Small RNA and degradome profiling reveals a role for miRNAs and their targets in the developing fibers of Gossypium barbadense

Abstract

SUMMARY microRNAs (miRNAs) are 20-24 nucleotide non-coding small RNAs that play important roles in plant development. The stages of cotton fiber development include initiation, elongation, secondary wall thickening (SWT) and maturation. We constructed seven fiber RNA libraries representing the initiation, elongation and SWT stages. In total, 47 conserved miRNA families and seven candidate miRNAs were profiled using small RNA sequencing. Northern blotting and real-time polymerase chain reaction (PCR) analyses revealed the dynamic expression of miRNAs during fiber development. In addition, 140 targets of 30 conserved miRNAs and 38 targets of five candidate miRNAs were identified through degradome sequencing. Analysis of correlated expression between miRNAs and their targets demonstrated that specific miRNAs suppressed the expression of transcription factors, SBP and MYB, a leucine-rich receptor-like protein kinase, a pectate lyase, a-tubulin, a UDP-glucuronic acid decarboxylase and cytochrome C oxidase subunit 1 to affect fiber development. Histochemical analyses detected the biological activity of miRNA156/157 in ovule and fiber development. Suppressing miRNA156/157 function resulted in the reduction of mature fiber length, illustrating that miRNA156/157 plays an essential role in fiber elongation.

Cross Talk between Nitric Oxide and Phytohormones Regulate Plant Development during Abiotic Stresses

“…Experiment with soybean seedlings showed that combined application of SNP (as NO donor) and SA alleviated the toxicity of NaCl-induced salt stress by increased proline accumulation and activation of CAT, APX, and GPX. Similar results were reported by Liu et al [96] and Dong et al [97] uptake under salt stress conditions [97].…”

Small RNA and degradome profiling reveals miRNA regulation in the seed germination of ancient eudicot Nelumbo nucifera

“…The degradome library was constructed as described previously [13]. Poly (A) RNA was extracted from total RNA of mixture of the five samples (1 μg of total RNA for each) using the Oligotex kit (Qiagen).…”

“…After amplifying 18 PCR cycles, the PCR product was gel-purified for deep sequencing. The sliced miRNA targets were identified according to the CleaveLand pipeline [13]. The potential targets were as followed: alignments with scores less than four (G: U pairs scored 0.5), and no mismatches were found at the site between the 10th and 11th nucleotides of the miRNAs.…”

“…Other studies have also suggested that whole-scale miRNA identification and targets analysis might reveal regulatory networks in plant growth and development [10]. Lately, degradome sequencing has been used to find target genes on Arabidopsis, rice, cotton and so on [11–13]. However, the miRNA targets in sacred lotus ( Nelumbo nucifera Gaertn.)…”

Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing

“…Advances in the understanding of miRNA-mediated gene regulation revealed that miRNAs play important roles in plant developmental switching and plant responses to environmental abiotic and biotic stresses as well as signal transduction (Jones-Rhoades et al, 2006; Li and Zhang, 2016). To date, several studies have investigated many miRNAs and their regulatory functions in the developmental processes of cotton fibers (Wang et al, 2012, 2015; Xue et al, 2013; Liu et al, 2014; Yu et al, 2014; Xie et al, 2015). Both computational prediction and experimental examinations have been widely employed to identify miRNAs in plants.…”