Identification of Differentially Expressed Genes Related to Floral Bud Differentiation and Flowering Time in Three Populations of Lycoris radiata
Abstract
:1. Introduction
2. Results
2.1. Cytological Characteristics during Floral Bud Differentiation in L. radiata
2.2. Statistics of Sequencing, Assembly, and Annotation of RNA-Seq in L. radiata
2.3. Differentially Expressed Genes (DEGs) Identification in L. radiata
2.4. GO and KEGG Annotation of DEGs
2.5. Key DEGs Related to Floral Bud Differentiation in L. radiata
2.6. Identification of Candidate Genes Associated with the Floral Transition by Weighted Gene Co-Expression Network Analysis (WGCNA)
2.7. qRT-PCR Validation of Expression of the Critical Flowering-Related Genes
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Collection
4.2. Cytological Observation
4.3. RNA Extraction, Library Construction, and Sequencing
4.4. Assembly and Functional Annotation
4.5. Gene Expression Level Analysis and Differential Expressed Genes (DEGs) Identification
4.6. Co-Expression Network Analysis with WGCNA
4.7. qRT-PCR Validation of RNA-seq Data
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Total Raw Reads (M) | Total Clean Reads (M) | Total Clean Bases (Gb) | Clean Reads Q20 (%) | Clean Reads Q30 (%) | Clean Reads Ratio (%) |
---|---|---|---|---|---|---|
E1_r1 | 49.08 | 42.9 | 6.43 | 97.24 | 92.92 | 87.4 |
E1_r2 | 49.08 | 42.75 | 6.41 | 97.11 | 92.6 | 87.11 |
E1_r3 | 49.08 | 43.01 | 6.45 | 97.06 | 92.47 | 87.63 |
E2_r1 | 49.08 | 43.11 | 6.47 | 97.03 | 92.41 | 87.83 |
E2_r2 | 49.08 | 42.82 | 6.42 | 97.23 | 92.91 | 87.25 |
E2_r3 | 50.83 | 43.18 | 6.48 | 97.1 | 92.62 | 84.95 |
L1_r1 | 47.33 | 42.24 | 6.34 | 97 | 92.33 | 89.24 |
L1_r2 | 49.08 | 43.41 | 6.51 | 96.97 | 92.3 | 88.45 |
L1_r3 | 47.33 | 42.46 | 6.37 | 96.86 | 92.01 | 89.71 |
L2_r1 | 47.33 | 43.25 | 6.49 | 97.73 | 93.57 | 91.38 |
L2_r2 | 47.33 | 43.5 | 6.52 | 97.62 | 93.31 | 91.91 |
L2_r3 | 47.33 | 42.68 | 6.4 | 97.85 | 93.91 | 90.18 |
M1_r1 | 49.08 | 42.94 | 6.44 | 97.09 | 92.53 | 87.5 |
M1_r2 | 49.08 | 42.78 | 6.42 | 97 | 92.35 | 87.17 |
M1_r3 | 49.08 | 42.81 | 6.42 | 97.03 | 92.42 | 87.22 |
M2_r1 | 47.33 | 43.45 | 6.52 | 97.94 | 94.16 | 91.81 |
M2_r2 | 47.33 | 43 | 6.45 | 97.81 | 93.84 | 90.86 |
M2_r3 | 47.33 | 42.83 | 6.42 | 97.9 | 94.08 | 90.5 |
Database | Annotated Number of Unigenes | Percentage of Total Unigenes |
---|---|---|
Total | 165,109 | 100% |
NR | 122,777 | 74.36% |
NT | 95,120 | 57.61% |
Swissprot | 96,085 | 58.19% |
KEGG | 100,063 | 60.60% |
KOG | 99,330 | 60.16% |
Pfam | 89,517 | 54.22% |
GO | 94,803 | 57.42% |
Intersection | 50,188 | 30.40% |
Overall | 127,400 | 77.16% |
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Cheng, G.; Zhang, F.; Shu, X.; Wang, N.; Wang, T.; Zhuang, W.; Wang, Z. Identification of Differentially Expressed Genes Related to Floral Bud Differentiation and Flowering Time in Three Populations of Lycoris radiata. Int. J. Mol. Sci. 2022, 23, 14036. https://doi.org/10.3390/ijms232214036
Cheng G, Zhang F, Shu X, Wang N, Wang T, Zhuang W, Wang Z. Identification of Differentially Expressed Genes Related to Floral Bud Differentiation and Flowering Time in Three Populations of Lycoris radiata. International Journal of Molecular Sciences. 2022; 23(22):14036. https://doi.org/10.3390/ijms232214036
Chicago/Turabian StyleCheng, Guanghao, Fengjiao Zhang, Xiaochun Shu, Ning Wang, Tao Wang, Weibing Zhuang, and Zhong Wang. 2022. "Identification of Differentially Expressed Genes Related to Floral Bud Differentiation and Flowering Time in Three Populations of Lycoris radiata" International Journal of Molecular Sciences 23, no. 22: 14036. https://doi.org/10.3390/ijms232214036