Xiaoshuang Wang , Yanqing Wang , Shihong Li , Yingliang Liu , Bin Zhu

School of Life Science, Guizhou Normal University, Guiyang 550025, China
Author    Correspondence author
Tree Genetics and Molecular Breeding, 2021, Vol. 11, No. 1   doi: 10.5376/tgmb.2021.11.0001
Received: 12 Aug., 2021    Accepted: 20 Aug., 2021    Published: 31 Aug., 2021

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.

Wang X.S., Wang Y.Q., Li S.H., Liu Y.L., and Zhu B., 2021, Analysis of codon usage bias in the Platycarya chloroplast genome, Tree Genetics and Molecular Breeding, 11(1): 1-11 (doi:10.5376/tgmb.2021.11.0001)

To detect the codon usage characteristics of chloroplast genomes in Platycarya genus, the CodonW、CUSP and SPSSAU software were employed to analyze the codon usage patterns of the chloroplast genomes protein-coding sequence in Platycarya longipes and Platycarya strobilacea in this research. Results show that the GC content of chloroplast genomes was 37.75% and 37.80%, the average GC content in the 3rd position was 27.16% and 27.25%. the range of effective codon number from 35.19 to 56.98, and there were more than 2/3 genes when ENC value greater than 45, which indicated a weak preference. According to the results of neutrality plot analysis, ENC-plot analysis and PR2-plot analysis, codon bias in most Platycarya chloroplast genes were affected by natural selection, while a few were affected by mutations or other factors. And based on the ENC value, five groups of high-expressed and low-expressed genes were identified, 16 codons were ended with A/U among the 18 optimal codons. The research has implications on codon optimization, enhancing the expression efficiency of exogenous gene and phylogenetic analysis.

Platycarya; Chloroplast genomes; Codon bias; Optimal codons