Abstract
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, small RNA and mRNA degradome sequencing were used to identify low- and high-temperature stress-responsive miRNAs and their targets in cotton (Gossypium hirsutum). Cotton seedlings were treated under different temperature conditions (4, 12, 25, 35, and 42 °C) and then the effects were investigated. In total, 319 known miRNAs and 800 novel miRNAs were identified, and 168 miRNAs were differentially expressed between different treatments. The targets of these miRNAs were further analysed by degradome sequencing. Based on studies from Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, the majority of the miRNAs are from genes that are likely involved in 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 mechanisms of plant response to extreme temperature stresses, and especially the roles of miRNAs under extreme temperatures.
Highlights
Small RNAs have emerged as key post-transcriptional gene regulatory molecules in plants and animals
We identified known miRNAs by using homologous analysis to find sRNA sequences with criteria for selection of a length of at least 18 nt, and a maximum of two mismatches compared to all known plant miRNA sequences deposited in miRBase21.0 in the five small RNA libraries
To validate whether the predicted target genes were really regulated by miRNAs under different temperature stresses, we conducted the expression analysis of the predicted target genes and their corresponding miRNAs, and the results revealed that the predicted target genes had an opposite expression profiles compared to the corresponding miRNAs (Fig. 7)
Summary
Small RNAs (sRNAs) have emerged as key post-transcriptional gene regulatory molecules in plants and animals. Much focus has been directed to the mechanisms of cotton fiber development, quality and yield[15] This includes analysis of miRNA expression during fiber development[16], miRNA expression in biotic stress[17] and abiotic stress responding to drought and salinity[18]. The aim of this study was to profile the miRNA and their target mRNAs in cotton subjected to low- and high-temperature stresses, using high-throughput sequencing analysis and degradome sequencing. These findings reveal a putative miRNA-mediated regulatory network with a critical role in the response to low- and high-temperature stress in this important crop
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