Analysis of codon usage patterns in chloroplast genome.

OBJECTIVE

In order to distinguish the traditional Chinese medicine and its adulterants effectively and develop a better understanding of the factors affecting synonymous codon usage, codon usage patterns of chloroplast genome, we determine the complete chloroplast (cp) genome of and clarify the main factors that influence codon usage patterns of 78 genes in chloroplast genome.

METHODS

The total genomic DNA of fresh leaves from a single individual of was extracted with EASYspin plus Total DNA Isolation Kit and 2 μg genome DNA was sequenced using Illumina Hiseq 2500 Sequencing Platform. The cp genome of was reconstructed with MITObim v1.8 and annotated in the program CPGAVAS2 with default parameters. Python script and Codon W were used to calculate the codon usage bias parameters.

RESULTS

The full length of cp genome was 155 851 bp, 132 different genes were annotated in this cp genome containing 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The codon usage models tended to use A/T-ending codons. The neutrality plot, ENC plot, PR2-Bias plot and correspondence analysis showed that both compositional constraint under selection and mutation could affect the codon usage models in cp genome. Furthermore, three optimal codons were identified and most of these three optimal codons ended with G/U.

CONCLUSION

The cp genome of has been characterized and the codon usage bias in cp genome is influenced by natural selection, mutation pressure and nucleotide composition. The results will provide much more barcode information for species discrimination and lay a foundation for future research on codon optimization of exogenous genes, genetic engineering and molecular evolution in