lncRNAs underlying tomato fruit ripening.Here it is reported that 3679 lncRNAs were discovered from wild-type tomato and ripening mutant fruit.The lncRNAs are transcribed from all tomato chromosomes,85.1%of which came from intergenic regions.Tomato lncRNAs are shorter and have fewer exons than protein-coding genes,a situation reminiscent of lncRNAs from other model plants.Furthermore,it was observed that 490 lncRNAs were significantly upregulated in ripening mutant fruits,and 187 lncRNAs were down-regulated,indicating that lncRNAs could be involved in the regulation of fruit ripening.In line with this,silencing of several novel tomato intergenic lncRNAs resulted in an obvious delay of ripening of wild-type fruit.End structure analysis suggested these lncRNAs had 5cap structures and 3polyA tails,which might be Pol Ⅱ-dependent transcripts.Overall,the results indicated that lncRNAs might be essential regulators of tomato fruit ripening,which sheds new light on the regulation of fruit ripening.