Comparative analysis of cotton small RNAs in response to salt stress. Gossypium hirsutum

Plants respond to stress by using multiple gene regulatory mechanisms including the post-transcriptional regulation of gene expression. The stresses suffered by plants under salinity include osmotic stress and ion stress. In this study, three cotton small RNA libraries were constructed and sequenced under normal consideration, osmotic and ionic stress. The length distribution of obtained small RNAs was significantly different between libraries. A total of 228 cotton miRNAs were identified. Of them 24 were novel miRNAs. There were 88 and 75 miRNAs with different expression in response to the influence of osmotic and ionic factors of saline stress, respectively. The identification of these small RNAs as well as elucidating their functional significance broadens our understanding of the post-transcriptional gene regulations in response to salt stress. Overall design: Three separate cDNA libraries of small RNAs were constructed using total RNA obtained from control samples (CK), the 4 h and 5 d samples. A total of 57,370,554 sequence reads were obtained from three libraries. After removing the 3p and 5p adapter sequences and filtering out low quality "n" sequences, 17,026,070, 15,731,477 and 22,590,391 clean reads remained in the CK, 4 h and 5 d samples, respectively.