Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Growth and Histology
2.2. Scanning Electron Micrography
2.3. Sample Preparation for RNA-seq
2.4. RNA-seq Library Preparation and Sequencing
2.5. Reference-Based Transcriptome Analysis
2.6. Differentially Expressed Genes and Functional Enrichment Analysis
3. Results and Discussions
3.1. Vernalization-Induced Developmental Changes in the Aquilegia SAM
3.2. Transcriptome Sequencing
3.3. GO Enrichment and KEGG Analysis
3.4. Gene Expression Clusters
3.4.1. Flowering Time Genes
3.4.2. MADS-Box Genes
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Pairwise Comparisons | GO Category | GO Term | Description |
---|---|---|---|
W0-W4 up | BP | GO:0070647 | Protein modification by small protein conjugation or removal |
W0-W6 up | BP | GO:0010033 | Response to organic substance |
W0-WB up | BP | GO:0070647 | Protein modification by small protein conjugation or removal |
W4-W6 up | BP | GO:0055086 | Nucleobase-containing small molecule metabolic process |
W4-WB up | BP | GO:0034660 | ncRNA metabolic process |
W6-WB up | BP | GO:0048856 | Anatomical structure development |
W0-W4 down | BP | GO:0055086 | Nucleobase-containing small molecule metabolic process |
W0-W6 down | BP | GO:0006091 | Generation of precursor metabolites and energy |
W0-WB down | BP | GO:0006091 | Generation of precursor metabolites and energy |
W4-W6 down | BP | GO:0006091 | Generation of precursor metabolites and energy |
W4-WB down | BP | GO:0006812 | Cation transport |
W6-WB down | BP | GO:0006091 | Generation of precursor metabolites and energy |
W0-W4 up | MF | GO:0003700 | DNA-binding transcription factor activity |
W0-W6 up | MF | GO:0003700 | DNA-binding transcription factor activity |
W0-WB up | MF | GO:0003700 | DNA-binding transcription factor activity |
W4-W6 up | MF | GO:0005198 | Structural molecule activity |
W4-WB up | MF | GO:0005198 | Structural molecule activity |
W6-WB up | MF | GO:0003700 | DNA-binding transcription factor activity |
W0-W4 down | MF | GO:0005198 | Structural molecule activity |
W0-W6 down | MF | GO:0005198 | Structural molecule activity |
W0-WB down | MF | GO:0005198 | Structural molecule activity |
W4-W6 down | MF | GO:0003700 | DNA-binding transcription factor activity |
W4-WB down | MF | GO:0015075 | Ion transmembrane transporter activity |
W6-WB down | MF | GO:0015075 | Ion transmembrane transporter activity |
W0-W4 up | CC | GO:0031974 | Membrane-enclosed lumen |
GO:0043233 | Organelle lumen | ||
GO:0070013 | Intracellular organelle lumen | ||
W0-W6 up | CC | GO:0005829 | Cytosol |
W0-WB up | CC | GO:0031974 | Membrane-enclosed lumen |
GO:0043233 | Organelle lumen | ||
GO:0070013 | Intracellular organelle lumen | ||
W4-W6 up | CC | GO:0005840 | Ribosome |
W4-WB up | CC | GO:0005840 | Ribosome |
W6-WB up | CC | GO:0031974 | Membrane-enclosed lumen |
GO:0043233 | Organelle lumen | ||
GO:0070013 | Intracellular organelle lumen | ||
W0-W4 down | CC | GO:0005840 | Ribosome |
W0-W6 down | CC | GO:0005840 | Ribosome |
W0-WB down | CC | GO:0098796 | Membrane protein complex |
W4-W6 down | CC | GO:0009579 | Thylakoid |
GO:0044434 | Chloroplast part | ||
GO:0044435 | Plastid part | ||
W4-WB down | CC | GO:0044435 | Plastid part |
W6-WB down | CC | GO:0098796 | Membrane protein complex |
Flowering Time Genes | Cluster Number |
---|---|
AqTFL | C0 |
FRIGIDA LIKE 3 | C0 |
FRIGIDA LIKE 4A | C0 |
AqGI | C0 |
AqVIN3A | C1 |
AqCLF | C1 |
AqCO | C2 |
AqFT3 | C3 |
AqMSI | C3 |
AqFT2 | C5 |
AqLFY | C6 |
AqUFO2 | C6 |
AqUFO2A | C6 |
AqSWN | C7 |
AqFT | C8 |
AqMFT | C8 |
FRIGIDA LIKE | C9 |
FRIGIDA LIKE 1 | C9 |
AqVIN3B | C9 |
AqVRN5 | C10 |
AqUFO1 | C11 |
MADS-Box TFs | Cluster Number |
---|---|
AqAGL61 | C2 |
AqAGL63 | C2 |
AaAGL63 LIKE | C2 |
AqAGL64 | C2 |
AqAGL86 LIKE | C2 |
AqAGL86 LIKE A | C2 |
AqAGl12 | C2 |
AqSOC1.3 | C2 |
AqSOC 1.4 | C2 |
AqAG1 | C2 |
AqBS | C2 |
AqAGL24.1 | C3 |
AqAGL80 LIKE | C3 |
AqAG2 | C4 |
AqAGL84 | C5 |
AqAGL85 | C5 |
AqAGL24.2 | C5 |
AqAGL65 | C5 |
TM8 LIKE | C6 |
AqSOC1.2 | C6 |
AqAGL15 | C8 |
AqAP3-1 | C8 |
AqAP3-2 | C8 |
AqAP3-3 | C8 |
AqAG1B | C8 |
AqSEP2B | C8 |
AqSEP3 | C8 |
AqAGL63 LIKE A | C8 |
AqFL3 | C9 |
SRF TYPE-TF | C10 |
AqAGL6 | C11 |
AqFL1A | C11 |
AqFL1B | C11 |
AqAP3-3b | C11 |
AqPI | C11 |
AqSEP1 | C11 |
AqSEP2A | C11 |
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Sharma, B.; Batz, T.A.; Kaundal, R.; Kramer, E.M.; Sanders, U.R.; Mellano, V.J.; Duhan, N.; Larson, R.B. Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James). Genes 2019, 10, 734. https://doi.org/10.3390/genes10100734
Sharma B, Batz TA, Kaundal R, Kramer EM, Sanders UR, Mellano VJ, Duhan N, Larson RB. Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James). Genes. 2019; 10(10):734. https://doi.org/10.3390/genes10100734
Chicago/Turabian StyleSharma, Bharti, Timothy A. Batz, Rakesh Kaundal, Elena M. Kramer, Uriah R. Sanders, Valerie J. Mellano, Naveen Duhan, and Rousselene B. Larson. 2019. "Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James)" Genes 10, no. 10: 734. https://doi.org/10.3390/genes10100734
APA StyleSharma, B., Batz, T. A., Kaundal, R., Kramer, E. M., Sanders, U. R., Mellano, V. J., Duhan, N., & Larson, R. B. (2019). Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James). Genes, 10(10), 734. https://doi.org/10.3390/genes10100734