Codon usage in genome of Listeria monocytogenes EGD-e

Objective To analyze the codon usage patterns and related factors by taking Listeria monocytogenes EGD-e as subject. Methods The codon usage patterns of Listeria monocytogenes was analyzed with EGD-e Online Codon W software; the factors in codon usage of Listeria monocytogenes EGD-e was presumed by using correspondence analysis and Nc-plot; the major preference codons in genome of Listeria monocytogenes EGD-e was defined by using high-expression codon. Results The GC content in the genome of Listeria monocytogenes EGD-e was only 37%, and the codon ended with U or A was used frequently; correspondence analysis showed that there was a significant correlation (R=-0.182, P0.01) between the gene position on the first axis and G+C content and a significant correlation (R=-0.740, P0.01) between the gene position on the first axis and CAI. Moreover, the correlation with the latter was significantly higher than the former. Conclusion The codon usage pattern in the genome of Listeria monocytogenes EGD-e had certain bias; the gene expression level of genes in Listeria monocytogenes EGD-e might be the main factor influencing codon usage bias. The codon usage bias was also affected by base composition, and gene length had little effect on codon usage bias. Finally, 27 codons were defined as the major preference codons in Listeria monocytogenes EGD-e, which provided a basis for genomics study of Listeria monocytogenes in the future.