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

Gene
Xiaoli ShiJingchu Luo

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 synon...Continue Reading

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Citations

Dec 8, 2009·Proceedings of the National Academy of Sciences of the United States of America·Haibao TangAndrew H Paterson
Apr 21, 2011·Molecular Biology and Evolution·Aline MuyleSylvain Glémin
Jun 25, 2010·Genome Biology·Kiwoong NamHans Ellegren
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Feb 10, 2009·PloS One·Gwenael Piganeau, Adam Eyre-Walker
Feb 21, 2006·Gene·Yi Xing, Christopher Lee
Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Zhiwen ChenCorrinne E Grover

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