Comparative Analysis of Codon Usage Patterns in Chloroplast Genomes of Cherries

Synonymous codon usage bias (SCUB) analysis is an effective method to explore species specificity, evolutionary relationships and mRNA translation, as well discover novel genes, which are important for understanding gene function molecular phylogeny. Cherries (Prunus subg. Cerasus) flowering plant germplasm resources edible ornamental purposes. In this study, we analyzed the patterns of 36 chloroplast genomes provide a scientific basis elucidating evolution Cerasus. The results showed that average GC content was 0.377, GC3 0.298, ENC value 49.69. Neutral-plot analysis, ENC-plot PR2-plot all indicated natural selection main factor in Cerasus, whereas correlation expression level GC1 also affect pattern. pattern consistent across species, 30 high-frequency codons were identified, with preference A/T endings; there 23 optimal codons, only GAU identified individuals; structural differences existed between clustering tree based on RSCU values phylogenetic CDS, importance locus mutations no-preference reconstruction. This study describes first time SCUB characterization Cerasus provides new insight phylogeny subgenus.