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Fig. 3 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 3. Most enriched metabolic pathways of the DEGs during the first 18 hpi with C. gloeosporioides. Only significant pathways with a Q-value below 1 are shown. Terpene metabolism clusters are highlighted.

Fig. 1 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 1. Determination of terpenoids in leaves challenged with C. gloeosporioides. (A) Total contents of monoterpenes and sesquiterpenes, (B–C) The contents of individual monoterpene and sesquiterpene identified. Data are average of two independent experiments.

Fig. 4 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 4. Schematic illustration of general terpenoid biosynthesis pathways showing identified unigenes from F. nilgerrensis leaf transcriptome data. The interconvertible precursors IPP and DMAPP, two phosphorylated C5 unites, are produced by the MVA and MEP pathways which are exchangeable from both compartmentations. The chloroplast is a major site for synthesis of hemiterpene (C5), monoterpenoids (C10), diterpenoids (C20) carotenoids (C40) and chlorophyll, while the cytosol and other organelle are responsible for synthesis of monoterpenoids (C10), sesquiterpene (C15) and triterpene (C30). But that is not strictly conclusive. Arrow with lines indicate reactions catalyzed by enzymes and the encoding genes, with unigenes identified in this experiment boxed. The color highlights are for better visualization. Abbreviations: AACT, acetoacetyl-CoA thiolase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DXR, 1-deoxy-D-xylulose 5-phosphate reductase; DXS, 1-deoxy-D-xylulose 5-phosphate synthase; HDR, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3- methyl-but-2-enyl diphosphate synthase; HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase; HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase; IDI, isopentenyl diphosphate isomerase; MCT, MEP cytidyltransferase; MDC, mevalonate-5-diphosphate decarboxylase; MDS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; MVK, mevalonate kinase. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 2. Global differentially-expressed-genes (DEG) in leaves of F. nilgerrensis after challenged by C. gloeosporioides. (A) DEG heatmap depicts clustering of the early upregulated genes (up to 18-h post challenge) and the late respondents (>24 h) in the upper and lower parts, respectively, with top GO terms indicated. (B) Major GO term enrichment in an early responsive gene cluster 7 showing that terpenoid biosynthesis genes are co-expressed with antipathogen immune-responsive pathway genes. Each time-point contains 2 biological replications and the expression data was zero-normalized before hierarchical clustering is performed (Pearson uncentered metric, average linkage ordering) using Cluster 3.0 version 1.58. Heatmap was examined and generated using Java Tree- View version 1.1.6r4. Gene Ontology (GO) enrichment analysis of the DEGs is implemented by the topGO R package-based Kolmogorov–Smirnov test.

Fig. 5 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 5. Heat maps depicting the transcript levels of terpenoid biosynthesis genes from F. nilgerrensis leaf transcriptome in response to C. gloeosporioides. (A) Fifty-six MVA and MEP pathway-associated genes. Annotation of the unigenes by homologous are listed in Table S4. (B) Fifty-nine terpene synthase-like or related genes. Annotation of the unigenes by homologous are listed in Table S5. Average FPKM (n = 2) were log2 transformed. The heatmap was generated by Prism GraphPad version 7.04.

opennotspecifiedSep 2020View details →

Fig. 3 in Transcriptional response of giant reed (Arundo donax L.) low ecotype to long-term salt stress by unigene-based RNAseq

Fig. 3. Distribution of transcription factors responsive to salt stress. Data are sorted by number of G34-S3 vs G34-CK DEGs.

opennotspecifiedSep 2020View details →

Fig. 2 in Transcriptional response of giant reed (Arundo donax L.) low ecotype to long-term salt stress by unigene-based RNAseq

Fig. 2. GO enrichment analysis for the DEGs in A. donax (G34-S3 vs G34-CK) The X-axis indicates the numbers related to the total number of GO terms, and the Y-axis indicates the subcategories. BP, biological processes; CC, cellular components; MF, molecular functions.

opennotspecifiedSep 2020View details →

Fig. 1 in Transcriptional response of giant reed (Arundo donax L.) low ecotype to long-term salt stress by unigene-based RNAseq

Fig. 1. Volcano plot showing the DEGs of G34-S3 vs G34-CK comparison. The up-regulated genes with statistically significance are represented by blue dots, the green dots represent the down-regulated genes and the red dots are DEGs with -log10padj <1.3, adopting log2FoldChange threshold of 0.58 (1.5 fold change). The X-axis is the gene expression change, and the Y-axis is the pvalue adjusted after normalization. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7 in SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots

Fig. 7. (A) Identification of positive transgenic hairy roots lines by PCR (A, 35S + SmbHLH3; B, hpt II; C, rol b; D, rol c). Numbers above represent individual transgenic lines and M represent DL2000 DNA marker. (B) The phenotypes of hairy roots. Hairy roots were cultured in 6,7-V liquid medium for 30 days before being photographed. (C) Relative quantitative analysis of SmbHLH3 expression in transgenic lines and control of S. miltiorrhiza hairy roots. Bars are means ± SD from three independent biological replicates. One-way ANOVA (followed by a Turkey comparison) was tested for significant differences among the means (indicated by different letters at P <0.01).

Fig. 5 in SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots

Fig. 5. Subcellular localization of SmbHLH3 protein in onion epidermal cells. Fluorescence was observed using a confocal laser scanning microscope at 24 h after incubation. The pictures showed bright field (TD), green fluorescent field (GFP), DAPI and overlay of three fields (Merge). The numerical reading of red ruler is 100 μm. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots

Fig. 2. Relative expression levels of phenolic acids biosynthetic pathway genes in transgenic hairy roots lines and the control. The results were analyzed using the comparative Ct method. The S. miltiorrhiza Actin gene was used as an internal control to normalize expression levels. The vertical bars show the SD values (n = 3). One-way ANOVA (followed by a Turkey comparison) was tested for significant differences among the means (indicated by different letters at P <0.01).

Fig. 3 in SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots

Fig. 3. Relative expression levels of tanshinone biosynthesis pathway genes in transgenic hairy roots lines and the control. The vertical bars show the SD values (n = 3). One-way ANOVA (followed by a Turkey comparison) was tested for significant differences among the means (indicated by different letters at P <0.01).

Fig. 4 in SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots

Fig. 4. Sequence analysis of SmbHLH3. (A) Deduced amino acid sequence of SmbHLH3. Predicted HLH domain was present in shaded area. (B) Phylogenetic analysis of SmbHLH3. A phylogenetic tree was constructed based on the amino acid sequences of SmbHLH3 and SibHLH3 (XP_011080018), EgbHLH3-like (XP_012836308.1), OebHLH3 (XP_022854140), StbHLH (XP_006352746), NsbHLH3 (XP_009803066), CbbHLH3 (PHT46573), AcbHLH3 (PSS14567), CabHLH3 (PHT80432), LnbHLH3- like (XP_019165044), OebHLH3-like (XP_022872401), CcbHLH3 (PHU16394), PabHLH3 (XP_021814813), AtbHLH3 (AT4G16430), AtbHLH13 (AAM10932), AtbHLH17 (AT2G46510) and all of the SmbHLHs that previously reported. These phylogenetic trees were constructed via MEGA6, using the neighbor-joining method with 500 bootstrap replicates.

Fig. 1 in SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots

Fig. 1. The chemical structures of three water-soluble phenolic acids (CA, caffeic acid; RA, rosemarinic acid; SAB, salvianolic acid B) (A) and four lipid-soluble tanshinone (T-I, tanshinone I; T-IIA, tanshinone IIA; CT, cryptotanshinone; DT-I, dihydrotanshinone I) (B) studied in this article.

Fig. 6 in SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots

Fig. 6. Expression pattern of SmbHLH3 in different tissues of S. miltiorrhiza. Bars are means ± SD from three independent biological replicates. One-way ANOVA (followed by a Turkey comparison) was tested for significant differences among the means (indicated by different letters at P <0.01).

Fig. 8 in SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots

Fig. 8. Contents of CA, RA, SAB (A) and T-I, T-IIA, CT, DT-I (B) in transgenic and the control hairy roots lines of S. miltiorrhiza. The vertical bars show the SD values (n = 3). One-way ANOVA (followed by a Turkey comparison) was tested for significant differences among the means (indicated by different letters at P <0.05).

opencc-by-4.0Jul 2023View details →

Transcriptional repression by a secondary DNA binding surface of DNA topoisomerase I safeguards against transcription overdrive

Molecular dynamics simulation input files and processed output trajectories.

opencc-by-4.0Sep 2023View details →

Response of exogenous melatonin on transcription and metabolism of soybean under drought stress

Response of exogenous melatonin on transcription and metabolism of soybean under drought stress

opengpl-3.0-or-laterOct 2023View details →

Single nuclei and spatial transcriptional in papillary and anaplastic thyroid cancers IRIBHM dataset

This dataset includes the R Seurat objects for single nuclei RNA-seq and spatial transcriptomics data associated with the publication "Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers".