title: Deciphering the roles of circRNAs on chilling injury in tomato.
abstract: Various circular RNAs (circRNAs) are newly identified in animals and plants through high-throughput deep sequencing which play important roles in miRNA function and transcriptional controlling. However, little is known regarding circRNAs in tomato fruit. In this study, we systematically parse the circRNAs in the whole genome using the combination methods of deep sequencing and bioinformatics. In all, 854 circRNAs were identified in our results, among them, 163 circRNAs exhibit chilling responsive expression. Intriguingly, several circRNAs were predicted to involved in chilling responsive process, such as redox reaction, cell wall degradation, Arginine and polyamine metabolism, heat and cold shock protein, energy metabolism, Jasmonic acid and abscisic acid metabolism, low temperature and salt responsive protein and low temperature-induced transcription factors(CBF and WRKY). Furthermore, 102 circRNAs were found to act as the corresponding 24 miRNAs sponges in tomato. These discoveries deciphered the unexpected complexity of the regulatory circRNAs and may open a window for understanding the functions of circRNAs in plants.
authors.affiliation: National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing 100097, China. Electronic address: zuojinhua@126.com.
authors.forename: Jinhua
authors.initials: J
authors.lastname: Zuo
authors.affiliation: National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing 100097, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
authors.forename: Benzhong
authors.initials: B
authors.lastname: Zhu
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
authors.forename: Yunbo
authors.initials: Y
authors.lastname: Luo
authors.affiliation: National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing 100097, China. Electronic address: gaolipu@nercv.org.
authors.forename: Lipu
authors.initials: L
authors.lastname: Gao
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D003080:Cold Temperature; D004734:Energy Metabolism / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000235:genetics* / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000235:genetics*; D000079962:RNA, Circular; D018749:RNA, Plant / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D000079962:RNA, Circular; D018749:RNA, Plant; D014157:Transcription Factors; D012313:RNA
keywords: Chilling injury; Tomato fruit; circRNAs