Analysis of Chloroplast Genome Characteristics and Codon Usage Bias of Styphnolobium japonicum f. oligophyllum

To investigate the codon usage bias (CUB) and its influencing factors in the chloroplast genome of Styphnolobium japonicum f. oligophyllum, we sequenced, assembled and annotated the genome using Illumina high-throughput sequencing, and systematically analyzed 52 protein-coding sequences. The chloroplast genome is 158,739 bp with a typical quadripartite structure, containing 129 functional genes. It presents a mean GC3 content of 28.26% and a mean ENC value of 45.40, indicating weak CUB and low gene expression. Among 31 preferred codons (RSCU > 1), 29 (93.5%) end with A/U. Neutrality plot, ENC-plot and PR2-plot analyses reveal that natural selection is the primary regulator of CUB. A total of 19 optimal codons were identified. These results provide fundamental reference data that may facilitate future genetic engineering efforts in S. japonicum f. oligophyllum.