Abstract
Codon usage bias, which exists in many genomes, is mainly determined by mutation and selection. To elucidate the genetic features and evolutionary history of herbaceous peony (Paeonia lactiflora), a well-known symbol of prosperity in China, we examined synonymous codon usage in 24,216 reconstructed genes from the P. lactiflora transcriptome. The mean GC content was 44.4%, indicating that the nucleotide content of P. lactiflora genes is slightly AT rich and GC poor. The P. lactiflora genome has a wide range of GC3 (GC content at the third synonymous codon position) distribution, with a significant correlation between GC12 and GC3. ENC (effective number of codons) analysis suggested that mutational bias played a major role in shaping codon usage. Parity Rule 2 (PR2) analysis revealed that GC and AU were not used proportionally. We identified 22 “optimal codons”, most ending with an A or U. Our results suggested that nucleotide composition mutation bias and translational selection were the main driving factors of codon usage bias in P. lactiflora. These results lay the foundation for exploring the evolutionary mechanisms and heterologous expression of functionally-important proteins in P. lactiflora.
Highlights
The genetic code is degenerate (64 codons for 20 amino acids and the termination signal), with most amino acids encoded by two to six synonymous codons used at different frequencies, a phenomenon known as codon usage bias (CUB) [1]
Codon usage bias for a single type of codon is greatly influenced by the overall nucleotide content of the genome [26]
The GC content at GC1 was extremely close to that at GC2, and the GC content at GC3 was the highest among codon positions. The results from this initial nucleotide composition analysis suggested that A/U-ending codons might be preferred over G/C-ending codons in the P. lactiflora genome
Summary
The genetic code is degenerate (64 codons for 20 amino acids and the termination signal), with most amino acids encoded by two to six synonymous codons used at different frequencies, a phenomenon known as codon usage bias (CUB) [1]. Many factors influence codon usage in various organisms, such as natural selection (e.g., gene expression level, tRNA abundance, protein length, gene translation initiation signals and protein structure) and mutational pressure (e.g., GC content, mutation frequency and pattern), as well as random genetic drift [2,3,4]. Since the genome sequence of P. lactiflora has still not been released, it is difficult to investigate codon usage bias in this species. We analyzed the nucleotide composition of coding sequences from the P. lactiflora genome, followed by correlation analysis of various factors that influence codon usage bias. The results of this study help elucidate the mechanism underlying the molecular evolution of this species, while providing a theoretical basis for improving the expression levels of exogenous genes by codon optimization
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
