Genome-Wide Analysis of the HD-Zip Gene Family in Chinese Cabbage (Brassica rapa subsp. pekinensis) and the Expression Pattern at High Temperatures and in Carotenoids Regulation
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Materials, Heat Stress Treatment, and Carotenoid Content Measurement
2.2. GenomeWide Identification of HD-Zip Genes
2.3. Multiple Sequence Alignment and Phylogenetic Analysis
2.4. Gene Structure, Motif, and Cis-Regulatory Elements Analysis
2.5. Synteny Analysis of HD-Zip Genes
2.6. Calculating the Ka, Ks, and 4DTv of HD-Zip Paralogs
2.7. Expression Pattern Analysis of HD-Zip Genes
3. Results
3.1. Whole-Genome Identification of HD-Zip Genes in Brassicaceae Plants
3.2. Phylogenetic Analysis of the HD-Zip Genes
3.3. Conserved Motif Analysis and Gene Structural Analysis of HD-Zip Genes
3.4. Cis-Acting Elements Analysis in the Putative Promoter of HD-Zip Genes
3.5. Chromosome Location and Gene Family Expansion Analysis of HD-Zip Genes in Brassicaceae Plants
3.6. Estimating Dates and Driving Forces for the Evolution of the HD-Zip Gene Family
3.7. Expression Patterns of HD-Zip Genes in Different Chinese Cabbage Varieties
4. Discussion
4.1. Whole-Genome Identification and Phylogenetic Analysis of HD-Zip Genes in Chinese Cabbage
4.2. The Evolution History of the HD-Zip Gene Family
4.3. The Potential Roles of Chinese Cabbage HD-Zip Transcription Factors
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Species | Genome Size | Chromosome Number (2n) | Whole Gene Number | HD-Zip Gene Number | |||
---|---|---|---|---|---|---|---|
I | II | III | IV | ||||
Brassica rapa | 351.06 | 20 | 46,250 | 39 | 18 | 10 | 26 |
Brassica oleracea | 561.16 | 18 | 59,064 | 41 | 20 | 10 | 25 |
Brassica napus | 924 | 38 | 108,190 | 74 | 38 | 19 | 53 |
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Yin, L.; Sun, Y.; Chen, X.; Liu, J.; Feng, K.; Luo, D.; Sun, M.; Wang, L.; Xu, W.; Liu, L.; et al. Genome-Wide Analysis of the HD-Zip Gene Family in Chinese Cabbage (Brassica rapa subsp. pekinensis) and the Expression Pattern at High Temperatures and in Carotenoids Regulation. Agronomy 2023, 13, 1324. https://doi.org/10.3390/agronomy13051324
Yin L, Sun Y, Chen X, Liu J, Feng K, Luo D, Sun M, Wang L, Xu W, Liu L, et al. Genome-Wide Analysis of the HD-Zip Gene Family in Chinese Cabbage (Brassica rapa subsp. pekinensis) and the Expression Pattern at High Temperatures and in Carotenoids Regulation. Agronomy. 2023; 13(5):1324. https://doi.org/10.3390/agronomy13051324
Chicago/Turabian StyleYin, Lian, Yudong Sun, Xuehao Chen, Jiexia Liu, Kai Feng, Dexu Luo, Manyi Sun, Linchuang Wang, Wenzhao Xu, Lu Liu, and et al. 2023. "Genome-Wide Analysis of the HD-Zip Gene Family in Chinese Cabbage (Brassica rapa subsp. pekinensis) and the Expression Pattern at High Temperatures and in Carotenoids Regulation" Agronomy 13, no. 5: 1324. https://doi.org/10.3390/agronomy13051324
APA StyleYin, L., Sun, Y., Chen, X., Liu, J., Feng, K., Luo, D., Sun, M., Wang, L., Xu, W., Liu, L., & Zhao, J. (2023). Genome-Wide Analysis of the HD-Zip Gene Family in Chinese Cabbage (Brassica rapa subsp. pekinensis) and the Expression Pattern at High Temperatures and in Carotenoids Regulation. Agronomy, 13(5), 1324. https://doi.org/10.3390/agronomy13051324