Deep Sequencing Reveals Small RNA-Mediated Responses to Low- and High-Temperature Stresses in Cotton

MicroRNAs (miRNAs) are one class of endogenous non-coding RNAs modulating the expression of target genes involved in plant development and stress tolerance, by degrading mRNA or repressing translation. In this study, temperature stress-responsive miRNAs and their targets in cotton (Gossypium hirsutum) were identified via small RNA and mRNA degradome sequencing. Cotton seedlings were treated under different low- and high-temperature conditions (4, 12, 25, 35, and 42 ℃) and then the effects were investigated. A total of 319 known miRNAs and 800 novel miRNAs were identified, and 168 miRNAs were significantly differentially expressed between different treatments. The targets of these miRNAs were further analysed by degradome sequencing. The majority of the miRNAs were identified as being involved in Gene Ontology- and KEGG-defined response to hormone stimulus, oxidation-reduction reaction, photosynthesis, plant–pathogen interaction and plant hormone signal transduction pathways. This study provides new insight into the molecular basis of response to extreme temperature stress and its regulation by miRNAs.