Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Measurement of Chlorophyll Content
2.3. Analysis of Plastid Ultrastructure by Transmission Electron Microscopy
2.4. RNA Extraction and Sequencing
2.5. Differential Expression Analysis
2.6. TF Identification
2.7. Weighted Gene Co-Expression Network Analysis
2.8. Quantitative Real-Time-PCR Analysis
3. Results
3.1. Chlorophyll Content of Green and White Ray Florets of Chrysanthemum
3.2. Morphology and Structure of Chloroplasts of Green and White Ray Florets
3.3. RNA-Seq Analysis of Green and White Pools
3.4. Gene Annotation and Functional Classification
3.5. DEG Analysis
3.6. Expression of Genes Involved in Chlorophyll Metabolism and Related Pathways
3.7. WGCNA of DEGs
3.8. Functional Enrichment Analysis of Key Modules
3.9. Identification of Hub TFs in the Black Module
3.10. qRT-PCR Validation of Hub Genes
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Samples | Library | Raw Reads | Clean Reads | Clean Bases | Error (%) | Q20 (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|---|---|---|
GS1_1 | FRAS192310180-1r | 69,909,924 | 67,974,534 | 10.2G | 0.02 | 98.22 | 94.50 | 41.89 |
GS1_2 | FRAS192310181-1r | 67,154,326 | 65,518,128 | 9.83G | 0.02 | 98.28 | 94.64 | 42.19 |
GS1_3 | FRAS192310182-1r | 79,385,102 | 77,582,694 | 11.64G | 0.02 | 98.16 | 94.41 | 42.38 |
WS1_1 | FRAS192310183-1r | 78,199,758 | 76,158,198 | 11.42G | 0.02 | 98.26 | 94.69 | 42.45 |
WS1_2 | FRAS192310184-1r | 68,968,074 | 67,390,906 | 10.11G | 0.02 | 98.25 | 94.55 | 42.33 |
WS1_3 | FRAS192310185-1r | 71,120,720 | 69,206,430 | 10.38G | 0.02 | 98.10 | 94.24 | 42.40 |
GS2_1 | FRAS192310186-1r | 74,730,896 | 72,493,234 | 10.87G | 0.02 | 98.19 | 94.48 | 42.38 |
GS2_2 | FRAS192310187-1r | 72,994,076 | 70,710,496 | 10.61G | 0.02 | 98.25 | 94.63 | 42.26 |
GS2_3 | FRAS192310188-1r | 73,085,728 | 71,432,126 | 10.71G | 0.02 | 98.11 | 94.23 | 42.16 |
WS2_1 | FRAS192310189-1r | 68,345,294 | 66,024,344 | 9.9G | 0.02 | 98.16 | 94.45 | 41.92 |
WS2_2 | FRAS192310190-1r | 81,521,172 | 79,358,278 | 11.9G | 0.02 | 98.19 | 94.56 | 41.69 |
WS2_3 | FRAS192310191-1r | 69,440,584 | 67,776,290 | 10.17G | 0.02 | 98.08 | 94.24 | 41.79 |
GS3_1 | FRAS192042324-1r | 76,123,912 | 74,489,046 | 11.17G | 0.03 | 97.90 | 93.72 | 41.99 |
GS3_2 | FRAS192042325-1r | 76,239,258 | 74,539,470 | 11.18G | 0.03 | 98.00 | 93.99 | 42.07 |
GS3_3 | FRAS192042326-1r | 75,168,204 | 73,433,218 | 11.01G | 0.03 | 97.92 | 93.74 | 42.05 |
WS3_1 | FRAS192042327-1r | 78,303,734 | 76,184,148 | 11.43G | 0.03 | 97.84 | 93.61 | 41.70 |
WS3_2 | FRAS192042328-1r | 78,068,928 | 76,158,448 | 11.42G | 0.03 | 97.92 | 93.77 | 41.68 |
WS3_3 | FRAS192042329-1r | 79,621,212 | 77,866,790 | 11.68G | 0.03 | 97.82 | 93.55 | 41.99 |
KEGG Pathway | No. in All Unigenes | No. in DEGs |
---|---|---|
Photosynthesis | 151 | 20 |
Photosynthesis—antenna proteins | 65 | 15 |
Chlorophyll metabolism | 113 | 24 |
Carbon fixation in photosynthetic organisms | 230 | 16 |
Glyoxylate and dicarboxylate metabolism | 204 | 12 |
Module | Number of DEGs Related to Key Processes in Chrysanthemum | |||||
---|---|---|---|---|---|---|
Total DEGs | Photosynthesis—Antenna Proteins | Photosynthesis | Carbon Fixation in Photosynthetic Organisms | Glyoxylate and Dicarboxylate Metabolism | Chlorophyll Metabolism | |
Red | 116 | 5 | 0 | 0 | 0 | 0 |
Black | 97 | 6 | 20 | 10 | 7 | 5 |
Other | 1621 | 0 | 0 | 0 | 0 | 0 |
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Fu, H.; Zeng, T.; Zhao, Y.; Luo, T.; Deng, H.; Meng, C.; Luo, J.; Wang, C. Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses. Genes 2021, 12, 449. https://doi.org/10.3390/genes12030449
Fu H, Zeng T, Zhao Y, Luo T, Deng H, Meng C, Luo J, Wang C. Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses. Genes. 2021; 12(3):449. https://doi.org/10.3390/genes12030449
Chicago/Turabian StyleFu, Hansen, Tuo Zeng, Yangyang Zhao, Tingting Luo, Huijie Deng, Chenwei Meng, Jing Luo, and Caiyun Wang. 2021. "Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses" Genes 12, no. 3: 449. https://doi.org/10.3390/genes12030449