Comparative Analysis of Circadian Transcriptomes Reveals Circadian Characteristics between Arabidopsis and Soybean
Abstract
:1. Introduction
2. Results
2.1. Comparison of Circadian Rhythmic Genes Unveils Distinctive Circadian Parameter Characteristics between Arabidopsis and Soybean
2.2. Comparative Analysis of Homologous Circadian Clock Genes Implies Intricate Circadian Regulatory Mechanisms Distinguishing Soybean from Arabidopsis
2.3. Circadian Parameter Alterations of Genes Provide Insights into the Circadian Control of Flowering and Maturity in Soybean
2.4. Circadian Control of Physiological Activities in Arabidopsis and Soybean
2.5. Differential Circadian Regulation of Physiological Activities in Arabidopsis and Soybean
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Sequencing Reads Acquisition, Read Alignment, and mRNA Quantification
4.3. Pre-Processing of Expression Data
4.4. Weighted Estimation of Rhythmic Parameters of Genes
- (1)
- Remove the slope trends by fitting a linear regression model to the gene expression data and keep residuals.
- (2)
- Perform Fast Fourier Transformation (FFT) of the time series data and keep main signals.
- (3)
- Estimate the initial period using FFT transformed data.
- (4)
- Perform non-linear regression fitting. The fitting was applied with weights obtained in the pre-processing. Amplitude was constrained to be non-negative. Period was constrained to be greater than 12 h but less than 36 h. Phase24 and Constant have no constraints. Phase was normalized as phase24, which is more than 0 but less than 24. Constant indicates the average expression level of the gene.
- (5)
- Predict the best-fit data and calculate circadian oscillation correlation between observed data and predicted data.
- (6)
- Genes without convergent fits were considered arrhythmic. Genes with the resulting best-fit Amplitude, Period, Phase24, Constant and their standard error and degree of freedom were used for downstream statistical analysis.
4.5. Analysis of Homologous Genes
4.6. Phase24 Plots
4.7. Gene Set Enrichment Analysis
4.8. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Arabidopsis thaliana | Glycine max | |||||||
---|---|---|---|---|---|---|---|---|
Type | GO ID | Description | NES 1 | p Value | Rank 2 | NES | p Value | Rank |
BP | GO:0042274 | ribosomal small subunit biogenesis | 2.7329 | 0.0001 | 5671 | −1.5852 | 0.0405 | 20,587 |
CC | GO:0005852 | eukaryotic translation initiation factor 3 complex | 2.3767 | 0.0001 | 5596 | −1.6797 | 0.0131 | 15,219 |
BP | GO:0055075 | potassium ion homeostasis | 1.7333 | 0.0126 | 9684 | −1.6109 | 0.0496 | 8780 |
CC | GO:0000502 | proteasome complex | 1.5905 | 0.0146 | 10,956 | −2.2152 | 0.0120 | 16,030 |
CC | GO:0005839 | proteasome core complex | 1.6584 | 0.0166 | 11,279 | −2.2368 | 0.0013 | 16,579 |
CC | GO:1905369 | endopeptidase complex | 1.5202 | 0.0229 | 10,956 | −2.4388 | 0.0169 | 16,030 |
BP | GO:0010499 | proteasomal ubiquitin-independent protein catabolic process | 1.5683 | 0.0364 | 11,279 | −2.0977 | 0.0033 | 16,579 |
CC | GO:0070993 | translation preinitiation complex | 1.4947 | 0.0488 | 5486 | −1.7524 | 0.0045 | 15,219 |
Arabidopsis thaliana | Glycine max | |||||||
---|---|---|---|---|---|---|---|---|
Term | NES 1 | p Value | FDR 2 | Rank 3 | NES | p Value | FDR | Rank |
ribonucleoprotein complex subunit organization | 1.965 | 0.000 | 0.003 | 5744 | −1.933 | 0.333 | 0.674 | 20,531 |
ribonucleoprotein complex assembly | 1.995 | 0.000 | 0.003 | 5744 | −1.943 | 0.333 | 0.674 | 20,531 |
ribosomal small subunit biogenesis | 2.745 | 0.000 | 0.003 | 5671 | −1.633 | 0.037 | 0.199 | 20,587 |
cytoplasmic translation | 2.741 | 0.000 | 0.003 | 5696 | −1.311 | 0.185 | 0.494 | 18,680 |
maturation of SSU-rRNA from tricistronic rRNA transcript | 2.491 | 0.000 | 0.003 | 7533 | −1.331 | 0.083 | 0.323 | 20,587 |
cytidine to uridine editing | −0.743 | 0.842 | 0.944 | 17,268 | 2.032 | 0.001 | 0.022 | 5953 |
phosphogluconate dehydrogenase (decarboxylating) activity | −0.882 | 0.598 | 0.819 | 11,493 | 1.780 | 0.008 | 0.075 | 5914 |
amyloplast | −0.939 | 0.520 | 0.769 | 10,958 | 1.752 | 0.013 | 0.104 | 11,820 |
carbon-oxygen lyase activity, acting on phosphates | −0.732 | 0.847 | 0.948 | 15,240 | 1.721 | 0.015 | 0.112 | 8267 |
protein kinase CK2 complex | −1.005 | 0.422 | 0.703 | 13,202 | 1.684 | 0.019 | 0.131 | 4358 |
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Wang, X.; Hu, Y.; Wang, W. Comparative Analysis of Circadian Transcriptomes Reveals Circadian Characteristics between Arabidopsis and Soybean. Plants 2023, 12, 3344. https://doi.org/10.3390/plants12193344
Wang X, Hu Y, Wang W. Comparative Analysis of Circadian Transcriptomes Reveals Circadian Characteristics between Arabidopsis and Soybean. Plants. 2023; 12(19):3344. https://doi.org/10.3390/plants12193344
Chicago/Turabian StyleWang, Xingwei, Yanfei Hu, and Wei Wang. 2023. "Comparative Analysis of Circadian Transcriptomes Reveals Circadian Characteristics between Arabidopsis and Soybean" Plants 12, no. 19: 3344. https://doi.org/10.3390/plants12193344