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. 2022 Dec;20(4):e43.
doi: 10.5808/gi.22045. Epub 2022 Dec 30.

The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family

Satyabrata Sahoo  1 , Ria Rakshit  2
Affiliations

The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family

Satyabrata Sahoo et al. Genomics Inform. 2022 Dec.

Abstract

Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformaticmethodologies were used to examine the pattern of coding sequences and the factors thatmight influence codon usage bias in the chloroplast genome of Atropa belladonna andother nightshade genomes. The chloroplast engineering being a promising field in modernbiotechnology, the characterization of chloroplast genome is very important. The resultsrevealed that the chloroplast genomes of Nicotiana tabacum, Solanum lycopersicum, Capsicum frutescens, Datura stramonium, Lyciumbarbarum, Solanum melongena, and Solanumtuberosum exhibited comparable codon usage patterns. In these chloroplast genomes, weobserved a weak codon usage bias. According to the correspondence analysis, the genesisof the codon use bias in these chloroplast genes might be explained by natural selection,directed mutational pressure, and other factors. GC12 and GC3S were shown to have nomeaningful relationship. Further research revealed that natural selection primarily shapedthe codon usage in A. belladonna and other nightshade genomes for translational efficiency. The sequencing properties of these chloroplast genomes were also investigated by investing the occurrences of palindromes and inverted repeats, which would be useful forfuture research on medicinal plants.

Keywords: Atropa belladonna; chloroplast genome; codon bias; codon usage; medicinal plants.

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Conflict of interest statement

Conflicts of Interest

No potential conflict of interest relevant to this article was reported.

Figures

Fig. 1.
Fig. 1.
Distribution of nucleotide composition at the synonymous third codon positions in protein-coding genes of Atropa belladonna chloroplast genome.
Fig. 2.
Fig. 2.
Distribution of GC content at the first, second, and third position of codons in protein-coding genes of Atropa belladonna chloroplast genome.
Fig. 3.
Fig. 3.
The PR2 plot of protein-coding genes of Atropa belladonna and other related chloroplast genomes in the nightshade family.
Fig. 4.
Fig. 4.
The neutrality plot of protein-coding genes of Atropa belladonna and other related chloroplast genomes in the nightshade family.
Fig. 5.
Fig. 5.
The frequencies of amino acids (AA) in protein-coding genes of Atropa belladonna chloroplast genome.
Fig. 6.
Fig. 6.
Codon Adaptation Index (CAI) plotted against NC for each protein-coding genes of Atropa belladonna chloroplast genome.
Fig. 7.
Fig. 7.
Modified relative codon bias strength (MRCBS) plotted against emPAI [40] for protein-coding genes of Atropa belladonna chloroplast genome.
Fig. 8.
Fig. 8.
Codon Adaptation Index (CAI) plotted against emPAI [40] for protein-coding genes of Atropa belladonna chloroplast genome.
Fig. 9.
Fig. 9.
Distribution of Codon Adaptation Index (CAI) of all protein-coding genes of Atropa belladonna chloroplast genome.
Fig. 10.
Fig. 10.
The GC and GC3s content of the protein-coding genes of Atropa belladonna chloroplast genome.
Fig. 11.
Fig. 11.
NC-GC3s plot for all protein-coding sequences of Atropa belladonna and other related chloroplast genomes in the nightshade family.
Fig. 12.
Fig. 12.
The relative and cumulative inertia of the first 40 factors from correspondence analysis based on the codon usage of Atropa belladonna chloroplast genes.
Fig. 13.
Fig. 13.
The distribution of codons on axis 1 versus axis 2 in correspondence analysis based on the codon usage of Atropa belladonna chloroplast genes.
Fig. 14.
Fig. 14.
Correspondence analysis of codon usage pattern for chloroplast genes in Atropa belladonna.
Fig. 15.
Fig. 15.
Phylogentic analysis of Atropa belladonna and other related genomes in the nightshade family.
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