Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias.

Xiaoli Shi; Xiyin Wang; Zhe Li; Qihui Zhu; Wen Tang; Song Ge; Jingchu Luo

doi:10.1016/j.gene.2006.03.003

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Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias.

Xiaoli Shi·Xiyin Wang·Zhe Li·Qihui Zhu·Wen Tang·Song Ge·Jingchu Luo

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Abstract

Understanding the correlation between synonymous substitution rate and GC content is essential to decipher the gene evolution. However, it has been controversial on their relationship. We analyzed the GC content and synonymous substitution rate in 1092 paralogues produced by two large-scale duplication events in the rice genome. According to the GC content at the third codon sites (GC3), the paralogues were classified into GC3-rich and GC3-poor genes. By referring to their outgroup sequences, we inferred the last common ancestor of sister paralogues and, consequently, calculated the average synonymous substitution rate for two gene classes. The results suggest that average synonymous substitution rate is lower in GC3-rich genes than that in GC3-poor genes, indicating that the synonymous substitution rate is negatively correlated with GC content in the rice genome. Through characterizing the synonymous nucleotide substitution pattern, we found a strong synonymous nucleotide substitution frequency bias from AT to GC in GC3-rich genes. This indicates possible limitations of commonly used methods developed to estimate the synonymous substitution rate. Their estimates might produce misleading results on correlation between the synonymous substitution rate and GC content.

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Base Composition Base Pairing Base Sequence Codon GC Rich Sequence Gene Duplication Gene Frequency Genes, Plant Likelihood Functions Models, Genetic Models, Statistical Mutation Oryza Comparative Study Journal Article Research Support, Non-U.S. Gov't

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Xiaoli Shi, Xiyin Wang, Zhe Li, Qihui Zhu, Wen Tang, Song Ge, Jingchu Luo. 2006-03-18. Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias.. https://doi.org/10.1016/j.gene.2006.03.003

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