High-Throughput Transcriptomic Analysis of Circadian Rhythm of Chlorophyll Metabolism under Different Photoperiods in Tea Plants
Abstract
:1. Introduction
2. Results
2.1. Chlorophyll and Carotenoid Content in Tea Plants Under Different Photoperiods
2.2. Quality Analysis of Tea Transcriptome Sequencing at Different Time Points
2.3. Functional Annotation and Classification
2.4. GO Analysis
2.5. KEGG Classification
2.6. KOG Classification
2.7. Screening of Differentially Expressed Genes in the Tea Transcriptome at Different Time Points
2.8. Screening of Different Genes in the Chlorophyll Metabolic Pathway in Tea Plants at Different Time Points
2.9. Fluorescence Quantitative PCR Verification
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Extraction and Measurement of Chlorophyll and Carotenoid Content
4.3. RNA Extraction, cDNA Library Construction and Sequencing
4.4. RNA-Seq Data and Enrichment Analysis of Differentially Expressed Genes
4.5. Functional Annotation Analysis
4.6. RT-qPCR Validation of Differentially Expressed Genes
4.7. Data Processing and Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Clean Reads | Clean Bases | Q20 Rate | Q30 Rate | GC Content |
---|---|---|---|---|---|
T0 h | 43,291,008 | 6,042,417,256 | 98.606% | 95.866% | 44.054% |
T6 h | 43,294,090 | 6,071,741,360 | 98.397% | 96.011% | 43.882% |
T12 h | 43,299,782 | 6,084,730,076 | 98.533% | 96.154% | 43.767% |
T18 h | 43,297,578 | 6,037,877,452 | 97.840% | 94.419% | 44.213% |
T24 h | 43,315,956 | 5,785,374,886 | 98.800% | 96.873% | 44.225% |
F24 h | 43,325,480 | 6,027,509,621 | 98.460% | 96.353% | 44.188% |
Item | Count | Percentage |
---|---|---|
All | 37,644 | 100.00% |
KEGG | 8050 | 21.38% |
Pathway | 4156 | 11.04% |
Nr | 27,713 | 73.62% |
Uniprot | 27,433 | 72.87% |
GO | 20,207 | 53.68% |
KOG (EuKaryotic Orthologous Groups) | 98 | 0.26% |
Pfam | 15,849 | 42.10% |
TF (Transcription factor) | 758 | 2.01% |
Comparison | Significant Diff Number | Up | Down |
---|---|---|---|
T0 h vs. T6 h | 713 | 353 | 360 |
T0 h vs. T12 h | 1292 | 366 | 926 |
T0 h vs. T18 h | 634 | 319 | 315 |
T0 h vs. T24 h | 496 | 157 | 339 |
T0 h vs. F24 h | 1121 | 485 | 636 |
Time | ZT 0-ZT 3 | ZT 3-ZT 6 | ZT 6-ZT 9 | ZT 9-ZT 12 | ZT 12-ZT 15 | ZT 15-ZT 18 | ZT 18-ZT 21 | ZT 21-ZT 24 | |
---|---|---|---|---|---|---|---|---|---|
Groups | |||||||||
6L6D | 6 h (09:00~15:00) | 6 h (15:00~21:00) | 6 h (21:00~ + 103:00) | 6 h (+ 103:00~ + 109:00) | |||||
24 L | 24 h (09:00~ + 109:00) |
Gene | Forward Primer Sequence (5′-3′) | Reverse Primer Sequence (5′-3′) |
---|---|---|
CsCHLE1.1 | TGAAGGCGAATCCAGAGT | ATACCGAGAGGCAGAAGAA |
CsCHLE1.2 | TGCCTCTCGGTATATGTGA | TCTCTTGAACTCTGGATTCTC |
CsCHLP1.1 | CCTTCATCATCTCCGCTAA | GCTCCAATCACAACATCAA |
CsCHLP1.2 | CATAGACCGCCGAGTAAC | TGAGGAAGAGACCGTTGA |
CsCLH1.1 | CGAAGCGTAGATGACCAA | GTGTTACAGGAGCAATAGTAG |
CsCLH1.2 | TTCAATCCACACTGCCTAA | TCTTCATTCTCACCATCCAA |
CsPOR1.1 | GTCGGCTCAATTACAGGTA | CCACATCACTCGCTTCTT |
CsPOR1.2 | GTTGATGATGGAGGACTTGA | CGGATTCTTCTTCGGATACA |
GAPDH | TTGGCATCGTTGAGGGTCT | CAGTGGGAACACGGAAAGC |
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Hu, Z.-H.; Sun, M.-Z.; Yang, K.-X.; Zhang, N.; Chen, C.; Xiong, J.-W.; Yang, N.; Chen, Y.; Liu, H.; Li, X.-H.; et al. High-Throughput Transcriptomic Analysis of Circadian Rhythm of Chlorophyll Metabolism under Different Photoperiods in Tea Plants. Int. J. Mol. Sci. 2024, 25, 9270. https://doi.org/10.3390/ijms25179270
Hu Z-H, Sun M-Z, Yang K-X, Zhang N, Chen C, Xiong J-W, Yang N, Chen Y, Liu H, Li X-H, et al. High-Throughput Transcriptomic Analysis of Circadian Rhythm of Chlorophyll Metabolism under Different Photoperiods in Tea Plants. International Journal of Molecular Sciences. 2024; 25(17):9270. https://doi.org/10.3390/ijms25179270
Chicago/Turabian StyleHu, Zhi-Hang, Meng-Zhen Sun, Kai-Xin Yang, Nan Zhang, Chen Chen, Jia-Wen Xiong, Ni Yang, Yi Chen, Hui Liu, Xing-Hui Li, and et al. 2024. "High-Throughput Transcriptomic Analysis of Circadian Rhythm of Chlorophyll Metabolism under Different Photoperiods in Tea Plants" International Journal of Molecular Sciences 25, no. 17: 9270. https://doi.org/10.3390/ijms25179270