**1. 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 [1–3]. To maintain the fruit quality, the pepper fruit must be cooled as quickly as possible after harvest [4]. However, pepper fruits are highly sensitive to cold and susceptible to

chilling injury (CI) when transported or stored below 7 ◦C [5]. The main symptoms of chilling injury damage include deterioration of the calyx, sunken lesions, seed browning, and surface pitting [6,7]. CI limits the storage life and leads to a significant degradation of the postharvest nutritional quality and product value. However, cold storage is generally the most effective technology to maintain the quality of postharvest horticultural crops. Thus, it is important to overcome the chilling stress in commercially important chilling-sensitive crops [5,8].

With the development of deep-sequencing technology, numerous non-coding RNAs (ncRNAs) have been discovered in recent years [9]. The ncRNAs can be classified according to their length and function [10,11]. For instance, small ncRNAs of 20–30 nt are mostly microRNAs (miRNAs) and small interfering RNAs (siRNAs), usually associated with transcriptional and translational effects [12]. Medium ncRNAs of 50–200 nt and long ncRNAs (lncRNAs) over 200 nt are associated with splicing, gene inactivation, and translation [13,14]. Unlike linear mRNAs, circRNAs form covalently closed loop structures which originate from tRNAs, exons, introns, or combinations of these molecules to form stable circular RNAs [15–21]. Recently, both lncRNAs and circRNAs have been suggested to have properties as "miRNA sponges", whereby they contribute to the regulation of gene expression by operating as competing RNA (ceRNA), influencing a number of distinct biological processes [22,23].

Previously, in a study focused on pepper miRNAs, a comprehensive bioinformatics analysis revealed 11 miRNAs and 54 putative target genes [24]. Via later deep sequencing, 59 known miRNAs and 310 novel miRNAs were found in hot and black pepper [25,26]. The targets of the miRNAs were analyzed and, in some cases, identified as factors associated with fruit development, quality, and stress response [26,27]. In another study, using strand-specific RNA-sequencing, 2505 putative lncRNAs were identified, and many were associated with functions involved in fruit development and quality in hot pepper [28]. To better understand the molecular mechanisms involved in preventing CI, transcriptome profiling analyses of peppers treated with methyl jasmonate (MeJA) and Brassinosteroids (BRs) were performed [5,29]. However, little effort has been focused on the regulation of miRNAs, circRNAs, and lncRNAs in conjunction with mRNA expression during bell pepper chilling, and, as such, the broader non-coding RNA network involved in chilling response remains unclear.

In this study, high-throughput sequencing was employed to explore the regulation of ncRNAs during bell pepper chilling. We identified 380 lncRNAs, 36 circRNAs, 18 miRNAs, and 4128 differentially expressed mRNAs in response to chilling in pepper fruit. In addition, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses revealed that several ncRNAs were involved in the chilling response, such as the WRKY and bHLH transcription factors, key enzymes, including polyphenol oxidase, catalase, peroxidase, and lipoxygenase involved in redox reaction, and cell wall metabolism-related enzymes, such as beta-galactosidase, pectate lyase, and polygalacturonase. Furthermore, the competing endogenous RNAs (ceRNAs) network of lncRNAs, circRNAs, mRNAs, and miRNAs was assessed by examining gene annotation to uncover influenced pathways and processes.
