Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Plant Materials
2.2. Total RNA Extraction, Library Construction, and RNA-seq
2.3. De Novo Assembly of Reads from RNA-seq and Functional Annotation
2.4. Cluster Analysis
2.5. Differential Gene Expression Analysis
2.6. Weighted Gene Co-Expression Network Analysis (WGCNA)
2.7. Quantitative Real-Time PCR
2.8. Statistical Analysis
3. Results
3.1. Qualitative Evaluation of RNA-seq Data
3.2. Comparison of Overall Expression Patterns between the Control and the Treatment
3.3. Differentially Expressed Genes Analysis
3.4. Weighted Gene Co-Expression Network Analysis (WGCNA)
3.5. Reconstruction of Gene Co-Expression Network
3.6. qRT-PCR Assay
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ROS | Reactive oxygen species |
SOD | Superoxidase dismutase |
PCA | Principal components analysis |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
DEGs | Differentially expressed genes |
WGCNA | Weighted gene co-expression network analysis |
HCEF1 | Fructose-1,6-bisphosphatase |
BZIP9 | Basic leucine zipper 9 |
ELIP | Early light induced proteins |
XTH | Xyloglucan endotransglucosylase/hydrolase |
HSPs | Heat shock protein |
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Days Post-Anthesis (DPA) | |||||
---|---|---|---|---|---|
Control sampling time | 50 (C1) | 60 (C2) | 70 (C3) | 80 (C4) | 90 (C5) |
Treatment sampling time | 50 (T1) | 60 (T2) | 70 (T3) | 80 (T4) | 90 (T5) |
Stages | Genes ID | Genes Name | Regulated | FDR | Log2FoldChange | Annotation Function |
---|---|---|---|---|---|---|
C1 vs. T1 | VIT_08s0007g04250 | VIT_208s0007g04250 | up | 3.24 × 10−68 | Inf | Probable glycosyltransferase |
VIT_05s0020g04840 | GDSL | up | 9.92 × 10−65 | 2.769179 | GDSL esterase/lipase | |
VIT_04s0044g01160 | VIT_204s0044g01160 | up | 1.29 × 10−55 | Inf | Probable cysteine desulfurase-like | |
VIT_02s0025g04950 | VIT_202s0025g04950 | up | 2.15 × 10−44 | Inf | Hypothetical protein | |
VIT_16s0039g02140 | PRK | up | 3.39 × 10−27 | Inf | Phosphoribulokinase, chloroplastic | |
VIT_16s0013g00870 | PEI1 | up | 3.59 × 10−24 | Inf | Zinc finger CCCH domain-containing protein | |
VIT_13s0067g03890 | KCS19 | down | 0.0069 | −1.36784 | 3-ketoacyl-CoA synthase 21 | |
C2 vs. T2 | VIT_04s0008g03940 | RD22 | up | 0.000148 | 2.746652 | Dehydration-responsive protein RD22 (Precursor) |
VIT_07s0005g01790 | LACS1 | up | 1.07 × 10−9 | 2.043324 | Long chain acyl-CoA synthetase 1 | |
VIT_06s0061g00550 | XTH32 | down | 4.39 × 10−49 | −2.0868 | Probable xyloglucan endotransglucosylase/hydrolase Protein 32 (Precursor) | |
VIT_06s0004g02560 | VIT_206s0004g02560 | down | 1.52 × 10−23 | −1.45724 | Ripening-related protein grip22 (Precursor) | |
VIT_16s0022g00960 | VIT_216s0022g00960 | down | 2.53 × 10−23 | −1.49248 | 21 kDa protein (Precursor) | |
VIT_08s0007g08330 | ADPG1 PGAZAT | down | 1.05 × 10−10 | −1.87416 | Polygalacturonase (Precursor) | |
C3 vs. T3 | VIT_11s0016g04920 | VIT_211s0016g04920 | up | 1.95 × 10−215 | 4.90208 | Early nodulin-93 OS=Glycine max (Soybean) |
VIT_02s0025g00430 | GH9B15 | up | 2.58 × 10−33 | 6.101505 | Endoglucanase (Precursor) | |
VIT_05s0020g04110 | ELIP1 | up | 1.86 × 10−8 | 3.826895 | Early light-induced protein 1 | |
VIT_18s0089g01270 | ATHSP22 | down | 3.22 × 10−31 | −3.35075 | 22.7 kDa class IV heat shock protein (Precursor) | |
VIT_02s0154g00320 | VIT_202s0154g00320 | down | 3.95 × 10−27 | −3.06725 | 14 kDa proline-rich protein DC2.15 (Precursor) | |
VIT_12s0028g02830 | VIT_212s0028g02830 | down | 2.45 × 10−27 | −2.89329 | Trans-resveratrol di-O-methyltransferase | |
VIT_12s0028g01880 | VIT_212s0028g01880 | down | 5.60 × 10−25 | −2.71443 | Trans-resveratrol di-O-methyltransferase |
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Wang, Z.-G.; Guo, L.-L.; Ji, X.-R.; Yu, Y.-H.; Zhang, G.-H.; Guo, D.-L. Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin. Genes 2019, 10, 514. https://doi.org/10.3390/genes10070514
Wang Z-G, Guo L-L, Ji X-R, Yu Y-H, Zhang G-H, Guo D-L. Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin. Genes. 2019; 10(7):514. https://doi.org/10.3390/genes10070514
Chicago/Turabian StyleWang, Zhen-Guang, Li-Li Guo, Xiao-Ru Ji, Yi-He Yu, Guo-Hai Zhang, and Da-Long Guo. 2019. "Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin" Genes 10, no. 7: 514. https://doi.org/10.3390/genes10070514
APA StyleWang, Z.-G., Guo, L.-L., Ji, X.-R., Yu, Y.-H., Zhang, G.-H., & Guo, D.-L. (2019). Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin. Genes, 10(7), 514. https://doi.org/10.3390/genes10070514