Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis.

Genomics
Xu-Yuan LiuShang-Qian Xie

Abstract

The protein-coding genes and pseudogenes of Cuscuta australis had the diverse contribution to the formation and evolution of parasitism. The codon usage pattern analysis of these two type genes could be used to understand the gene transcription and translation. In this study, we systematically analyzed the codon usage patterns of protein-coding sequences and pseudogenes sequences in C. australis. The results showed that the high frequency codons of protein coding sequences and pseudogenes had the same A/U bias in the third position. However, these two sequences had converse bias at the third base in optimal codons: the protein coding sequences preferred G/C-ending codons while pseudogene sequences preferred A/U-ending codons. Neutrality plot and effective number of codons plot revealed that natural selection played a more important role than mutation pressure in two sequences codon usage bias. Furthermore, the gene expression level had a significant positive correlation with codon usage bias in C. australis. Highly-expressed protein coding genes exhibited a higher codon bias than lowly-expressed genes. Meanwhile, the high-expression genes tended to use G/C-ending synonymous codons. This result further verified the optimal codon...Continue Reading

Citations

Jan 12, 2021·Journal of Basic Microbiology·Yaqin WuYoujun Shang
Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Zhiwen ChenCorrinne E Grover
Aug 14, 2020·Genomics·Muhammad Nasir IqbalIskander Tlili

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