Solanum habrochaites

To identify tomato miRNAs involved in chilling response, two small RNA libraries and two degradome libraries from chilling-treated(4°C/4°C for 1h,4h, 8h, 12h, 24h and 48h) and non-chilling-treated (25°C/20°C for 1h,4h, 8h, 12h, 24h and 48h)leaves of LA1777' (S. habrochaites) seedlings were constructed. A total of 4342604 and 7231609 clean reads were obtained by high-throughput sequencing of the two libraries, respectively. 161 conserved miRNAs and 236 novel miRNAs were identified in the two librayies. Of these miRNAs, 192 were upregulated, whereas 205 were downregulated in response to chilling stress. Among these, 23 miRNAs and 26 miRNAs were significantly upregulated and downregulated in response to chilling stress, respectively.Through degradome sequencing,62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Target gene functional analysis revealed that most target genes played positive role in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzymes and genes involved in cell wall formation. Overall design: tomato miRNA-seq and Degradome-seq after chilling