MicroRNAs and targets in senescent litchi fruit during ambient storage and post-cold storage shelf life

BACKGROUND: Litchi has a high commercial value due to its bright color and rich nutrients. However, it deteriorates with the pericarp turning brown within 1–2 days after harvest. The factors that mediate litchi fruit senescence are complicated. MicroRNAs act as negative regulators involved in almost every physiological process. To understand the mechanism of litchi fruit senescence and pericarp browning at the miRNA level, five small RNA libraries and a degradome library prepared from the pericarp of litchi fruit subjected to ambient storage and post-cold storage shelf life were sequenced. RESULTS: By aligning the sRNA reads onto the litchi unigene assembly, 296 miRNAs belonging to 49 known miRNA families were first identified from litchi. In addition, 11 litchi-specific miRNAs were identified. Among these, 167 known miRNAs were identified to cleave 197 targets, and three litchi-specific miRNAs were found to have five targets. Through combined analysis of stem-loop quantitative real-time polymerase chain reaction (qRT-PCR) and transcriptome profiling, 14 miRNA-target pairs were found to be actively involved in litchi fruit senescence-related processes, including energy regulation, anthocyanin metabolism, hormone signaling, and pathogen-infection defense. CONCLUSIONS: A network of miRNA-targets that regulate litchi fruit senescence has been proposed, revealing the miRNA-mediated regulation in senescent litchi fruit. This will aid in developing new strategies to postpone the senescence of litchi fruit and other horticultural products. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-015-0509-2) contains supplementary material, which is available to authorized users.