Analysis of Codon Usage Bias in the Chloroplast Genome of <i>Ananas comosus</i>
Welcome to Chinese Journal of Tropical Crops,

Chinese Journal of Tropical Crops ›› 2022, Vol. 43 ›› Issue (3): 439-446.DOI: 10.3969/j.issn.1000-2561.2022.03.001

• Omics & Biotechnology •     Next Articles

Analysis of Codon Usage Bias in the Chloroplast Genome of Ananas comosus

YANG Xiangyan, CAI Yuanbao*(), TAN Qinliang, QIN Xu, HUANG Xianya, WU Mi   

  1. Guangxi Subtropical Crops Research Institute / Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530001, China
  • Received:2021-08-09 Revised:2021-12-06 Online:2022-03-25 Published:2022-03-23
  • Contact: CAI Yuanbao


The codon usage bias of chloroplast genome affects the genes expression efficiency, which provides important information for chloroplast genetic engineering and species genetic improvement. To determine the codon usage characteristic of the chloroplast genome and its main influencing factors in pineapple (Ananas comosus), the codon usage pattern and its preference of pineapple chloroplast genome were analyzed using bioinformatics softwares. The average GC content of codons of pineapple chloroplast genes was 38.31%, the average GC content of codons from the first position to the third position was 46.78%, 39.61% and 28.53%, respectively, and the average GC contents at the first and second positions of codons were significantly higher than that at the third position. The value range of effective number of codons (ENC) was 38.48—61.00, and its average value was 47.21, indicating weak codon bias. GC1 was significantly correlated with GC2, GCall was significantly positively correlated with GC1, GC2 and GC3, and GC3 was not significantly correlated with GC1 and GC2. ENC was not significantly correlated with GC1, but significantly and extremely significantly correlated with GC2 and GC3, respectively. Codon number (N) was only significantly correlated with GC3, which indicating that the base composition of the third position in the three positions of the codon mainly affects codon number. RSCU analysis showed that among the 29 codons with RSCU>1, 12 codons ended with A, 16 codons ended with U, and 1 codon ended with G. Neutrality plot analysis showed that there was not significant correlation between GC12 and GC3, and the correlation coefficient and regression coefficient was 0.065 and 0.085, respectively. ENC-plot analysis showed most genes were distributed near the standard curve, and most ENC ratios were distributed in the interval of -0.05—0.05. PR2-plot analysis showed that all genes were unevenly distributed in the four regions of the PR2 plan, and the use frequency of pyrimidine T/C at the third position of codon was higher than that of purine A/G. Bias analysis of Neutrality plot, ENC-plot and PR2-plot suggested that natural selection and mutation as the main factors affect the codon usage bias of pineapple chloroplast genome. Analysis of optimal codons and RSCU showed that most of the 29 codons with RSCU>1 and the 18 optimal codons ended with A or U. The results provide scientific basis for codon optimization of exogenous genes and improvement of their expression efficiency.

Key words: pineapple (Ananas comosus), chloroplast genome, codon usage bias, optimal codons

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