Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling.

Jinhua Zuo,Benzhong Zhu,Yunbo Luo,Yunxiang Wang,Lipu Gao,Qing Wang

doi:10.3390/ijms19072001

Abstract

Increasing evidence suggests that long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have roles during biotic and abiotic stress, though their exact contributions remain unclear. To explore their biological functions in response to chilling in bell pepper, we examined their accumulation profiles by deep sequencing and identified 380 lncRNAs, 36 circRNAs, 18 miRNAs, and 4128 differentially expressed mRNAs in the chilled versus the non-chilled fruit. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed differentially expressed genes and putative ncRNA targets, including transcription factors of multiple classes, such as myeloblastosis (MYB), basic helix-loop-helix (bHLH), and ethylene response factor (ERF) transcription factors (TFs), enzymes involved in bio-oxidation and oxidative phosphorylation (serine/threonine-protein kinase, polyphenol oxidase, catalase, peroxidase, lipoxygenase, and ATPase), and cell wall metabolism-related enzymes (beta-galactosidase, pectate lyase, pectinesterase, and polygalacturonase). On the basis of the accumulation profiles, a network of putatively interacting RNAs associated with bell pepper chilling was developed, which pointed to ncRNAs that could provide the foundation for further developing a more refined understanding of the molecular response to chilling injury.

Highlights

Bell pepper (Capsicum annuum) is important from both nutritional and commercial standpoints because of its high vitamin C content and its widespread production throughout tropical, sub-tropical, and temperate regions [1,2,3]
9848 long non-coding RNAs (lncRNAs) were found: 84 were known lncRNAs, and 9764 were novel lncRNAs found in the control and chilling samples (Table S1)
We developed candidate competing RNA (ceRNA) relationships through the miRNA target relationship and obtained 2972 pairs of ceRNA relationships

Summary

Introduction

Bell pepper (Capsicum annuum) is important from both nutritional and commercial standpoints because of its high vitamin C content and its widespread production throughout tropical, sub-tropical, and temperate regions [1,2,3]. To maintain the fruit quality, the pepper fruit must be cooled as quickly as possible after harvest [4]. Pepper fruits are highly sensitive to cold and susceptible to chilling injury (CI) when transported or stored below 7 ◦C [5]. CI limits the storage life and leads to a significant degradation of the postharvest nutritional quality and product value. Cold storage is generally the most effective technology to maintain the quality of postharvest horticultural crops. It is important to overcome the chilling stress in commercially important chilling-sensitive crops [5,8]

Methods

Results

Conclusion