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Fig. 2 in Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves

Fig. 2. Genes involved in Paris saponin biosynthesis. (a) Genes participated in the MVA and MEP pathways. (b) Genes participated in the downstream of saponin backbone biosynthesis.

Fig. 4 in Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves

Fig. 4. An overview of DEG expression patterns and GO enrichments. (a) Heatmap of expression values for all DEGs. (b) GO enrichments of DEGs, with displaying the top fifteen subcategories for each category.

Fig. 7 in Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves

Fig. 7. QRT-PCR validation of RNA-Seq data. Expression profiles of eight selected genes were determined by transcriptome and qRT-PCR data. The left vertical axis represents the relative expression of the gene based on qRT-PCR. The right vertical axis represents the expression level of the gene based on transcriptome sequencing. The asterisk above the bar chart denotes statistical significance based on the qRT-PCR data (* denotes P value <0.05, ** denotes P value <0.01, ns denotes P value> 0.05).

Fig. 1 in Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves

Fig. 1. The bioactive compound content and transcriptome characters. (a) Total content of three typical types of Paris saponins in leaves and rhizomes during the vegetative and fruiting stages. VL: leaves at vegetative stage, VR: rhizomes at vegetative stage, FL: leaves at fruiting stage, and FR: rhizomes at fruiting stage. (b) Proportion of three types of Paris saponins in leaves and rhizomes. (c) Distribution of the expressed unigenes in tissues during the two stages (log2 (TPMþ1)> 0). (d) Boxplot of unigene expression profiles.

Fig. 3 in Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves

Fig. 3. DEG statistics. (a) Venn diagram of DEGs from the four paired comparisons. (b) The number of up-down regulated DEGs of the four paired comparisons.

Fig. 3 in Transcriptome and metabolome profiling unveiled mechanisms of tea (Camellia sinensis) quality improvement by moderate drought on pre-harvest shoots

Fig. 3. Transcriptome analysis of DEGs. (A) Venn diagram of DEGs. (B–D) Biological processes of corresponding DEGs related to differentially accumulated metabolites in groups of CK vs. MI, CK vs. MO, and CK vs. SE.

Fig. 1 in Transcriptome and metabolome profiling unveiled mechanisms of tea (Camellia sinensis) quality improvement by moderate drought on pre-harvest shoots

Fig. 1. Metabolomic analysis of differentially accumulated metabolites. (A) Venn diagram of differentially accumulated metabolites. (B) The top five most abundant categories. A, amino acids and derivatives; F, flavonoids; N, nucleotide and derivatives; L, lipids; O, organic acids. Blue dot, categories with less metabolites. (C) Accumulation tendencies of the five categories under diferent SWCs.. CK, control (21–24% SWC); MI, milder drought (15–18% SWC); MO, moderate drought (12–15% SWC); SE, severe drought (9–12% SWC). (D) KEGG enrichment of group CK vs. MI from metabolic data. (E) KEGG enrichment of group CK vs. MO from metabolic data. (F) KEGG enrichment of group CK vs. SE from metabolic data. Plot: mean with standard deviation (SD). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Transcriptome and metabolome profiling unveiled mechanisms of tea (Camellia sinensis) quality improvement by moderate drought on pre-harvest shoots

Fig. 6. Regulation of lipid metabolisms under different SWCs. (A) Phospholipid metabolism, glycerolipid metabolism, and fatty acid biosynthesis, and the expression tendencies of corresponding differentially accumulated lipids. (B) Connection network of 16 DEGs and 30 differentially accumulated lipids according to PCC> 0.9. Blue dots indicate DEGs, and pink dots denote closely correlated lipids. Colors from green to red in heatmaps represent the relative expression patterns of DEGs; colors from blue to pink represent the accumulated pattern of related metabolites. The compounds index in A and B are referred to in Supplementary Table S6-1. CK, control; MI, mild drought; MO, moderate drought; SE, severe drought. ADH3, alcohol dehydrogenase 3; AFP1-like, ninja-family protein AFP1-like; ALA2_like, phospholipid-transporting ATPase 2; AOS, allene oxide synthase; CIPK5-like, CBL-interacting protein kinase 5-like; DAD1, phospholipase A(1) DAD1; DGK7-like, diacylglycerol kinase 7-like; GDSL-1, GDSL esterase/lipase At5g33370-like; GDSL-2, GDSL esterase/lipase At4g26790-like; GDSL-3, GDSL esterase/lipase 1-like; GDSL-4, GDSL esterase/lipase At1g33811; KCS-12/19-like, 3-ketoacyl-CoA synthase 12/19-like; LTP1-like, non-specific lipid-transfer protein 1-like; MGLL, caffeoylshikimate esterase-like, the isozyme gene of monoglyceride lipase; MTACP, acyl carrier protein; PL A1-Ibeta2, phospholipase A1-Ibeta2; PLD1-like, phospholipase D alpha 1-like. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Transcriptome and metabolome profiling unveiled mechanisms of tea (Camellia sinensis) quality improvement by moderate drought on pre-harvest shoots

Fig. 5. Underlying regulation of flavonoid biosynthesis under different SWCs. (A) Expressions of differentially accumulated flavonoids. (B) Underlying regulation mechanism of flavonoid biosynthesis pathway. (C) Connection network of 11 DEGs and 32 differentially accumulated flavonoids according to PCC> 0.9. Blue dots indicate DEGs, and pink dots denote flavonoids. In B and C, the colors from green to red in the heatmap show the relative expression pattern of DEGs, and the colors from blue to pink represent the relative accumulated pattern of closely related metabolites. The compounds index in A and C are referred to in Supplementary Tables S5-1. CK, control; MI, mild drought; MO, moderate drought; SE, severe drought. ANR, anthocyanidin reductase; ANS, anthocyanidin synthase; AS-like, hydroquinone glucosyltransferase-like; C, catechin; DFR, dihydroflavonol 4-reductase; EC, epicatechin; ECG, epicatechin gallate; EGCG, epigallocatechin gallate; FLS, flavonol synthase/flavanone 3-hydroxylase; GC, gallocatechin; LAR, leucoanthocyanidin reductase; PKSB, type III polyketide synthase B; UFGT, anthocyanidin 3-Oglucosyltransferase; UGT83A1, UDP-glycosyltransferase 83A1; UGT94P1, beta-D-glucosyl crocetin beta-1,6-glucosyltransferase-like. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in Transcriptome and metabolome profiling unveiled mechanisms of tea (Camellia sinensis) quality improvement by moderate drought on pre-harvest shoots

Fig. 4. Levels of quality-associated compounds for different SWCs. (A) Total differentially accumulated flavonoids, isoflavonoids, and C- and O- glycosylflavonoids. (B) Levels of catechins, theanine, and theobromine. (C) Levels of glycerophospholipids, glycerolipids, and fatty acids. Plot: mean with SD.

Fig. 2 in Comparative transcriptome analysis infers bulb derived in vitro cultures as a promising source for sipeimine biosynthesis in Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) - High value Himalayan medicinal herb

Fig. 2. (A–E) Differential gene expression analysis in comparative F. roylei transcriptome: (A) Heat-map showing differential gene expression in the bulb (PKW) vs callus (PK2); bulb (PKW) vs in vitro regenerated plantlets (PK1) and callus (PK2) vs in vitro regenerated plantlets (PK1); (B) Venn diagram represents the differential gene expression in PKW vs PK1; PKW vs PK2; PK2 vs PK1, (C–E) Volcano plots represents the differential gene expression in PKW vs PK1; PKW vs PK2; PK2 vs PK1 as colour description image, where p-value & log2 fold-change in red colour represents genes with log2 fold-change cut off 2 and p-value <=0.05; p-value in blue colour represents genes with no cut off on log2 fold-change and p-value <=0.05. Whereas, log2 fold-change in green colour represents genes with fold-change cut off 2 but no p-value cut off and non-significant (NS) in grey colour represents genes with no filter on log2 fold-change and p-value, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Comparative transcriptome analysis infers bulb derived in vitro cultures as a promising source for sipeimine biosynthesis in Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) - High value Himalayan medicinal herb

Fig. 1. (A–F) Functional annotations and unigenes classification of comparative F. roylei transcriptome: (A) Unigenes annotation with top 15 different plant species; (B) Top 5 pathway representation as per Kyoto Encyclopedia of Genes and Genomes; (C) Gene Ontology classification under the cellular component, molecular function, and biological process categories; (D) COG (Cluster of Orthologous Groups of proteins) classification into nine different categories; (E) Unigenes classification into major transcription factor families; (F) Gene family and sub-family classification using TAIR database.

Fig. 4 in Comparative transcriptome analysis infers bulb derived in vitro cultures as a promising source for sipeimine biosynthesis in Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) - High value Himalayan medicinal herb

Fig. 4. Comparative expression pattern validation for the sipeimine biosynthetic pathway genes as obtained from RNA-Seq data and qRT-PCR.

Fig. 3 in Comparative transcriptome analysis infers bulb derived in vitro cultures as a promising source for sipeimine biosynthesis in Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) - High value Himalayan medicinal herb

Fig. 3. Proposed sipeimine biosynthetic pathways in F. roylei. Heat-map showing gene expression in the bulb, callus, and regenerated plantlets. The genes were mapped using TPM (transcripts per kilobase million) values and colour-coded by increasing relative expression. The broken dotted arrow represents putative terminal biosynthesis steps. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Comparative transcriptome analysis reveals the regulatory effects of acetylcholine on salt tolerance of Nicotiana benthamiana

Fig. 6. Differentially expressed genes related to the plant hormone signal transduction pathway in the comparison (NaCl vs NaCl + ACh). (A) diagram of auxin, gibberellin, brassinosteroid and salicylic acid signalling transduction pathways; (B) information and expression patterns of differentially expressed genes involved in auxin, gibberellin, brassinosteroid and salicylic acid signalling transduction pathways. Red means upregulated expression of genes, and green means downregulated expression of genes. The number in each sample name represents the sample order. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Comparative transcriptome analysis reveals the regulatory effects of acetylcholine on salt tolerance of Nicotiana benthamiana

Fig. 3. Functional annotation of differentially expressed genes (DEGs) based on gene ontology categorization. The left Y-axis represents the significantly enriched GO terms (p <0.05) pathways. The Xaxis represents the percentage of DEGs belonging to the corresponding pathway. The sizes of bubbles represent the number of DEGs in the corresponding pathway, and the colours of the bubbles represent the enrichment p-value of the corresponding pathway. The left y-axis shows the Gene Ontology terms. Biological process, cellular component and molecular function are indicated by different colours. Only significantly enriched GO terms (p <0.05) are shown. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 8 in Comparative transcriptome analysis reveals the regulatory effects of acetylcholine on salt tolerance of Nicotiana benthamiana

Fig. 8. Quantitative real-time PCR (RT-qPCR) validation of selected differentially expressed genes detected in Nicotiana benthamiana leaves. The expression levels obtained by RT-qPCR are represented in black lines, RT-qPCR data showed the mean values from three replicates, and the error bars represent the SE of the means, while the corresponding expression data for RNA-seq are represented in the white histogram. CN, control; CN + ACh, 10 μM acetylcholine; NaCl, 150 mM NaCl stress; NaCl + ACh, 150 mM NaCl stress plus 10 μM acetylcholine.

Fig. 5 in Comparative transcriptome analysis reveals the regulatory effects of acetylcholine on salt tolerance of Nicotiana benthamiana

Fig. 5. Heatmap representing the differentially expressed genes (DEGs) involved in cell wall extensibility of Nicotiana benthamiana leaves as influenced by NaCl alone or in combination with acetylcholine treatment (NaCl + ACh). Red means upregulated expression of genes, and green means downregulated expression of genes. The number in each sample name represents the sample order. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Comparative transcriptome analysis reveals the regulatory effects of acetylcholine on salt tolerance of Nicotiana benthamiana

Fig. 1. Changes in reactive oxygen species accumulation and production and antioxidant enzyme activity in Nicotiana benthamiana leaves 5 days after treatment with acetylcholine (ACh) under salt stress. (a) leaves were stained with NBT and DAB, (b) Fv/Fm, (c) Superoxide content, (d) Hydrogen peroxide content, (e) Ascorbate peroxidase activity and (d) Catalase activity as influenced by salt stress alone or in combination with ACh treatment. Data are means of three replications ±SE. Means with the same lowercase letters are not significantly different at p <0.05, according to Duncan's multiple range test. CN: control; CN + ACh, 10 μM acetylcholine; NaCl, 150 mM NaCl stress; NaCl + ACh, 150 mM NaCl stress plus 10 μM acetylcholine.

Fig. 7 in Comparative transcriptome analysis reveals the regulatory effects of acetylcholine on salt tolerance of Nicotiana benthamiana

Fig. 7. Heatmap representing the differentially expressed genes involved in transcription factors extensibility of Nicotiana benthamiana leaves as influenced by NaCl alone or in combination with acetylcholine treatment (NaCl + ACh). Red means upregulated expression of genes, and green means downregulated expression of genes. The number in each sample name represents the sample order. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)