Genome-Wide Analysis of KNOX Genes: Identification, Evolution, Comparative Genomics, Expression Dynamics, and Sub-Cellular Localization in Brassica napus
Abstract
1. Introduction
2. Results
2.1. Identification and Chromosome Map of KNOX Proteins and Genes from Brassica
2.2. Phylogenetic and Classification Analyses of KNOX Protein Family
- To analyze the evolutionary patterns of KNOX, we constructed a comprehensive phylogenetic tree for 150 KNOX proteins, including the following: 32 from B. napus, 16 from Populus trichocarpa/Zea mays, 15 from B. rapa, 14 from B. oleracea, 13 from Oryza sativa, 11 from Brachypodium distachyon, 9 from Arabidopsis thaliana, 8 from Fragaria vesca, 7 from Medicago truncatula, 4 from Physcomitrella patens/Selaginella moellendorffii, and 1 from O. lucimarinus (Figure 2; Supplement File S1). Subsequently, excluding PpKNAT2a/2b and OlKNAT7 due to their inability to be classified into Class I or Class II despite sharing the same domain organization as others (similar results were obtained using different phylogenetic trees constructed by Neighbor-Joining or Maximum Likelihood methods), we successfully categorized the remaining set of 147 KNOX proteins into three distinct classes. Notably in Brassica species specifically, B. napus not only encompasses all KNOX proteins found in both B. rapa and B. oleracea but also exhibits an additional three unique members within its repertoire (Figure 2; Supplement File S1).
2.2.1. Phylogenetic and Domain Analyses of Class I
2.2.2. Phylogenetic and Domain Analyses of Class II
2.2.3. Phylogenetic and Domain Analyses of Class-III
2.3. Analysis of Cis-Acting Elements of BnKNOX Gene Promoters and Gene Structure in B. napus
2.4. Gene Collinearity and Duplication of BnKNOXs in B. napus
2.5. Expression Patterns of BnKNOXs in Different Tissues from BrassicaEDB
2.6. BnKNOXs Expression Levels of in Reproductive Organs by qRT-PCR
2.7. Subcellular Localization Analysis
3. Discussion
3.1. Conservation and Evolution of KNOX Proteins in Plants
3.2. KNOX Orthologs Among B. napus, B. rapa and B. oleracea
3.3. KNOX Gene Duplication and Diversity in B. napus, B. rapa and B. oleracea
3.4. Potential Roles of BnKNOX Genes Related to Plant Growth and Development
4. Materials and Methods
4.1. KNOX Protein Identification and Chromosome Map Construction
4.2. Analysis of Protein Domain Organization
4.3. Phylogenetic Analysis
4.4. Analysis of Cis-Acting Elements of BnKNOXs Promoters and Gene Structures in B. napus
4.5. Collinearity Analysis
4.6. Expression Levels of BnKNOXs in Different Tissues
4.7. Validation of Expression Levels of BnKNOXs by qRT-PCR
4.8. Subcellular Localization of the BnKNOX::GFP Fusion Protein
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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He, X.; Zheng, R.; Chen, Y.; Tan, C. Genome-Wide Analysis of KNOX Genes: Identification, Evolution, Comparative Genomics, Expression Dynamics, and Sub-Cellular Localization in Brassica napus. Plants 2025, 14, 2167. https://doi.org/10.3390/plants14142167
He X, Zheng R, Chen Y, Tan C. Genome-Wide Analysis of KNOX Genes: Identification, Evolution, Comparative Genomics, Expression Dynamics, and Sub-Cellular Localization in Brassica napus. Plants. 2025; 14(14):2167. https://doi.org/10.3390/plants14142167
Chicago/Turabian StyleHe, Xiaoli, Ruiyi Zheng, Yan Chen, and Chengfang Tan. 2025. "Genome-Wide Analysis of KNOX Genes: Identification, Evolution, Comparative Genomics, Expression Dynamics, and Sub-Cellular Localization in Brassica napus" Plants 14, no. 14: 2167. https://doi.org/10.3390/plants14142167
APA StyleHe, X., Zheng, R., Chen, Y., & Tan, C. (2025). Genome-Wide Analysis of KNOX Genes: Identification, Evolution, Comparative Genomics, Expression Dynamics, and Sub-Cellular Localization in Brassica napus. Plants, 14(14), 2167. https://doi.org/10.3390/plants14142167