Analysis of Codon Preferences in Medicago ruthenica based on Transcriptome Data

Abstract

Background: The study investigated codon usage bias in Medicago ruthenica transcriptome coding sequences, aiming to lay the foundation for optimizing codon composition and enhancing heterologous gene expression in Medicago ruthenica. Methods: In this research, Medicago ruthenica was used as the research material and 11,581 high-quality transcript gene sequences were selected from transcriptome data. Codon usage patterns and preferences were analyzed using software such as CodonW, R and Excel. Result: The study revealed that the effective number of codons (ENC) ranged from 28.8 to 61.0. The average GC content of codons in expressed genes of Medicago ruthenica was 0.40 and the average GC content of the third nucleotide position of synonymous codons (GC3s) was 0.33. Analysis through ENC-plot, neutrality plot and bias analysis suggested that codon usage bias in the Medicago ruthenica transcriptome may be the result of a combination of factors including selection and mutation. Fifteen optimal codons were selected, with ten ending in ‘A’ and five ending in ‘U’, indicating a preference for ‘A/U’ ending codons in the Medicago ruthenica transcriptome. The frequency of codon usage in Medicago ruthenica was compared to five other organisms, including Arabidopsis thaliana, Glycine max, Nicotiana tabacum, yeast and Escherichia coli, revealing significant differences with E. coli and relatively smaller differences with Nicotiana tabacum.