SRNAome and degradome sequencing analysis reveals specific regulation of sRNA in response to chilling injury in tomato fruit.
Plant genomes encode diverse small RNA classes that function in distinct gene-silencing pathways. To elucidate the intricate regulation of microRNAs (miRNAs) and endogenous small-interfering RNAs (siRNAs) in response to chilling injury in tomato fruit, the deep sequencing and bioinformatic methods were combined to decipher the small RNAs landscape in the control and chilling-injured groups. Except for the known miRNAs and ta-siRNAs, 85 novel miRNAs and 5 ta-siRNAs members belonging to 3 TAS families (TAS5, TAS9 and TAS10) were identified, 34 putative phased small RNAs and 740 cis/trans-natural antisense small-interfering RNAs (nat-siRNAs) were also found in our results which enriched the tomato small RNAs repository. A large number of genes targeted by those miRNAs and siRNAs were predicted to be involved in the chilling injury responsive process and five of them were verified via degradome sequencing. Based on the above results, a regulatory model that comprehensively reveals the relationships between the small RNAs and their targets was set up. This work provides a foundation for further study of the regulation of miRNAs and siRNAs in the plant in response to chilling injury.
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.
Jinhua
J
Zuo
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.
Qing
Q
Wang
Laboratory of Postharvest Physiology and Technology of Fruits and Vegetables, Department of Food Science, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
Cong
C
Han
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.
Zheng
Z
Ju
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.
Dongyan
D
Cao
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.
Benzhong
B
Zhu
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.
Yunbo
Y
Luo
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.
Lipu
L
Gao
D003080:Cold Temperature; D019295:Computational Biology; D005638:Fruit / Q000235:genetics* / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000235:genetics* / Q000502:physiology; D035683:MicroRNAs / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics
D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering