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.
Highlights
The introduction the genetic code refers to the sequences of DNA and RNA nucleotides that determine amino acid sequences in proteins
Studies of codon usage have determined that several factors may influence codon usage patterns, including mutational bias and natural selection
If translational selection pressure influences codon usage, the bias should be significantly positively correlated with expression levels, with some translation-preferred codons appearing more frequently than others
Summary
The introduction the genetic code refers to the sequences of DNA and RNA nucleotides that determine amino acid sequences in proteins. Different codons that encode the same amino acid are termed synonymous codons. Studies of codon usage have determined that several factors may influence codon usage patterns, including mutational bias and natural selection. Little is known about codon usage bias in Epichloë endophytes, a group of clavicipitaceous fungi (Clavicipitaceae, Ascomycota) that live in systemic symbioses with cool-season grasses of the subfamily Pooideae [15,16]. This mutualistic symbiotic association confers on the host a number of bioprotective benefits by producing secondary fungal metabolites that alter host metabolism [17]. Our results lay the groundwork for analyses of genetic evolution in E. festucae
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