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(A) Venn diagram of DEGs in the three comparison groups. The three circles represent different comparison groups, and their overlaps indicate the number of common DEGs identified in these comparison groups. (B) Number of DEGs in the three comparison groups. The orange rectangles indicate the up-regulated DEGs and the blue rectangles indicate the down-regulated DEGs. (C) The hierarchical cluster analysis of DEGs from three comparison groups of different tissues. The rows in the graph represent DEGs, the columns represent samples, and the colors are log-transformed and normalized to the FPKM values. The brighter color represents a higher (red) or lower (green) expression level.
Source publication
Rheum officinale Baill. is an important traditional Chinese medicinal herb, its dried roots and rhizomes being widely utilized to cure diverse diseases. However, previous studies mainly focused on the active compounds and their pharmacological effects, and the molecular mechanism underlying the biosynthesis of these ingredients in R. officinale is...
Contexts in source publication
Context 1
... COG annotation, 41,568 annotated unigenes were classified into 25 categories, with a high proportion of "posttranslational modification, protein turnover, chaperones" (2596, 6.25%), "translation, ribosomal structure and biogenesis" (2267, 5.45%), and "carbohydrate transport and metabolism" (1927,4.64%) ( Figure S2A). Then, 74,696 unigenes were divided into 25 KOG categories based on the biological functions of their orthologous proteins. ...
Context 2
... total of 36,789 unigenes annotated in the KEGG database was mapped into the following five categories: "metabolism" (9878 unigenes), "genetic information processing" (9516 unigenes), "cellular processes" (2086 unigenes), "environmental information processing" (550 unigenes), and "organismal systems" (412 unigenes). Among the subcategories, "carbohydrate metabolism" (ko01200, 2190 unigenes) and "ribosome" (ko03010, 1896 unigenes) were predominant ( Figure S2B). Furthermore, 9878 unigenes from 96 metabolism pathways were further counted, and a total of 856 unigenes was involved in secondary metabolic pathways such as phenylpropanoid biosynthesis, terpenoid biosynthesis, flavonoid biosynthesis, tropane, piperidine, and pyridine alkaloid biosynthesis. ...
Context 3
... total of 261 DEGs was commonly present between paired comparisons (Ro_R vs. Ro_L, Ro_R vs. Ro_S, and Ro_S vs. Ro_L) (Figure 2A). Moreover, the pairwise comparisons of Ro_R vs. Ro_L, Ro_R vs. Ro_S, and Ro_S vs. Ro_L (control vs. treated) resulted in a total of 3641 DEGs (54.44% up-regulated and 45.56% down-regulated), 3308 DEGs (55.44% upregulated and 44.46% down-regulated), and 2380 DEGs (43.03% up-regulated and 56.97% down-regulated), respectively ( Figure 2B). ...
Context 4
... total of 261 DEGs was commonly present between paired comparisons (Ro_R vs. Ro_L, Ro_R vs. Ro_S, and Ro_S vs. Ro_L) (Figure 2A). Moreover, the pairwise comparisons of Ro_R vs. Ro_L, Ro_R vs. Ro_S, and Ro_S vs. Ro_L (control vs. treated) resulted in a total of 3641 DEGs (54.44% up-regulated and 45.56% down-regulated), 3308 DEGs (55.44% upregulated and 44.46% down-regulated), and 2380 DEGs (43.03% up-regulated and 56.97% down-regulated), respectively ( Figure 2B). All 5884 DEGs obtained from each comparison group of three different tissues were screened for hierarchical clustering analysis, and the heatmap of the DEGs showed that the gene expression profiles of roots, stems, and leaves of R. officinale were similar ( Figure 2C). ...
Context 5
... the pairwise comparisons of Ro_R vs. Ro_L, Ro_R vs. Ro_S, and Ro_S vs. Ro_L (control vs. treated) resulted in a total of 3641 DEGs (54.44% up-regulated and 45.56% down-regulated), 3308 DEGs (55.44% upregulated and 44.46% down-regulated), and 2380 DEGs (43.03% up-regulated and 56.97% down-regulated), respectively ( Figure 2B). All 5884 DEGs obtained from each comparison group of three different tissues were screened for hierarchical clustering analysis, and the heatmap of the DEGs showed that the gene expression profiles of roots, stems, and leaves of R. officinale were similar ( Figure 2C). ...
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Zingiber roseum is a perennial herb in the Zingiberaceae family. The plant is native to Bangladesh, and rhizomes are frequently used in traditional medicine to cure gastric ulcers, asthma, wounds, and rheumatic disorders. Therefore, the present study aimed to analyse the antipyretic, anti-inflammatory, and analgesic properties of Z. roseum rhizome...
Citations
... This study highlights the de novo assembly of the S. rosmarinus leaf and stem transcriptome. The application of this sequencing technique is in studying function annotation of genes, identification of genes involved in the synthesis of secondary metabolites, investigations of the secondary metabolites' differential expression in several tissues, gene expression, and their regulation, different environmental factors, and gene expression networks [73,74]. Our result shows the relevance with transcriptome sequencing of Justicia adhatoda L. leaves [75]. ...
... A few prior investigations identified the molecular mechanism behind the tissue-specific distribution of secondary metabolites by screening differentially expressed genes (DEGs) from a specific secondary metabolite biosynthesis pathway in various tissues and their functional annotation [74,76]. After the coding regions prediction of assembled unigenes, only 38,288 unigenes were found as coding unigenes, which were further processed for functional annotation with public databases, and a total of 28,757 (75.1%) unigenes could be successfully annotated in the public database. ...
... Molecular markers are conserved short sequences of the genome, unaffected by the environment so, used to establish genetic relationships between the species [96,97] and for genetic conservation in plants [80]. SSR markers are made up of 1-6 nucleotide tandem repeat sequences that are highly polymorphic, found in coding and non-coding regions, have broad genomic coverage, are reproducible, and are inexpensive [74,94]. SSRs are frequently employed in plant genetic engineering, conservation of germplasm, and development because they originate from expressed gene areas [95,98]. ...
Background
The Salvia rosmarinus spenn. (rosemary) is considered an economically important ornamental and medicinal plant and is widely utilized in culinary and for treating several diseases. However, the procedure behind synthesizing secondary metabolites-based bioactive compounds at the molecular level in S. rosmarinus is not explored completely.
Methods and results
We performed transcriptomic sequencing of the pooled sample from leaf and stem tissues on the Illumina HiSeqTM X10 platform. The transcriptomics analysis led to the generation of 29,523,608 raw reads, followed by data pre-processing which generated 23,208,592 clean reads, and de novo assembly of S. rosmarinus obtained 166,849 unigenes. Among them, nearly 75.1% of unigenes i.e., 28,757 were interpreted against a non-redundant protein database. The gene ontology-based annotation classified them into 3 main categories and 55 sub-categories, and clusters of orthologous genes annotation categorized them into 23 functional categories. The Kyoto Encyclopedia of Genes and Genomes database-based pathway analysis confirmed the involvement of 13,402 unigenes in 183 biochemical pathways, among these unigenes, 1,186 are involved in the 17 secondary metabolite production pathways. Several key enzymes involved in producing aromatic amino acids and phenylpropanoids were identified from the transcriptome database. Among the identified 48 families of transcription factors from coding unigenes, bHLH, MYB, WRKYs, NAC, C2H2, C3H, and ERF are involved in flavonoids and other secondary metabolites biosynthesis.
Conclusion
The phylogenetic analysis revealed the evolutionary relationship between the phenylpropanoid pathway genes of rosemary with other members of Lamiaceae. Our work reveals a new molecular mechanism behind the biosynthesis of phenylpropanoids and their regulation in rosemary plants.
... RNA sequencing studies in RPC are shedding light on the intricacies of anthraquinone biosynthesis in rhubarb. Our previous studies had pinpointed candidate unigenes engaged in the MVA, MEP, shikimate and polyketide pathways in RPC [37,38], providing valuable insights into the molecular basis of the organ-specific gene expression in rhubarb. However, the genetic mechanism of the anthraquinone biosynthetic pathway in RPC is still largely unknown. ...
Background
Rhubarb is one of common traditional Chinese medicine with a diverse array of therapeutic efficacies. Despite its widespread use, molecular research into rhubarb remains limited, constraining our comprehension of the geoherbalism.
Results
We assembled the genome of Rheum palmatum L., one of the source plants of rhubarb, to elucidate its genome evolution and unpack the biosynthetic pathways of its bioactive compounds using a combination of PacBio HiFi, Oxford Nanopore, Illumina, and Hi-C scaffolding approaches. Around 2.8 Gb genome was obtained after assembly with more than 99.9% sequences anchored to 11 pseudochromosomes (scaffold N50 = 259.19 Mb). Transposable elements (TE) with a continuous expansion of long terminal repeat retrotransposons (LTRs) is predominant in genome size, contributing to the genome expansion of R. palmatum. Totally 30,480 genes were predicted to be protein-coding genes with 473 significantly expanded gene families enriched in diverse pathways associated with high-altitude adaptation for this species. Two successive rounds of whole genome duplication event (WGD) shared by Fagopyrum tataricum and R. palmatum were confirmed. We also identified 54 genes involved in anthraquinone biosynthesis and other 97 genes entangled in flavonoid biosynthesis. Notably, RpALS emerged as a compelling candidate gene for the octaketide biosynthesis after the key residual screening.
Conclusion
Overall, our findings offer not only an enhanced understanding of this remarkable medicinal plant but also pave the way for future innovations in its genetic breeding, molecular design, and functional genomic studies.
... The study on the biosynthesis and transcriptional regulation mechanism of anthraquinones will help to artificially manipulate its secondary metabolic pathway and reconstruct the biosynthetic pathway with bioengineering to enhance the yield of anthraquinones. Previously, we identified the candidate enzyme genes involved in the MVA, MEP, shikimate and polyketide pathways for R. tanguticum and R. officinale, which provide insights for the inference of the accumulation differences of anthraquinones in different tissues for Rheum species [36,49]. In the present study, anthraquinone-related enzyme genes were also identified, and these genes will provide more candidates for the genetic manipulation of anthraquinone biosynthesis in R. palmatum complex. ...
Geoherb usually represents high-quality medicinal herbs with better clinical therapeutic effects, and elucidating the geoherbalism is essential for the quality improvement of traditional Chinese Medicine. However, few researches were conducted to clarify the geoherbalism based on a large scale of transcriptomics. In the present study, we compared the transcriptomes of Rheum palmatum complex derived from top-geoherb and non-geoherb areas to show the geoherbalism properties of rhubarb. A total of 412.32 Gb clean reads were obtained with unigene numbers of 100,615 after assembly. Based on the obtained transcriptome datasets, key enzyme-encoding genes involved in the anthraquinones biosynthesis were also obtained. We also found that 21 anthraquinone-related unigenes were differentially expressed between two different groups, and some of these DEGs were correlated to the content accumulation of five free anthraquinones, indicating that the gene expression profiles may promote the geoherbalism formation of rhubarb. In addition, the selective pressure analyses indicated that most paired orthologous genes between these two groups were subject to negative selection, and only a low proportion of orthologs under positive selection were detected. Functional annotation analyses indicated that these positive-selected genes related to the functions such as gene expression, substance transport, stress response and metabolism, indicating that discrepant environment also enhanced the formation of geoherbalism. Our study not only provided insights for the genetic mechanism of geoherbalism of rhubarb, but also laid more genetic cues for the future rhubarb germplasms improvement and utilization.
... RNA sequencing is a high-throughput sequencing method thathas been an integral part of metabolome research in non-model species with relatively high rapidity. This sequencing technology is effective to study the annotation and to elucidate various transcripts responsible for the biosynthetic pathways, gene expression analysis, and distribution of secondary metabolites in different tissues [52].The Illumina sequencing of the root tissue of Sida cordifolia revealed 59,484,771 reads, which were further processed to remove the adapter and redundant sequences. The de novo assembler TRINITY was used to assemble the transcripts, and a total of 187,215 numbers of transcripts were identified. ...
Sida cordifolia is a medicinal shrub that is conventionally used in the Indian system of medicine;however, the genes contributing to its medicinal properties have been minimally explored, thus limiting its application. High-throughputsequencing and Liquid Chromatography with tandem mass spectrometry(LC-MS/MS) technologies were applied to unravel the medicinally important bioactive compounds. As a result, transcriptomic sequencing generated more than 12 GB of clean data, and 187,215 transcripts were obtained by de novoassembly. These transcripts were broadly classified into 20 classes, based on the gene ontology classification, and 6551 unigenes were annotated using Kyoto Encyclopedia of Genes and Genomes (KEGG) database with more than 142 unigenes involved in the biosynthesis of secondary metabolites. LC-MS/MS analysis of three tissues of Sida cordifolia revealed that acacetin and procyanidin are some important metabolites identified thatcontribute to its medicinal value. Several key enzymes witha crucial role in phenylpropanoid and flavonoid biosynthetic pathways were identified, especially phenylalanine ammonia lyase, which might be an important rate-limiting enzyme. Real-Time Quantitative Reverse Transcription Polymerase chain reaction (qRT-PCR) analysis revealed enzymes, such as Phenylalanine ammonia lyase (PAL), Cinnamyl alcohol dehydrogenase 1 (CAD), Cinnamoyl-CoA reductase 1 (CF1) and Trans cinnamate 4-monooxygenase(TCM), which were predominantly expressed in root compared to leaf and stem tissue. The study provides a speculative insight for the screening of active metabolites and metabolic engineering in Sida cordifolia.
Background
Rheum palmatum L. has important medicinal value because it contains biologically active anthraquinones. However, the key genes and TFs involved in anthraquinone biosynthesis and regulation in R. palmatum remain unclear.
Methods
Based on full length transcriptome data, in this study, we screened the differentially expressed genes in the anthraquinone biosynthesis pathway. The R2R3-MYB family genes of R. palmatum were systematically identified based on full-length transcriptome sequencing followed by bioinformatics analyses. The correlation analysis was carried out by using co-expression analysis, protein interaction analysis, and real-time fluorescence quantitative analysis after MeJA treatment. The RpMYB81 and RpMYB98 genes were amplified by RT-PCR, and their subcellular localization and self-activation characteristics were analyzed.
Results
Comparative transcriptome analysis results revealed a total of 3525 upregulated and 6043 downregulated DEGs in the CK versus MeJA group; 28 DEGs were involved in the anthraquinone pathway. Eleven CHS genes that belonged to the PKS family were differentially expressed and involved in anthraquinone biosynthesis. Twelve differentially expressed MYBs genes were found to be co-expressed and interact with CHS genes. Furthermore, 52 MYB genes were identified as positive regulators of anthraquinone biosynthesis and were further characterized . Three MYB genes including RpMYB81 , RpMYB98 , and RpMYB100 responded to MeJA treatment in R. palmatum , and the levels of these genes were verified by qRT-PCR . RpMYB81 was related to anthraquinone biosynthesis. RpMYB98 had an interaction with genes in the anthraquinone biosynthesis pathway. RpMYB81 and RpMYB98 were mainly localized in the nucleus. RpMYB81 had self-activation activity, while RpMYB98 had no self-activation activity.
Conclusion
RpMYB8 1, RpMYB98 , and RpMYB100 were significantly induced by MeJA treatment. RpMYB81 and RpMYB98 are located in the nucleus, and RpMYB81 has transcriptional activity, suggesting that it might be involved in the transcriptional regulation of anthraquinone biosynthesis in R. palmatum .
The molecular mechanisms of Rhizoma Chuanxiong (Chuanxiong, CX) and Rhei Radix et Rhizoma (Dahuang, DH) in treating acute kidney injury (AKI) and subsequent renal fibrosis (RF) were investigated in this study by applying network pharmacology and experimental validation. The results showed that aloe-emodin, (-)-catechin, beta-sitosterol, and folic acid were the core active ingredients, and TP53, AKT1, CSF1R, and TGFBR1 were the core target genes. Enrichment analyses showed that the key signaling pathways were the MAPK and IL-17 signaling pathways. In vivo experiments confirmed that Chuanxiong and Dahuang pretreatments significantly inhibited the levels of SCr, BUN, UNAG, and UGGT in contrast media-induced acute kidney injury (CIAKI) rats (p < 0.001). The results of Western blotting showed that compared with the control group, the protein levels of p-p38/p38 MAPK, p53, and Bax in the contrast media-induced acute kidney injury group were significantly increased, and the levels of Bcl-2 were significantly reduced (p < 0.001). Chuanxiong and Dahuang interventions significantly reversed the expression levels of these proteins (p < 0.01). The localization and quantification of p-p53 expression in immunohistochemistry technology also support the aforementioned results. In conclusion, our data also suggest that Chuanxiong and Dahuang may inhibit tubular epithelial cell apoptosis and improve acute kidney injury and renal fibrosis by inhibiting p38 MAPK/p53 signaling.
Gall oak (Quercus infectoria) is a native tree of Iran, whose gall extract is used to treat many diseases. The presence of abundant secondary metabolites with various bioactivities in this plant has made it medically important. Despite its medicinal value, due to the lack of genomic information, the biosynthetic pathways of these compounds in this species are still unknown. The current research was aimed at observing, characterizing, and investigating the biosynthetic pathways of these compounds in Q.infectoria. De novo transcriptome assembly was conducted using the RNA sequencing technique. A total of 89,335 unigenes were generated, of which 6928 unigenes showed differential expression in leaves compared to root tissue. Gene ontology examination of DEGs revealed GO-term enrichment was related to cellular processes and enzyme activity. KEGG enrichment analysis for DEGs showed that most unigenes were related to metabolic pathways and biosynthesis of secondary metabolites. Moreover, 39 families of transcription factors were identified, of which the C2H2, bZIP, bHLH, and ERF TFs had the highest frequency. In the absence of a reference genome, the overall study of transcriptome will provide a reference for future functional and comparative studies. Moreover, the data obtained from sequencing and de novo assembly can be a valuable scientific resource for Q.infectoria.
