Analysis of Codon Usage Bias in the Chloroplast Genome of Hemsleya chinensis

To analyze the codon usage pattern and its underlying factors in the Hemsleya chinensis chloroplast genome, we conducted a systematic analysis of its codon usage. This study provides a molecular basis for subsequent phylogenetic reconstruction within the Hemsleya genus and elucidates the evolutionary mechanisms of codon usage in chloroplast genomes.This study employed high-throughput sequencing to assemble and analyze the chloroplast genome of H. chinensis. The results revealed a typical quadripartite circular chloroplast genome structure with a total length of 157,735 bp and a GC content of 37.07%. Genome annotation identified 116 functional genes, of which 52 protein-coding sequences (CDS) were selected Codon usage bias analysis showed a gradient decrease in the GC content across the three codon positions: GC₁ (46.53%), GC₂ (39.29%), and GC₃ (28.58%). The average effective number of codons (ENC) was 47.17, significantly higher than the conventional threshold of 35.00, while the codon adaptation index (CAI) ranged from 0.11 to 0.31. Natural selection was identified as the primary driver of codon usage bias. Through relative synonymous codon usage (RSCU) analysis, 14 optimal codons end with A/U, such as GCA (Ala), UGU (Cys), and GAA (Glu), were identified.