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. 2016 Jul 15;17(7):1138.
doi: 10.3390/ijms17071138.

Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae

Xiuzhang Li  1 , Hui Song  2 , Yu Kuang  3 , Shuihong Chen  4 , Pei Tian  5 , Chunjie Li  6 , Zhibiao Nan  7
Affiliations

Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae

Xiuzhang Li et al. Int J Mol Sci. .

Abstract

Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59%) in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU) values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C.

Keywords: Epichloë festucae; codon usage bias; grass endophyte; natural selection; optimal codons.

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Figures

Figure 1
Figure 1
Neutrality plots (GC12 vs. GC3).GC12 stands for the average value of GC content in the first and second position of the codons (GC1 and GC2). While GC3 refers to the GC content in the third position. The solid line is the linear regression of GC12 against GC3, R2 = 0.0146, p < 0.01.
Figure 2
Figure 2
The frequency distribution of effective number of codons (ENC) ratio.
Figure 3
Figure 3
Effective number of codons ENC-plot showing relationship between ENC and GC3s.
See this image and copyright information in PMC

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