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ORIGINAL RESEARCH article
Front. Genet.
Sec. Genomics of Plants and the Phytoecosystem
Volume 15 - 2024 |
doi: 10.3389/fgene.2024.1401013
This article is part of the Research Topic Genetic, Evolution, and Utilization of Crop Germplasm in Crop Improvement View all 5 articles
Analysis of codon usage patterns in complete plastomes of four medicinal Polygonatum species (Asparagaceae)
Provisionally accepted- 1 College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- 2 Yunnan Agricultural University, Kunming, Yunnan, China
Polygonati Rhizoma and Polygonati odorati Rhizoma, known as "Huangjing" and "Yuzhu" in China, are medicinal Polygonatum 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 Polygonatum species chloroplast genomes has not been systematically studied. In our study, a detailed analysis of CUB was performed in the medicinal Polygonatum species chloroplast genomes. We investigated the codon bias of 204 plastid protein-coding genes (PCGs) in 4 medicinal Polygonatum species using CodonW and CUSP online software. Through the analysis of the codon bias index, we found that the medicinal Polygonatum species chloroplast genomes had weak codon usage bias. In addition, our results also showed a high preference for AT bases in medicinal Polygonatum 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 Polygonatum species. Furthermore, the result of RSCU-based cluster analysis showed that the genetic relationship between different medicinal Polygonatum species could be well reflected. This study provided an essential understanding of CUB and evolution in the medicinal Polygonatum species chloroplast genomes.
Keywords: Polygonatum species, Chloroplast genome, codon usage bias, Mutation pressure, natural selection, evolution
Received: 14 Mar 2024; Accepted: 23 Aug 2024.
Copyright: © 2024 Shi, Yuan, Huang and Wen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Guosong Wen, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
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