Transcriptional Controls for Early Bolting and Flowering in Angelica sinensis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Total RNA Isolation and Illumina Sequencing
2.3. Sequence Filtration, Assembly and Unigene Expression Analysis
2.4. Basic Annotation of DEGs and Gene Cluster Analysis
2.5. qRT-PCR Validation
2.6. GA Quantification and Identification
2.7. Soluble Sugar Measurement
2.8. Statistical Analysis
3. Results
3.1. Global Gene Analysis
3.2. DEGs Linked with Bolting and Flowering
3.3. Flower-Regulating DEGs Inarticulately Expressed with EBF
3.4. Sucrose and GA Accumulation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Bolted | Unbolted | |
---|---|---|
Unfiltered data | ||
Data of reads number (million) | 60.73 | 52.48 |
Reads length | 150 | 150 |
GC (%) | 44.69 | 45.12 |
Data of reads number×read length (million) | 9110 | 7872 |
Q20 (%) | 98.50 | 98.47 |
Q30 (%) | 95.25 | 95.18 |
Filtered data 1 | ||
Data of reads number (million) | 60.66 | 52.41 |
Data of reads number×read length (million) | 9098 | 7862 |
Q20 (%) | 98.56 | 98.53 |
Q30 (%) | 95.34 | 95.26 |
Mapped data 2 | ||
Data of unique mapped reads (million) | 44.70 | 37.40 |
Data of multiple mapped reads (million) | 7.80 | 6.40 |
Mapping ratio (%) | 86.56 | 83.57 |
Compiled data | ||
Total number of unigenes | 72,502 | |
Total Length (bp) (million) | 64.14 | |
N50 (bp) | 1534 | |
Max length (bp) | 15,601 | |
Min length (bp) | 201 | |
Average Length (bp) | 884 | |
GC content (%) | 41.17 |
BLASTx Searching against Specific Platforms | Values | Percentage (%) |
---|---|---|
NR | 44,708 | 61.66 |
SwissProt | 30,471 | 42.03 |
KOG | 22,959 | 31.67 |
KEGG | 18,056 | 24.90 |
GO | 12,473 | 17.20 |
Gene Name | Gene ID | Protein Name | log2 Ratio (BRPKM/UBRPKM) |
---|---|---|---|
Floral development (8) | |||
Genes favoring flowering | |||
SOC1 | XP_017245180.1 | MADS-box protein SOC1 | 1.06 |
MADS8 | XP_017257209.1 | MADS-box transcription factor 8 | 7.21 |
AGL8 | XP_017244085.1 | Agamous-like MADS-box protein AGL8 | 4.16 |
AGL12 | XP_017218759.1 | Agamous-like MADS-box protein AGL12 | 3.42 |
DEFA | XP_017253634.1 | Floral homeotic protein DEFICIENS | 1.11 |
AP1 | AGX01569.1 | Floral homeotic protein APETALA 1 | 4.29 |
Genes disfavoring flowering | |||
AP2 | XP_017231882.1 | Floral homeotic protein APETALA 2 | −6.14 |
ANT | XP_017254585.1 | AP2-like ethylene-responsive transcription factor ANT | −3.27 |
Sucrose pathway (11) | |||
Genes favoring flowering | |||
SUS1 | XP_017219197.1 | Sucrose synthase isoform 1 | 1.31 |
SUS3 | XP_017225961.1 | Sucrose synthase 3 | 1.40 |
SUS7 | XP_017244457.1 | Sucrose synthase 7 | −2.70 |
INVA | CAA76145.1 | Alkaline/neutral invertase A, mitochondrial | 1.41 |
INVB | XP_017254796.1 | Probable alkaline/neutral invertase B | 1.22 |
INVE | XP_017258042.1 | Alkaline/neutral invertase E, chloroplastic | 1.09 |
AMY1.1 | XP_017218607.1 | Alpha-amylase | 1.03 |
BAM1 | XP_017219233.1 | Beta-amylase 1, chloroplastic | 1.62 |
BAM3 | XP_017236738.1 | Beta-amylase 3, chloroplastic | 1.05 |
BAM9 | XP_017219710.1 | Inactive beta-amylase 9 | 1.30 |
Genes disfavoring flowering | |||
INV Inh | KZV43516.1 | Invertase inhibitor | −1.83 |
GA pathway (7) | |||
Genes favoring flowering | |||
KO | XP_017253618.1 | Ent-kaurene oxidase, chloroplastic | 2.04 |
GA20OX1 | XP_017239190.1 | Gibberellin 20 oxidase 1 | 1.77 |
Genes disfavoring flowering | |||
GA2OX1 | API85599.1 | Gibberellin 2-beta-dioxygenase 1 | −1.41 |
GAI | XP_017238853.1 | DELLA protein GAI | −3.49 |
GA2OX6 | XP_017243791.1 | Gibberellin 2-beta-dioxygenase 6 | 2.53 |
GA2OX8 | XP_017220109.1 | Gibberellin 2-beta-dioxygenase 8 | 1.65 |
GAIP | XP_017217018.1 | DELLA protein GAIP | 2.15 |
Photoperiodic induction (14) | |||
Genes favoring flowering | |||
CO3 | XP_017232180.1 | Zinc finger protein CO3 | 2.58 |
COL2 | XP_017231361.1 | Zinc finger protein CONSTANS-LIKE 2 | 3.5 |
HD3A | XP_017216959.1 | Protein HEADING DATE 3A | 13.41 |
FTIP1 | XP_019421416.1 | FT-interacting protein 1 | 2.13 |
FD | XP_017256913.1 | Protein FD | 3.26 |
HDR1 | XP_019170400.1 | Protein HEADING DATE REPRESSOR 1 | 2.12 |
SVP | XP_017245967.1 | MADS-box protein SVP | −1.25 |
Genes disfavoring flowering | |||
COL3 | XP_017221909.1 | Zinc finger protein CONSTANS-LIKE 3 | −2.79 |
COL16 | XP_017244294.1 | Zinc finger protein CONSTANS-LIKE 16 | −1.33 |
AS1 | XP_017249788.1 | Transcription factor AS1 | −2.23 |
CDF2 | XP_017221059.1 | Cyclic dof factor 2 | 3.03 |
MIP1A | XP_017253198.1 | B-box domain protein 30 | 2.58 |
MIP1B | XP_017253198.1 | B-box domain protein 31 | 3.50 |
EFM | XP_017241902.1 | EARLY FLOWERING MYB PROTEIN | 1.12 |
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Li, M.; Li, J.; Wei, J.; Paré, P.W. Transcriptional Controls for Early Bolting and Flowering in Angelica sinensis. Plants 2021, 10, 1931. https://doi.org/10.3390/plants10091931
Li M, Li J, Wei J, Paré PW. Transcriptional Controls for Early Bolting and Flowering in Angelica sinensis. Plants. 2021; 10(9):1931. https://doi.org/10.3390/plants10091931
Chicago/Turabian StyleLi, Mengfei, Jie Li, Jianhe Wei, and Paul W. Paré. 2021. "Transcriptional Controls for Early Bolting and Flowering in Angelica sinensis" Plants 10, no. 9: 1931. https://doi.org/10.3390/plants10091931