Analysis of Codon Usage Bias in Xyloglucan Endotransglycosylase (XET) Genes

• Published in: International journal of molecular sciences 2023-03, Vol.24 (7), p.6108
• Main Authors: Xiong, Bo, Wang, Tie, Huang, Shengjia, Liao, Ling, Wang, Xun, Deng, Honghong, Zhang, Mingfei, He, Jiaxian, Sun, Guochao, He, Siya, Wang, Zhihui
• Format: Article
• Language: English
• Subjects: Abiotic stress; Amino acids; Base composition; Bias; Cluster analysis; Codon; Codon - genetics; Codon Usage; codon usage bias; Codons; Evolution & development; Genes; Genetic distance; Genetic research; Genomes; Glycosyltransferases - genetics; Natural selection; optimal codons; Phylogeny; Xyloglucan; Xyloglucan endotransglycosylase
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms24076108

Xyloglucan endotransglycosylase ( ) genes are widely distributed in most plants, but the codon usage bias of genes has remained uncharacterized. Thus, we analyzed the codon usage bias using 4500 codons of 20 genes to elucidate the genetic and evolutionary patterns. Phylogenetic and hierarchical cluster analyses revealed that the 20 genes belonged to two groups. The closer the genetic distance, the more similar the codon usage preference. The codon usage bias of most genes was weak, but there was also some codon usage bias. AGA, AGG, AUC, and GUG were the top four codons (RSCU > 1.5) in the 20 genes. had a stronger codon usage bias, and there were eight optimal codons of (i.e., AGA, AUU, UCU, CUU, CCA, GCU, GUU, and AAA). The RSCU values underwent a correspondence analysis. The two main factors affecting codon usage bias (i.e., Axes 1 and 2) accounted for 54.8% and 17.6% of the total variation, respectively. Multiple correspondence analysis revealed that genes were widely distributed, with Group 1 genes being closer to Axis 1 than Group 2 genes, which were closer to Axis 2. Codons with A/U at the third codon position were distributed closer to Axis 1 than codons with G/C at the third codon position. , , , , and were biased toward codons ending with G/C. In contrast, , , and were strongly biased toward codons ending with A/U, indicating that these genes have a strong codon usage bias. Translational selection and base composition (especially A and U at the third codon position), followed by mutation pressure and natural selection, may be the most important factors affecting codon usage of 20 genes. These results may be useful in clarifying the codon usage bias of genes and the relevant evolutionary characteristics.