Abstract
Codon usage bias plays an important role in shaping genomes and genes in unicellular species and multicellular species. Here, we first analyzed codon usage bias in seven Epichloë species and their peramine-coding genes. Our results showed that both natural selection and mutation pressure played a role in forming codon usage bias in seven Epichloë species. All seven Epichloë species contained a peramine-coding gene cluster. Interestingly, codon usage bias of peramine-coding genes were not affected by natural selection or mutation pressure. There were 13 codons more frequently found in Epichloë genome sequences, peramine-coding gene clusters and orthologous peramine-coding genes, all of which had a bias to end with a C nucleotide. In the seven genomes analyzed, codon usage was biased in highly expressed coding sequences (CDSs) with shorter length and higher GC content. Genes in the peramine-coding gene cluster had higher GC content at the third nucleotide position of the codon, and highly expressed genes had higher GC content at the second position. In orthologous peramine-coding CDSs, high expression level was not significantly correlated with CDS length and GC content. Analysis of selection pressure identified that the genes orthologous to peramine genes were under purifying selection. There were no differences in codon usage bias and selection pressure between peramine product genes and non-functional peramine product genes. Our results provide insights into understanding codon evolution in Epichloë species.
Highlights
The genetic code constitutes of 64 triplet codons encoding for 20 amino acids, with synonymous codons coding for the same amino acid
A recent study on codon usage bias in E. festucae showed that both natural selection and mutation pressure played a role in forming codon usage bias in E. festucae, and that codon usage bias was influenced by coding sequences (CDSs) length (Li et al, 2016)
We conducted a comprehensive analysis of codon usage bias in seven Epichloë genomes and their peraminecoding genes
Summary
The genetic code constitutes of 64 triplet codons encoding for 20 amino acids, with synonymous codons coding for the same amino acid. Synonymous codons occur at different frequencies in genomes/genes, a phenomenon referred as codon usage bias (Hershberg and Petrov, 2008; Plotkin, 2011). Mutational pressure and natural selection are considered to be the two major factors. Codon Usage Bias in Epichloë Organism Lab ID. Epichloë amarillans Epichloë bromicola Epichloë festucae Epichloë glyceriae Epichloë sylvatica Epichloë typhina Epichloë typhina subsp. E4668 AL0434 E894 E277 E7368 E8 E5819 Host. Agrostis hyemalis Bromus tomentellus Festuca trachyphylla Glyceria striata Brachypodium sylvaticum Lolium perenne Poa nemoralis. Total CDSs in this study GC1 content
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