Abstract
Plant long non-coding RNA (lncRNA) undergoes dynamic regulation and acts in developmental and stress regulation. In this study, we surveyed the expression dynamics of lncRNAs in grapevine (Vitis vinifera L.) under cold stress using high-throughput sequencing. Two-hundred and three known lncRNAs were significantly up-regulated and 144 known lncRNAs were significantly down-regulated in cold-treated grapevine. In addition, 2 088 novel lncRNA transcripts were identified in this study, with 284 novel lncRNAs significantly up-regulated and 182 novel lncRNAs significantly down-regulated in cold-treated grapevine. Two-hundred and forty-two differentially expressed grapevine lncRNAs were predicted to target 326 protein-coding genes in a cis-regulatory relationship. Many differentially expressed grapevine lncRNAs targeted stress response-related genes, such as CBF4 transcription factor genes, late embryogenesis abundant protein genes, peroxisome biogenesis protein genes, and WRKY transcription factor genes. Sixty-two differentially expressed grapevine lncRNAs were predicted to target 100 protein-coding genes in a trans-regulatory relationship. The expression of overall target genes in both cis and trans-regulatory relationships were positively related to the expression of lncRNAs in grapevines under cold stress. We identified 31 known lncRNAs as 34 grapevine micro RNA (miRNA) precursors and some miRNAs may be derived from multiple lncRNAs. We found 212 lncRNAs acting as targets of miRNAs in grapevines, involving 150 miRNAs; additionally, 120 grapevine genes were predicted as targets of grapevine miRNAs and lncRNAs. We found one gene cluster that was up-regulated and showed the same expression trend. In this cluster, many genes may be involved in abiotic stress response such as WRKY, Hsf, and NAC transcription factor genes.
Highlights
In eukaryotes, many transcripts are non-coding RNAs[1,2]
To systematically identify long non-coding RNA (lncRNA) related to cold stress in grapevine, we performed whole transcriptome RNA-seq of grapevine cv
A previous study reported the existence of lncRNAs in plants[37]
Summary
Many transcripts are non-coding RNAs (ncRNAs)[1,2]. Long ncRNA (lncRNA) is a type of ncRNA that is generally >200 nt long and has no discernable coding potential[3,4]. The Arabidopsis microRNA target mimics the IPS1 lncRNA and the decoy ASCO-lncRNA14,23 This illustrates the competing endogenous RNA (ceRNA) theory, which is well-supported and is widely accepted[17,24]. Growing evidence supports the view that non-coding RNAs, including lncRNAs, play important roles in regulating responses to a variety of abiotic and biotic stressors[25,26,27]. MiRNA, another non-coding RNA, was shown to be involved in various abiotic stress responses such as cold stress (chilling or freezing) in plants[33,34,35,36]. LncRNAs compete with other miRNA sponges, such as target gene mRNA, to play important roles in eukaryotes[30,37,38,39,40]. Our aims were to identify the cold-responsive lncRNAs and determine if or how cold stress response in grapevine is related to lncRNA regulation
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