Comparative Analysis of Codon Usage Patterns in Chloroplast Genomes of Cherries

Abstract

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

Decoding Evolution of Rubioideae: Plastomes Reveal Sweet Secrets of Codon Usage, Diagnostides, and Superbarcoding

“…The relative synonymous codon usage (RSCU) in chloroplast genomes shows a preference for using specific codons that might be a result of natural selection or mutational pressure [54]. Evolution might affect chloroplast genomes by changing their structure, content, and creation of nucleotide differences.…”

“…Evolution might affect chloroplast genomes by changing their structure, content, and creation of nucleotide differences. Most plastome codons end with A or T (we are using a thymine instead of uracil for a convenience because our analysis is based on DNA material), which might be an effect of many million years of development of chloroplast genomes [43,[54][55][56][57][58]. However, the RSCU is sometimes very similar in the case of specific codons.…”

Sequencing and Phylogenetic Analysis of the Chloroplast Genome of Three Apricot Species

“…The total cp genome lengths of P. armeniaca, P. sibirica, and kernel consumption apricot were 157,951, 158,224, and 157,994 bp, respectively. The cp genomes showed a typical tetrad structure, including two IRs (26,373 bp) that were separated by LSC (86,217-86,358 bp) and SSC (18,,120 bp) regions. Of the total cp genome, the protein-coding region accounted for (49.63-49.72%); tRNA and rRNA accounted for (1.77-1.78%), and (5.72-5.73%), respectively; meanwhile, introns and intergenic spacers (IGSs) accounted for (11.40-11.41%) and (31.34-31.47%), respectively.…”

“…With improvements in sequencing technology, the complete cp genome of Nicotiana tabacum was obtained for the first time in 1986 [17]. More recently, the cp genomes of Prunus cerasus (sour cherry) [18], P. phaeosticta (dark-spotted cherry) [19], P. kansuensis (Chinese bush peach) [20], and P. japonica (Japanese bush cherry) [21] were sequenced and analyzed, and their phylogenetic positions and genetic relationships were determined.…”