title: Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play versatile roles in plants, functioning in processes such as growth, development and stress responses. Chilling is a common abiotic stress that seriously affects plants growth and development. Recently, chilling-responsive miRNAs have been detected in several plant species. However, little is known about the miRNAs in the model plant tomato. 'LA1777' (Solanum habrochaites) has been shown to survive chilling stress due to its various characteristics.
  
  
  RESULTS
  Here, two small RNA libraries and two degradome libraries were produced from chilling-treated (CT) and non-chilling-treated (NT) leaves of S. habrochaites seedlings. Following high-throughput sequencing and filtering, 161 conserved and 236 novel miRNAs were identified in the two libraries. Of these miRNAs, 192 increased in the response to chilling stress while 205 decreased. Furthermore, the target genes of the miRNAs were predicted using a degradome sequencing approach. It was found that 62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Additionally, nine miRNAs and six target genes were validated by quantitative real-time PCR (qRT-PCR). Target gene functional analysis showed that most target genes played positive roles in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzyme and genes involved in cell wall formation.
  
  
  CONCLUSIONS
  Tomato is an important model plant for basic biological research. In this study, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, and the target genes were analyzed by degradome sequencing. The work helps identify chilling-responsive miRNAs in tomato and increases the number of identified miRNAs involved in chilling stress. Furthermore, the work provides a foundation for further study of the regulation of miRNAs in the plant response to chilling stress.
authors.forename: Xue
authors.initials: X
authors.lastname: Cao
authors.affiliation: Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P,R, China. wzh@njau.edu.cn.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wu
authors.forename: Fangling
authors.initials: F
authors.lastname: Jiang
authors.forename: Rong
authors.initials: R
authors.lastname: Zhou
authors.forename: Zeen
authors.initials: Z
authors.lastname: Yang
mesh_terms: D003080:Cold Temperature; D019295:Computational Biology; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D034622:RNA Interference; D020871:RNA Stability; D012333:RNA, Messenger; D015203:Reproducibility of Results; D013312:Stress, Physiological / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger