Analyses of Codon Usage Patterns and Codon Usage Bias in Peach (Prunus persica)
1 Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China
2 College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
3 College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
4 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801, U.S.A
Molecular Plant Breeding, 2022, Vol. 13, No. 28 doi: 10.5376/mpb.2022.13.0028
Received: 25 Nov., 2022 Accepted: 02 Dec., 2022 Published: 09 Dec., 2022
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This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Li R.Y., Zhang X.D., Ma X.Y., Guo R., Yan S.B., Jin G., and Zhou P., 2022, Analyses of codon usage patterns and codon usage bias in peach (Prunus persica), Molecular Plant Breeding, 13(28): 1-11 (doi: 10.5376/mpb.2022.13.0028)
To further study the characteristics of peach codon usage, this study analyzed codon usage biases and codon usage patterns of peach genome, based on the statistical calculations of related GC content, effective number of codons (ENC) and relative synonymous codons (RSCU) from 26 873 coding sequences. The results showed that there were obvious biases in codon usage of peach, and 4 out of 61 codons (UCA, ACA, GCA and GAA) were defined as the optimal codons, all of which end with Adenine at the third codon position. Further analyses of codon usage frequency among peach and other 9 relative species in Rosaceae found that the codon usage patterns in the relative genus were similar. These results also suggested that there was a positive correlation between the copy number of tRNA genes and the occurrence frequency of corresponding amino acids (and specific codons) in the peach genome. These results revealed codon usage patterns in Peach and provide an important reference for the relevant studies on codon usage mechanism and the genetic engineering.
Peach; Codon usage pattern; Codon usage bias