Comparative Analysis of Codon Usage Patterns in Chloroplast Genomes of Maple (Genus Acer)

Maple (Acer genus), deciduous perennial trees belong to the Sapindaceae family, thrive naturally across Asia, Europe and North America. In addition to their wide use in woodwork and pharmaceuticals, Acer species are favored choices for contemporary landscape design because of their large stature, intricate foliage patterns, vibrant colors, distinctive fruit shapes (paired winged samaras), and extensive genetic diversity. Understandably, they play a pivotal role in enhancing urban ecosystems and contributing to landscape construction. The aim of this study was to investigate the genomic characteristics and extent of codon usage bias (CUB) variation in the chloroplast (cp.) genome of ten sections of the genus Acer. Synonymous codon usage order (SCUO) indicated a weak codon usage bias (CUB) in the cp. genes of various Acer species. Notably, the third position of the codons exhibited a significant correlation with the overall nucleotide composition, suggesting that both natural selection and mutation pressure may have influenced the CUB. The Effective Number of Codon (ENC)-plot, Parity Rule 2 (PR2), and neutrality analyses showed that the codon bias of Acer cp. genetic material was influenced by several factors. While our analyses suggest a significant role for natural selection in shaping codon usage bias, as indicated by the ENC-plot analysis deviating from neutrality expectations, the contribution of mutation pressure and potentially genetic drift cannot be entirely excluded. These findings provide insights into codon usage patterns, which may be useful for future studies aiming to optimize codon usage for exogenous gene expression in the Acer cp. genome.