In-silico Analysis of Codon Usage Bias in 14 Lardizabalaceae Species

Codon usage bias (CUB) is crucial in species evolution and gene expression regulation. This study analyzed the CUB patterns in the chloroplast genomes of 14 Lardizabalaceae species to identify factors influencing codon usage variation. Using CodonW 1.4.2 and the CUSP program, we extracted and analyzed 1,182 protein-coding sequences (CDS) from these genomes. We examined nucleotide composition, relative synonymous codon usage (RSCU), ENC-GC3 plots, neutrality plots, and PR2-bias plots. The CDS length ranged from 79 to 85 base pairs (bp), with guanine-cytosine (GC) content between 38.46 percent and 39.37 percent, indicating a preference for adenine-thymine (AT)-rich sequences. RSCU and neutrality plot analysis suggested that natural selection predominantly shapes CUB, with weaker mutational pressure. Methionine (AUG) and tryptophan (UGG) showed no codon bias, while UAG and UGA exhibited variation in translation termination preferences. ENC-GC3 plot indicated the dual influence of mutation and selection, reflecting a complex evolutionary process. PR2-bias plots revealed a balanced preference for purines (G, A) and pyrimidines (C, T). Our findings suggest that CUB in Lardizabalaceae chloroplast genomes is primarily governed by natural selection, with a minor contribution from mutational pressure. These results highlight the evolutionary forces shaping codon usage, with potential implications for understanding gene expression, genetic variability, and adaptation in the Lardizabalaceae family.