MicroRNAs and their targets in cucumber shoot apices in response to temperature and photoperiod

Xiaohui Zhang,Mengmeng Duan,Yunsong Lai,Jiangping Song,Haiping Wang,Wei Zhang,Tongjin Liu,Jalil Ahmad,Xiaoxue Zhang,Yang Qiu,Xixiang Li

doi:10.1186/s12864-018-5204-x

Abstract

BackgroundThe cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and long vs. short photoperiod.ResultsA total of 164 known miRNAs derived from 68 families and 203 novel miRNAs from 182 families were identified. Their 4611 targets were predicted using psRobot and TargetFinder, amongst which 349 were validated by degradome sequencing. Fourteen targets of six miRNAs were differentially expressed between the treatments. A total of eight known and 16 novel miRNAs were affected by temperature and photoperiod. Functional annotations revealed that “Plant hormone signal transduction” pathway was significantly over-represented in the miRNA targets. The miR156/157/SBP-Boxes and novel-mir153/ethylene-responsive transcription factor/senescence-related protein/aminotransferase/acyl-CoA thioesterase are the two most credible miRNA/targets combinations modulating the plant’s responsive processes to the temperature-photoperiod changes. Moreover, the newly evolved, cucumber-specific novel miRNA (novel-mir153) was found to target 2087 mRNAs by prediction and has 232 targets proven by degradome analysis, accounting for 45.26–58.88% of the total miRNA targets in this plant. This is the largest sum of genes targeted by a single miRNA to the best of our knowledge.ConclusionsThese results contribute to a better understanding of the miRNAs mediating plant adaptation to combinations of temperature and photoperiod and sheds light on the recent evolution of new miRNAs in cucumber.

Highlights

The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology
Zhang et al BMC Genomics (2018) 19:819 cucumber shoot apexes grown in differential temperatures in previous studies [11]
Results sRNA sequencing and miRNA identification To reveal the roles of miRNAs in plant adaptation to temperature-photoperiod environments, small RNAs were pyrosequenced from the shoot apical tissues of cucumber plants grown in four differential temperature-photoperiod treatments (16 h light at 28 °C /8 h dark at 25 °C, HL; 8 h light at 28 °C /16 h dark at 25 °C, HS; 16 h light at 20 °C /8 h dark at 15 °C, LL; 8 h light at 20 °C /16 h dark at 15 ° C, LS)

Summary

Introduction

The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. A series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs low temperature and long vs short photoperiod. The plant genome responds to environments via epigenetic, transcriptional and post-transcriptional regulations [8]. Small RNAs play fundamental roles in post-transcriptional regulation via mRNA cleavage and translation inhibition and link up these three levels of regulation in the way of epigenetic reprogramming [24, 25]

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