Metabolite and Transcriptomic Changes Reveal the Cold Stratification Process in Sinopodophyllum hexandrum Seeds
<p>Changes in seed morphological, physiological, and biochemical features of <span class="html-italic">S</span>. <span class="html-italic">hexandrum</span> at five different stratification stages: Morphology of seed embryo (<b>A</b>,<b>B</b>). Changes in embryo rate and germination rate (<b>C</b>). Contents of soluble protein, starch, and soluble sugar (<b>D</b>–<b>F</b>). Activities of pyruvate kinase (PK), glucose-6-phosphate dehydrogenase (G-6-PDH), and succinate dehydrogenase (SDH) (<b>G</b>–<b>I</b>). Values are average with their standard deviations (<span class="html-italic">n</span> = 3) with three biological replicates. Different lowercase represents a significant difference (<span class="html-italic">p</span> < 0.05).</p> "> Figure 2
<p>The metabolite analysis of <span class="html-italic">S. hexandrum</span> seeds during different stratification stages: the heatmap visualizes the total metabolites with each metabolite’s content normalized for complete linkage hierarchical clustering, where red indicates high abundance and green indicates low abundance (<b>A</b>). Bar graph analysis of total DEMs (<b>B</b>). PCA analysis of metabolites (<b>C</b>). DEMs Venn diagram (<b>D</b>). Correlation heat map between DEMs (<b>E</b>).</p> "> Figure 3
<p>KEGG pathway analysis of DEMs in SM1_vs_SM0 (<b>A</b>). KEGG pathway analysis of DEMs in SM2_vs_SM0 (<b>B</b>). KEGG pathway analysis of DEMs in SM3_vs_SM0 (<b>C</b>). KEGG pathway analysis of DEMs in SM4_vs_SM0 (<b>D</b>). The Rich factor refers to the ratio of the number of differentially expressed genes enriched in a particular pathway to the total number of genes annotated to that pathway. A higher Rich factor indicates a greater degree of enrichment. A smaller Q-value indicates a more significant enrichment.</p> "> Figure 4
<p>Analysis of total Unigenes and annotation status of Unigenes in various databases (<b>A</b>). Distribution and probability density display of stratified sample data (<b>B</b>). Assessment of biological replication correlation among samples using r. The closer the absolute value of r is to 1 (depicted in redder shades), the stronger the correlation (<b>C</b>). Legend shows the number of annotated orthologous clusters and genes, with different clusters represented by distinct colors (<b>D</b>). The horizontal axis represents the secondary GO terms, while the vertical axis represents the number of genes annotated to each GO term (<b>E</b>). The horizontal axis represents the functional categories of KOG IDs, while the vertical axis represents the number of genes within each category. The categories are distinguished by unique colors, and the legend provides the code and its functional description (<b>F</b>).</p> "> Figure 5
<p>Volcano plot of differentially expressed genes between ST1_vs_ST0 (<b>A</b>), ST2_vs_ST0 (<b>B</b>), ST3_vs_ST0 (<b>C</b>), and ST4_vs_ST0 (<b>D</b>); red and green dots represent the significantly upregulated and downregulated genes. Heat map of differentially expressed genes based on hierarchical clustering analysis between ST1_vs_ST0 (<b>E</b>), ST2_vs_ST0 (<b>F</b>), ST3_vs_ST0 (<b>G</b>), and ST4_vs_ST0 (<b>H</b>) as follows: darker colors represent higher expression levels of differentially expressed genes, while lighter colors indicate the opposite.</p> "> Figure 6
<p>DEGs enriched on different GO terms and KEGG pathways: GO terms of DEGs in ST1_vs_ST0 (<b>A</b>). GO terms of DEGs in ST2_vs_ST0 (<b>B</b>). GO terms of DEGs in ST3_vs_ST0 (<b>C</b>). GO terms of DEGs in ST4_vs_ST0 (<b>D</b>). KEGG pathway analysis of DEGs in ST1_vs_ST0 (<b>E</b>). KEGG pathway analysis of DEGs in ST2_vs_ST0 (<b>F</b>). KEGG pathway analysis of DEGs in ST3_vs_ST0 (<b>G</b>). KEGG pathway analysis of DEGs in ST4_vs_ST0 (<b>H</b>). The Rich factor refers to the ratio of the number of differentially expressed genes enriched in a particular pathway to the total number of genes annotated to that pathway. A higher Rich factor indicates a greater degree of enrichment. A smaller Q-value indicates a more significant enrichment.</p> "> Figure 6 Cont.
<p>DEGs enriched on different GO terms and KEGG pathways: GO terms of DEGs in ST1_vs_ST0 (<b>A</b>). GO terms of DEGs in ST2_vs_ST0 (<b>B</b>). GO terms of DEGs in ST3_vs_ST0 (<b>C</b>). GO terms of DEGs in ST4_vs_ST0 (<b>D</b>). KEGG pathway analysis of DEGs in ST1_vs_ST0 (<b>E</b>). KEGG pathway analysis of DEGs in ST2_vs_ST0 (<b>F</b>). KEGG pathway analysis of DEGs in ST3_vs_ST0 (<b>G</b>). KEGG pathway analysis of DEGs in ST4_vs_ST0 (<b>H</b>). The Rich factor refers to the ratio of the number of differentially expressed genes enriched in a particular pathway to the total number of genes annotated to that pathway. A higher Rich factor indicates a greater degree of enrichment. A smaller Q-value indicates a more significant enrichment.</p> "> Figure 7
<p>The KEGG combined analysis of DEMs and DEGs: Combined analysis of DEGs and DEMs involved in S1_vs_S0 (<b>A</b>). Combined analysis of DEGs and DEMs involved in S2_vs_S0 (<b>B</b>). Combined analysis of DEGs and DEMs involved in S3_vs_S0 (<b>C</b>). Combined analysis of DEGs and DEMs involved in S4_vs_S0 (<b>D</b>). The horizontal coordinate represents the enrichment factor of the pathway in different histologies, and the vertical coordinate represents the name of the KEGG pathway; the gradient of red-yellow-green represents the change in the significance of enrichment from high-moderate-low, indicated by <span class="html-italic">p</span>-value; the shape of bubbles represents different omics, and the size of the bubbles represents the number of DEMs or DEGs—the larger the number, the bigger the point.</p> "> Figure 8
<p>Weighted gene co-expression network analysis (WGCNA) of genes during stratification stages: Clustering dendrogram of samples based on their Euclidean distance (<b>A</b>). Hierarchical cluster tree showing co-expression modules identified by WGCNA and heat map analysis of the samples with different modules (<b>B</b>). Module–metabolite association; each row corresponds to a module, and each column represents a specific hormone (<b>C</b>). The color of each cell at the row–column intersection indicates the correlation coefficient between a module and the hormones.</p> "> Figure 9
<p>The co-expression network analysis of DEMs and DEGs based on Pearson correlation: Interaction network of DEGs and DEMs involved in ST1_vs_ST0 (<b>A</b>). Interaction network of DEGs and DEMs in ST2_vs_ST0 (<b>B</b>). Interaction network of DEGs and DEMs involved in ST3_vs_ST0 (<b>C</b>). Interaction network of DEGs and DEMs in ST4_vs_ST0 (<b>D</b>). Edges colored in pink and blue represent DEMs and DEGs, respectively; solid line and dotted line represent positive and negative correlations, The length of the lines in the network diagram does not have any practical significance. As determined by a Pearson correlation coefficient > 0.80, <span class="html-italic">p</span> < 0.05.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Stratification
2.3. Observation of Seed Embryo Morphology and Rate
2.4. Determination of Seed Germination Rate
2.5. Determination of Physiological and Biochemical Substances
2.6. Metabolomics Analysis of Targeted Phytohormone
2.7. Differential Metabolites Selected
2.8. Transcriptomic Analysis
2.9. Hierarchical Cluster Analysis
2.10. Weighted Correlation Network Analysis
2.11. Statistical Analysis
3. Results and Discussion
3.1. Morphological and Phytochemical Changes during Seed Stratification
3.2. The Metabolome Analysis during Seed Stratification
3.2.1. Targeted Metabolome Analysis
3.2.2. The Functional Analysis of DEMs at Different Stratification Stages
3.3. The Transcriptome Analysis during Seed Stratification
3.3.1. Transcriptome Analysis
3.3.2. The Functional Analysis of DEGs at Different Stratification Stages
3.4. Metabolome and Transcriptome Integrated Analysis
3.4.1. The KEGG Combined Analysis of DEMs and DEGs
3.4.2. Weighted Gene Co-Expression Network Analysis
3.4.3. The Co-Expression Network Analysis of DEGs and DEMs
4. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Abbreviation | Metabolite | Class |
---|---|---|
mT9G | Meta-Topolin-9-glucoside | Cytokinin |
tZRMP | 9-Ribosyl-trans-zeatin 5′-monophosphate | Cytokinin |
2MeScZR | 2-Methylthio-cis-zeatin riboside | Cytokinin |
KR | Kinetin riboside | Cytokinin |
tZ | Trans-Zeatin | Cytokinin |
cZRMP | Cis-Zeatin riboside monophosphate | Cytokinin |
IPR | N6-isopentenyladenosine | Cytokinin |
2MeSiPR | 2-Methylthio-N6-isopentenyladenosine | Cytokinin |
BAP | 6-Benzyladenine | Cytokinin |
2MeSiP | 2-Methylthio-N6-isopentenyladenine | Cytokinin |
iP7G | N6-Isopentenyl-adenine-7-glucoside | Cytokinin |
iPRMP | N-6-iso-pentenyladenosine-5′-monophosphate | Cytokinin |
cZR | Cis-Zeatin riboside | Cytokinin |
IP | N6-isopentenyladenine | Cytokinin |
pT9G | 4-[[(9-beta-D-Glucopyranosyl-9H-purin-6-yl) amino] methyl] phenol | Cytokinin |
2MeScZ | 2-Methylthio-cis-zeatin | Cytokinin |
cZROG | Cis-Zeatin-O-glucoside riboside | Cytokinin |
cZ | cis-Zeatin | Cytokinin |
IAA-Gly | Indole-3-acetyl glycine | Auxin |
IAA-Glu | Indole-3-acetyl glutamic acid | Auxin |
IA | 3-Indoleacrylic acid | Auxin |
IAA-Leu | N-(3-Indolylacetyl)-L-leucine | Auxin |
IAA-Phe | N-(3-Indolylacetyl)-L-phenylalanine | Auxin |
IAA-Trp | Indole-3-acetyl-L-tryptophan | Auxin |
ILA | Indole-3-lactic acid | Auxin |
OxIAA | 2-oxindole-3-acetic acid | Auxin |
TRP | L-tryptophan | Auxin |
IAA | Indole-3-acetic acid | Auxin |
TRA | Tryptamine | Auxin |
MEIAA | Methyl indole-3-acetate | Auxin |
Indole | Indole | Auxin |
ICAld | Indole-3-carboxaldehyde | Auxin |
ICA | Indole-3-carboxylic acid | Auxin |
IAA-Phe-Me | Indole-3-acetyl-L-phenylalanine methyl ester | Auxin |
IAA-Asp | Indole-3-acetyl-L-aspartic acid | Auxin |
GA9 | Gibberellin A9 | Gibberellin |
GA53 | Gibberellin A53 | Gibberellin |
GA7 | Gibberellin A7 | Gibberellin |
GA3 | Gibberellin A3 | Gibberellin |
GA6 | Gibberellin A6 | Gibberellin |
GA19 | Gibberellin A19 | Gibberellin |
GA1 | Gibberellin A1 | Gibberellin |
GA5 | Gibberellin A5 | Gibberellin |
GA20 | Gibberellin A20 | Gibberellin |
OPC-6 | 3-oxo-2-(2-(Z)-Pentenyl) cyclopentane-1-hexanoic acid | Jasmonic acid |
MEJA | Methyl jasmonate | Jasmonic acid |
JA | Jasmonic acid | Jasmonic acid |
OPDA | Cis (+)-12-Oxophytodienoic acid | Jasmonic acid |
H2JA | Dihydrojasmonic acid | Jasmonic acid |
SA | Salicylic acid | Salicylic acid |
Phe | L-Phenylalanine | Salicylic acid |
t-CA | Trans-Cinnamic acid | Salicylic acid |
ABA | Abscisic acid | Abscisic acid |
MLT | Melatonine | Melatonin |
5DS | 5-Deoxystrigol | Strigolactone |
Module | Hub Genes | Module | Hub Genes |
---|---|---|---|
Black | Cluster-103188.0 | Magenta | Cluster-140764.5 |
Blue | Cluster-16348.6 | Mid night blue | Cluster-141210.0 |
Brown | Cluster-3253.1464 | Pink | Cluster-135750.4 |
Cyan | Cluster-123911.19 | Purple | Cluster-127961.0 |
Green | Cluster-132019.0 | Red | Cluster-139658.0 |
Green yellow | Cluster-85301.32 | Salmon | Cluster-57738.15 |
Grey60 | Cluster-4422.225 | Tan | Cluster-138313.7 |
Light cyan | Cluster-114960.0 | Turquoise | 1 Cluster-112157.0 |
Yellow | Cluster-112291.0 |
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Ning, R.; Li, C.; Fan, T.; Ji, T.; Xu, W. Metabolite and Transcriptomic Changes Reveal the Cold Stratification Process in Sinopodophyllum hexandrum Seeds. Plants 2024, 13, 2693. https://doi.org/10.3390/plants13192693
Ning R, Li C, Fan T, Ji T, Xu W. Metabolite and Transcriptomic Changes Reveal the Cold Stratification Process in Sinopodophyllum hexandrum Seeds. Plants. 2024; 13(19):2693. https://doi.org/10.3390/plants13192693
Chicago/Turabian StyleNing, Rongchun, Caixia Li, Tingting Fan, Tingting Ji, and Wenhua Xu. 2024. "Metabolite and Transcriptomic Changes Reveal the Cold Stratification Process in Sinopodophyllum hexandrum Seeds" Plants 13, no. 19: 2693. https://doi.org/10.3390/plants13192693