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

**Jinhua Zuo 1,2,3,4,5,\* ID , Yunxiang Wang <sup>6</sup> , Benzhong Zhu <sup>7</sup> , Yunbo Luo <sup>7</sup> , Qing Wang 1,2,3,4,\* and Lipu Gao 1,2,3,4,\***


Received: 21 May 2018; Accepted: 27 June 2018; Published: 9 July 2018

**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.

**Keywords:** analysis; non-coding RNA; transcriptomes; bell pepper; chilling injury
