Background: Somatic embryogenesis (SE), by which somatic cells of higher plants can dedifferentiate and reorganize into new plants, is a notable illustration of cell totipotency. However, the precise molecular mechanisms regulating SE remain unclear. To characterize the molecular events of this unique process, transcriptome analysis, in combination with biochemical and histological approaches, were conducted in cotton, a typical plant species in SE. Genome-wide profiling of gene expression allowed the identification of novel molecular markers characteristic of this developmental process. Results: RNA-Seq was used to identify 5,076 differentially expressed genes during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process, associated with morphological, histological changes and endogenous indole-3-acetic acid (IAA) alteration. Bioinformatics analysis showed that the genes were enriched for basic processes such as metabolic pathways and biosynthesis of secondary metabolites. Unigenes were abundant for the functions of protein binding and hydrolase activity. Transcription factor–encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein/indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE. Conclusion: We report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis.

MicroRNAs (miRNAs) have been involved in regulation of diverse spectrum of plant development processes in many species. In cotton, few miRNAs have been well characterised in floral organ development. Floral organ, which should be finely tuned, is a crucial factor affecting the yield of cotton. Therefore, it is well worth revealing the function of miRNAs in regulation of floral organ development. Here, we report the role of miRNA156/157 in regulation of floral organ size in cotton. Over-expression of the GhmiRNA157 precursor in cotton (Gossypium hirsutum) resulted in smaller floral organs, fewer ovules and decreased seed production due to suppression of cell proliferation and cell elongation. Five SQUAMOSA promoter-binding protein-like (SPL) genes were identified as targets of GhmiRNA157 using a RNA ligase-mediated rapid amplification of cDNA end approach, and the expression level of miR157-targeted GhSPLs decreased in the miR157 over-expression lines, indicating the presence of the miR157/SPL axis in cotton. Two MADS-box genes, orthologs of AtAGL6 and SITDR8, which are associated with floral organ development and reproductive production, were repressed in the miR157 over-expression lines. In addition, auxin-inducible genes were also down-regulated, and auxin signal visualized by a DR5::GUS reporter was attenuated in the miR157 over-expression lines. Our results indicate that the miR157/SPL axis controls floral organ growth and ovule production by regulating MADS-box genes and auxin signal transduction. The work further elucidates the mechanism of floral organ development and provides helpful molecular basis for improvement of cotton yield.

Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease characterized by expansion of the fibroblast and myofibroblast population and extracellular matrix deposition. Although the pathogenic mechanisms of IPF remain to be fully elucidated, there is emerging evidence that fibroblasts and myofibroblasts may be derived partially from alveolar epithelial cells by epithelial‑mesenchymal transition (EMT). In the present study, A549 cells were treated with different concentrations of Wnt1 and the results indicated that the mRNA and protein expression levels of vimentin, α‑smooth muscle actin (α‑SMA) and collagen Ⅰ gradully increased and those of E‑cadherin gradully decreased in a concentration‑dependent manner. Furthermore, the A549 cells were transfected with β‑catenin plasmid cells, revealing phenotypic changes in the cells from a pebble to a fusiform shape. The mRNA and protein expression levels of of vimentin, α‑SMA and collagen Ⅰ increased significantly, whereas those of E‑cadherin decreased significantly. The present study examined the roles of alveolar epithelial cell injury and profibrogenic cytokine release in EMT and their association with the Wnt/β‑catenin signaling pathway in a mouse model of bleomycin‑induced pulmonary fibrosis. Bronchoalveolar fluid was obtained 7 days after treatment with bleomycin and the A549 cells were incubated for 48 h. An increase in the expression levels of the mesenchymal markers, α‑SMA, vimentin and collagen Ⅰ, and a concomitant decrease in the expression of the epithelial marker, E‑cadherin were observed. This corresponded with an increased expression of β‑catenin. When the A549 cells were infected with a lentivirus expressing β‑catenin shRNA, no significant increase was observed in the expression of the mesenchymal cell markers and the expression of E‑cadherin did not decrease. These findings demonstrated that activation of the Wnt signaling pathway was capable of inducing an EMT program in the lung epithelial cells through β‑catenin and that injured alveolar epithelium activated the Wnt/β‑catenin signaling pathway, thereby inducing the expansion of the fibroblast/myofibroblast population through EMT. These results suggested that β‑catenin was involved in the formation of lung fibrosis and may provide a theoretical basis for the treatment of IPF.

Plants frequently modulate their hormonal signaling pathways in response to stress, thereby regulating the synthesis of secondary metabolites and adapting to fluctuations in their surroundings. The APETALA2/ethylene-responsive factor (AP2/ERF) domain transcription factors are important in regulating abiotic stress tolerance. The accumulation of asperosaponin VI in the root was significantly enhanced under low temperature stress, which exhibited a correlation with the AP2/ERF family. However, the involvement of AP2/ERF in regulating asperosaponin VI biosynthesis under cold stress remains ambiguous. Under cold stress conditions below 10 °C, we observed the accumulation of asperosaponin VI and an increase in jasmonic acid (JA) levels. This response was attributed to the activation of the JA synthesis pathway induced by low temperatures. Additionally, a comprehensive analysis of the full-length transcriptome of Dipsacus asper identified a total of 80 DaAP2/ERF transcription factors, which exhibited significant homology with Arabidopsis thaliana and Citrus ERFs based on phylogenetic analysis. Furthermore, qRT-PCR analysis demonstrated that both cold stress and methyl jasmonate (MeJA) induction upregulated DaERF108 expression. The expression of DaERF108 is notably upregulated in the leaves and during the early stages of growth and development of D. asper, while subcellular localization analysis confirmed its presence in the nucleus. The overexpression of DaERF108 significantly enhanced the accumulation of oleanolic acid, a precursor of asperosaponin VI, and activated the triterpenoid biosynthesis pathway in Arabidopsis roots. Additionally, the overexpression of DaERF108 induced the activation of the terpenoid synthesis pathway under cold stress conditions. Notably, there was a positive correlation between DaERF108 expression and genes involved in asperosaponin VI biosynthesis, particularly with 3-hydroxy-3-methylglutaryl coenzyme A synthase (DaHMGS). The interaction between DaERF108 and the GCC-box element in the DaHMGS promoter was demonstrated by LUC and Y1H assays, leading to enhanced activity. These findings suggest that DaERF108 specifically binds to the G-box element, thereby regulating DaHMGS gene expression, activating the JA signaling pathway, and promoting asperosaponin VI biosynthesis in response to cold stress.