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

Abstract

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; evolution; mutation pressure; natural selection.

FIGURE 1

Polygonatum kingianum Coll. et Hemsl. (A) individual, (B) whorled leaf, (C) flower and umbel, (D) anatomy of flower, (E) leaves.

FIGURE 2

Plastome map of Polygonatum kingianum. Genes inside and outside the circle were transcribed clockwise and counter-clockwise, respectively. Cp genome structure:LSC, large single copy region; SSC, small single copy region; IR, inverted repeat. The genes belonging to different functional groups are different color-coded. In the inner circle, the lighter gray indicates the AT content, and the darker gray indicates the GC content.

FIGURE 3

The related GC content of tested cp genes in medicinal Polygonatum species. The color variation is closely related to GC, GC1, GC2, and GC3 content. Green-to-red color indicates low to high percentage (%).

FIGURE 4

RSCU values for 21 amino acids (64 codons) in all tested cp genes of medicinal Polygonatum species. The different colors on the bar graph correspond to the color of the codon below the X-axis.

FIGURE 5

Neutrality plot analysis (GC12 vs. GC3) of cp genes in the medicinal Polygonatum species. R represents the Pearson’s correlation coefficient.

FIGURE 6

ENC-GC3s plot analysis of 51 tested cp genes in medicinal Polygonatum species. The yellow expected curve shows codon usage bias is only affected by mutation pressure.

FIGURE 7

Cp genes number distribution of ENC frequency ratio.

FIGURE 8

Parity Rule 2 (PR2) plot analysis of 51 cp genes in four medicinal Polygonatum species. The frequency of base A, T, G, and C at the third position of codons are denoted by A3s, T3s, G3s, C3s.

FIGURE 9

Spearman’s correlation analysis heatmap of different codon usage indicators of four medicinal Polygonatum species. The color of the color block changes from blue to red, indicating that the correlation index is rising. An asterisk indicates a significant association (p < 0.05); two asterisks indicate a extremely significant correlation (p < 0.01).

FIGURE 10

Hierarchical clustering analysis based on the RSCU of codons in chloroplast CDSs.