Transcriptome-based Medicago varia Codon Preference Analysis

Background: The study explored codon usage bias in medicago varia transcriptome coding sequences, aiming to provide data support for understanding gene expression and enhancing Molecular breeding methods in medicago varia. Methods: In this study, Medicago varia was used as the research material and 11722 complete open reading frame sequences were screened from the transcriptome sequencing results. Codon usage patterns and preferences were analyzed using software such as CodonW, R and Excel. Result: According to the 11722 complete open reading frame sequences screened from the transcriptome sequencing results, Codon was used to calculate the Codon preference index. A total of 41354958 Unigenes were obtained. A total of 80757 Unigenes (39.66%) were annotated, with the majority being annotated in the NR database. GO annotations include 20 Biological processes, 16 Cellular components and 11 molecular function GO terms, respectively. 25713 genes were annotated into KOG, including 25 subclasses. The content of average GC was 42.87%, respectively. The study revealed that the effective number of codons (ENC) ranged from 23.9 to 61.0. Mutation and selection affected the codon preference. Medicago varia preferred 30 codons and preferred the third base of the codon as A/U, so it can be inferred that Medicago prefers the third codon with A/U.