Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species
Abstract
:1. Introduction
2. Results
2.1. Identification and Nucleotide Composition of HSP20 Genes
2.2. Codon Usage Indices of HSP20 Genes
2.3. ENc-GC3s Plot Analysis
2.4. PR2-Plot Analysis
2.5. Neutrality Plot
2.6. Correlation Coefficient Analysis of Codon Usage Indices
2.7. Relationship between ENc and Gene Expression Level
2.8. Identification of Optimal Codons
2.9. Comparison of Evolutionary Relationship and Cluster Analysis
2.10. PCA of RSCU Values with Species and Subfamilies
3. Discussion
4. Materials and Methods
4.1. Identification of HSP20 Genes
4.2. Codon Usage Bias Analysis
4.3. ENc-GC3s Plot
4.4. PR2-Plot Analysis
4.5. Neutrality Plot
4.6. Correlation Analysis of Codon Usage Bias Indices
4.7. The Relationship between CUB and Gene Expression Level
4.8. Determination of Optimal Codons
4.9. Phylogenetic and Clustering Analysis
4.10. Principal Component Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
Abbreviations
References
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Ji, H.; Liu, J.; Chen, Y.; Yu, X.; Luo, C.; Sang, L.; Zhou, J.; Liao, H. Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species. Plants 2024, 13, 468. https://doi.org/10.3390/plants13040468
Ji H, Liu J, Chen Y, Yu X, Luo C, Sang L, Zhou J, Liao H. Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species. Plants. 2024; 13(4):468. https://doi.org/10.3390/plants13040468
Chicago/Turabian StyleJi, Huiyue, Junnan Liu, Yineng Chen, Xinyi Yu, Chenlu Luo, Luxi Sang, Jiayu Zhou, and Hai Liao. 2024. "Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species" Plants 13, no. 4: 468. https://doi.org/10.3390/plants13040468