Analysis of codon usage patterns in complete plastomes of four medicinal Polygonatum species (Asparagaceae)

Polygonati Rhizoma and Polygonati odorati Rhizoma, known as "Huangjing" and "Yuzhu" in China, are medicinal <i>Polygonatum</i> species resources with top-grade medical and edible properties. The chloroplast (cp) genome has been used to study species diversity, evolution, and breeding of species for applications in genetic engineering. Codon usage bias (CUB), a common and complex natural phenomenon, is essential for studies of codon optimization of exogenous genes, genetic engineering, and molecular evolution. However, the CUB of medicinal <i>Polygonatum</i> species chloroplast genomes has not been systematically studied. In our study, a detailed analysis of CUB was performed in the medicinal <i>Polygonatum</i> species chloroplast genomes. We investigated the codon bias of 204 plastid protein-coding genes (PCGs) in 4 medicinal <i>Polygonatum</i> species using CodonW and CUSP online software. Through the analysis of the codon bias index, we found that the medicinal <i>Polygonatum</i> species chloroplast genomes had weak codon usage bias. In addition, our results also showed a high preference for AT bases in medicinal <i>Polygonatum</i> species chloroplast genomes, and the preference to use AT-ending codons was observed in these species chloroplast genomes. The neutrality plot, ENC plot, PR2-Bias plot, and correspondence analysis showed that compared with mutation pressure, natural selection was the most important factor of CUB. Based on the comparative analysis of high-frequency codons and high expression codons, we also determined the 10-11 optimal codons of investigative medicinal <i>Polygonatum</i> species. Furthermore, the result of RSCU-based cluster analysis showed that the genetic relationship between different medicinal <i>Polygonatum</i> species could be well reflected. This study provided an essential understanding of CUB and evolution in the medicinal <i>Polygonatum</i> species chloroplast genomes.