| Salvia miltiorrhiza B.(S. miltiorrhiza) is a Chinese herbal medicine with significant medical and scientific research value. In production, the quality and quantity are affected by diseases and stresses. In plants, Salicylic acid(SA) plays an important role in responding to biotic and abiotic stresses, but the research that reported the SA signaling regulation factor and regulation mechanism in S. miltiorrhiza is very few. In this study, the RNA sequencing(RNA-seq) was employed to evaluate the transcriptional profiles in S. miltiorrhiza cells after 0, 2 and 8h SA induction, which generated a large number of S. miltiorrhiza genetic resources and the SA signaling related genes were obtained. In addition, the relative expression of SA signaling element genes were verified by q RT-PCR. Aimed to clarify the effect of SA on the transcriptome of S. miltiorrhiza, reveal the SA signal transduction pathway and provide help for further understanding the mechanism of SA mediated resistance mechanism. Achieved the following main conclusions:1. 26.22 Gb clean data were generated. The sequence dataset were submitted to the Short Read Archive(SRA) of the National Center for Biotechnology Information(NCBI) database(accession number SRX1423774).2. 50778 unigenes were assembled from the clean data. By aligned to the NR, Swiss-Prot, GO, COG and KEGG databases, 24181(47.62%) unigenes were annotated, of these 17867 unigene were annotated to the GO database, 7881 unigene were categorized into 25 COG families and 4960 unigene were mapped to 137 KEGG pathway.3. Expression pattern of the differentially expressed genes(DEGs) showed that, a total of 5316 DEGs were generated. The DEGs included 1584 only up-regulated, 1492 only down-regulated and 2240 inconsistently regulated unigenes. The GO enrichment analysis showed that a majority of the only up-regulated DEGs were related to response to stimulus,while most of only down-regulated DEGs were enriched in the developmental and cellular process. 532 DEGs were assigned to 104 KEGG pathways, of which the most abundant KEGG pathways in our analysis are ‘Plant hormone signal transduction’(46 DEGs) and ‘Plant-pathogen interaction’(35 DEGs).4. A total of 32 candidate novel genes coding SA signaling component proteins were identified; 13 candidate genes related to H2O2 metabolism, 9 unigenes invlolved in hormone synthesis and 15 unigenes invlolved in hormone signal transduction in addition to SA were significantly overexpressed under SA induction,which indicated that these genes may play important roles in the SA signaling network of S. miltiorrhiza. In addition, we identified a total of 1188 candidate genes encoding 56 transcription factor(TF) families, among these the NAC and GRAS family are the most representative TF families in the only up-regulated TFs, while the b HLH and HD-ZIP family are the top two TF families among the only down-regulated TFs. Besides, many unigenes coding ERF, b ZIP and MYB families protein showed to be differentially expressed after SA induction. It indicated that these TF families may be involved in the responses to disease and environmental stress in S. miltiorrhiza.5. The q RT-PCR validation results showed that: the trend of expression profiling of 18 selected SA signaling related genes based on q RT-PCR were similar to those texted by RNA-seq, which corroborated the reliability of our RNA-seq technology. |
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