Evaluating Selection and Mutation Influences on Codon Usage Patterns in the Chloroplast Genomes of Amaranthus species

Abstract

Amaranthus is a genus characterized by taxonomic complexity and ecological diversity, gaining importance in agriculture and genomics. We report in-depth codon usage bias (CUB) analysis of 18 Amaranthus species chloroplast genomes to make inroads into the evolutionary forces responsible for their genomic structure. We analyzed various codon usage parameters, including relative synonymous codon usage (RSCU), effective number of codons (ENC), GC Content, nucleotide composition, and positional bias. Our results indicated a strong inclination towards A/T-ending codons and a generally AT-rich nucleotide composition, especially at the third codon position, across all species. The ENC values varied from 34.05 to 58.87, reflecting a moderate codon usage bias. Neutrality plot analysis revealed weak correlations between GC3 and GC12 (slope 0.095–0.141), implying that natural selection, rather than mutation pressure, predominantly influences codon preferences. ENC-GC3s plots corroborated this, with most genes positioned below the expected curve, and PR2-bias plots demonstrated an imbalance favoring T and G over A and C at the third codon position. Correspondence analysis (COA) further confirmed that both mutational and selective forces affect codon usage variation. We identified 31 high-frequency codons and 12 optimal codons, with speciesspecific codon preferences, indicating subtle evolutionary adaptations. This study offers new insights into the molecular evolution and codon optimization of Amaranthus, providing valuable information for phylogenetics, functional genomics, and biotechnological applications within the genus.