Gene Duplication and Functional Diversification of MADS-Box Genes in Malus × domestica following WGD: Implications for Fruit Type and Floral Organ Evolution
Abstract
:1. Introduction
2. Results
2.1. The Expansion in the Number of MADS-Box Genes across Different Fruit Types Is Correlated with WGD in Rosaceae
2.2. The Retention of Duplicated Genes in Maleae following WGD and Subsequent Chromosome Rearrangement
2.3. Four MADS-Gene Orthologous Groups Are Expressed in Plant Tissues
2.4. The MADS18 Genes Derived from WGD in M. × domestica Have Undergone Differential Evolution
2.5. The MADS6 Genes Derived from Both WGD and Tandem Duplication in M. × domestica Exhibit Differential Evolution
3. Discussion
3.1. Changes in Chromosomes and Genes Following the WGD Event in Rosaceae
3.2. The Expansion of the MADS-Box Gene Family Is Associated with Different Fruit Types in Rosaceae
3.3. MADS18 and MADS6 Are Expanded through WGD and Gene Duplication
3.4. MADS18 and MADS6 Have Different Expression Levels in Apple Fruits at Different Stages and Different Flower Organs
4. Materials and Methods
4.1. Collection of Publicly Available Genomic and Transcriptome Data
4.2. Phylogenetic Analysis and Time Inference
4.3. GO Term Enrichment
4.4. Gene Family Expansion and Contraction
4.5. Collinearity and Sequence Similarity Analysis
4.6. Ancestral Chromosome Karyotype Reconstruction and Evolution
4.7. Analysis of WGD and Gene Duplication
4.8. Transcriptome Analysis
4.9. Conserved Domain Search and Protein Structure Prediction
4.10. Plant Material and qRT-PCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Wang, B.; Xiao, Y.; Yan, M.; Fan, W.; Zhu, Y.; Li, W.; Li, T. Gene Duplication and Functional Diversification of MADS-Box Genes in Malus × domestica following WGD: Implications for Fruit Type and Floral Organ Evolution. Int. J. Mol. Sci. 2024, 25, 8962. https://doi.org/10.3390/ijms25168962
Wang B, Xiao Y, Yan M, Fan W, Zhu Y, Li W, Li T. Gene Duplication and Functional Diversification of MADS-Box Genes in Malus × domestica following WGD: Implications for Fruit Type and Floral Organ Evolution. International Journal of Molecular Sciences. 2024; 25(16):8962. https://doi.org/10.3390/ijms25168962
Chicago/Turabian StyleWang, Baoan, Yao Xiao, Mengbo Yan, Wenqi Fan, Yuandi Zhu, Wei Li, and Tianzhong Li. 2024. "Gene Duplication and Functional Diversification of MADS-Box Genes in Malus × domestica following WGD: Implications for Fruit Type and Floral Organ Evolution" International Journal of Molecular Sciences 25, no. 16: 8962. https://doi.org/10.3390/ijms25168962
APA StyleWang, B., Xiao, Y., Yan, M., Fan, W., Zhu, Y., Li, W., & Li, T. (2024). Gene Duplication and Functional Diversification of MADS-Box Genes in Malus × domestica following WGD: Implications for Fruit Type and Floral Organ Evolution. International Journal of Molecular Sciences, 25(16), 8962. https://doi.org/10.3390/ijms25168962