Table_1_Genome-Wide Identification of Circular RNAs in Response to Low-Temperature Stress in Tomato Leaves.XLS

Abiotic stress adversely inhibits the growth and development of plants, by changing the expression of multiple genes. Circular RNAs (circRNAs), as a class of non-coding RNAs, function in transcriptional and posttranscriptional regulation. Yet, the involvement of circRNAs in abiotic stress response is rarely reported. In this study, the participation and function of circRNAs in low-temperature (LT)-induced stress response were investigated in tomato leaves. We generated genome-wide profiles of circRNAs and mRNAs in tomato leaves grown at 25°C room temperature (RT) and 12°C LT. Our results show that 1,830 circRNAs were identified in tomato leaves in both RT and LT treatments, among which 1,759 were differentially induced by the LT treatment. We find that the identified circRNAs are mainly located at exons of genes, but less distributed at introns of genes or intergenic regions. Our results suggest that there are 383 differentially expressed circRNAs predicted to function as putative sponges of 266 miRNAs to target 4,476 mRNAs in total. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis assays indicate that multiple pathways were enriched in both differentially expressed genes induced by LT and parental genes of differentially expressed circRNAs induced by LT, revealing the key functions of circRNAs and the corresponding targeted genes in response to LT stress. Our results suggest that circRNAs may be involved in regulating metabolism (i.e., carbohydrate, amino acid, lipid, and energy), signal transduction, and environmental adaptation-related pathways and that these circRNAs were predicted to regulate the expression of transcription factors, genes in signal transduction pathways, and genes related to the Ca2+ channel through targeting the corresponding proteins, such as WRKY, NAC, cytochrome P450, and calmodulin binding protein. Taken together, our study uncovers that multiple circRNAs are isolated and differently regulated in response to LT stress and provides the resource and potential networks of circRNA–miRNA–mRNA under LT stress for further investigations in tomato leaves.非生物胁迫（Abiotic stress）通过改变多个基因的表达水平，对植物生长发育产生显著抑制作用。环状RNA（Circular RNAs, circRNAs）作为一类非编码RNA（non-coding RNAs），可在转录及转录后层面发挥调控功能。然而，目前关于circRNAs参与非生物胁迫响应的研究报道尚少。本研究以番茄叶片为材料，探究了环状RNA在低温（low-temperature, LT）诱导的胁迫响应中的参与情况与功能。我们分别对在25℃室温（room temperature, RT）及12℃低温环境下生长的番茄叶片中的circRNAs与mRNAs进行了全基因组表达谱分析。结果显示，在室温与低温处理的番茄叶片中共鉴定出1830个circRNAs，其中1759个的表达在低温处理下发生显著差异。进一步分析发现，所鉴定的circRNAs主要分布于基因外显子区域，而在基因内含子区域及基因间区的分布较少。本研究预测，共有383个差异表达circRNAs可作为266种miRNA的潜在海绵，进而靶向调控总计4476个mRNAs的表达。此外，基因本体（Gene Ontology, GO）及京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）富集分析显示，低温诱导的差异表达基因与差异表达circRNAs的宿主基因均富集到多条通路，这揭示了circRNAs及其靶向基因在低温胁迫响应中的关键作用。研究结果表明，circRNAs可能参与调控碳水化合物、氨基酸、脂质及能量代谢、信号转导以及环境适应相关通路；此外，这些circRNAs可通过靶向WRKY、NAC、细胞色素P450、钙调素结合蛋白等相关蛋白，调控转录因子、信号转导通路基因及钙离子通道相关基因的表达。综上，本研究成功鉴定出多个响应低温胁迫的差异表达circRNAs，并为番茄叶片低温胁迫下circRNA–miRNA–mRNA调控网络的进一步研究提供了数据资源与潜在研究模型。