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Liu Hui, Wang Meng-Xing, Yue Wen-Jie, Xing Guang-Wei, Ge Ling-Qiao, Nie Xiao-Jun, Song Wei-Ning. Analysis of codon usage in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.)[J]. Plant Science Journal, 2017, 35(3): 362-371. DOI: 10.11913/PSJ.2095-0837.2017.30362
Citation: Liu Hui, Wang Meng-Xing, Yue Wen-Jie, Xing Guang-Wei, Ge Ling-Qiao, Nie Xiao-Jun, Song Wei-Ning. Analysis of codon usage in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.)[J]. Plant Science Journal, 2017, 35(3): 362-371. DOI: 10.11913/PSJ.2095-0837.2017.30362
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Analysis of codon usage in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.)

  • College of Agronomy, Northwest Agriculture and Forestry University, Shaanxi 712100, China

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This work was supported by grants from the National Natural Science Foundation of China (31401373) and Fundamental Research Funds for the Northwest Agriculture and Forestry University (2452015003).

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  • Received Date: November 07, 2016
  • Available Online: October 31, 2022
  • Published Date: June 27, 2017
    Graphical Abstract
    • Abstract
  • Codon usage bias (CUB) is an important evolutionary feature in a genome,which provides important information for studying organism evolution,gene function,and exogenous gene expression.The CUB and its influencing factors in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.) were preliminarily analyzed in this study based on 53 length-filtered CDS sequences.Results showed that the effective number of codons (ENC) ranged from 37.14 to 61,indicating that codon bias was weak.Relative synonymous codon usage (RSCU) analysis found 32 codons with a RSCU value of more than 1,of which 28 ended with A or T,suggesting that the third codon preferred A or U.Neutrality analysis showed no significant correlation between GC12 and GC3,and the regressive slope was 0.2129,suggesting natural selection mainly contributed to the CUB.ENC-plot (ENC vs GC3S) analysis showed that most genes followed the parabolic line of trajectory,but several genes with low ENC values below the expected curve were also observed.Furthermore,correspondence analysis of RSCU demonstrated that the first axis could explained 17.92% of variation,which was the major factor influencing codon bias.The first axis showed a significant correlation between ENC and GC3S,whereas no significant correlation was found for CBI and GC.Finally,nine codons were identified as optimal codons.We concluded that both natural selection and mutation have impacted the formation of CUB in the Broomcorn millet chloroplast genome.
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    • References (36)
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