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. 2021 Sep 23:9:e12173.
doi: 10.7717/peerj.12173. eCollection 2021.

Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species

Jiajing Sheng  1 , Xuan She  2 , Xiaoyu Liu  1 , Jia Wang  3 , Zhongli Hu  2
Affiliations

Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species

Jiajing Sheng et al. PeerJ. .

Abstract

Miscanthus is not only a perennial fiber biomass crop, but also valuable breeding resource for its low-nutrient requirements, photosynthetic efficiency and strong adaptability to environment. In the present study, the codon usage patterns of five different Miscanthus plants and other two related species were systematically analyzed. The results indicated that the cp genomes of the seven representative species were preference to A/T bases and A/T-ending codons. In addition, 21 common high-frequency codons and 4-11 optimal codons were detected in the seven chloroplast genomes. The results of ENc-plot, PR2-plot and neutrality analysis revealed the codon usage patterns of the seven chloroplast genomes are influenced by multiple factors, in which nature selection is the main influencing factor. Comparative analysis of the codon usage frequencies between the seven representative species and four model organisms suggested that Arabidopsis thaliana, Populus trichocarpa and Saccharomyces cerevisiae could be considered as preferential appropriate exogenous expression receptors. These results might not only provide important reference information for evolutionary analysis, but also shed light on the way to improve the expression efficiency of exogenous gene in transgenic research based on codon optimization.

Keywords: Chloroplast genome; Codon optimization; Codon usage pattern; Miscanthus species.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Codon content in all protein-coding genes of the seven Miscanthus and related cp genomes.
From left to right: M. floridulus, M. giganteus, M. sacchariflorus, M. sinensis, M. transmorrisonensis, Saccharum spontaneum and Sorghum bicolor.
Figure 2
Figure 2. ENc-plot of chloroplast genomes of seven Misacanthus and related species.
Figure 3
Figure 3. PR2-plot of chloroplast genomes of seven Misacanthus and related species.
Figure 4
Figure 4. Neutrality plot of chloroplast genomes of seven Misacanthus and related species.
Figure 5
Figure 5. Correspondence analysis of chloroplast genomes of seven Misacanthus and related species.
See this image and copyright information in PMC

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