Molecular Biology Reports

, Volume 36, Issue 8, pp 2039–2046 | Cite as

Analysis of synonymous codon usage patterns in different plant mitochondrial genomes

  • Meng ZhouEmail author
  • Xia Li


Codon usage in mitochondrial genome of the six different plants was analyzed to find general patterns of codon usage in plant mitochondrial genomes. The neutrality analysis indicated that the codon usage patterns of mitochondrial genes were more conserved in GC content and no correlation between GC12 and GC3. T and A ending codons were detected as the preferred codons in plant mitochondrial genomes. The Parity Rule 2 plot analysis showed that T was used more frequently than A. The ENC-plot showed that although a majority of the points with low ENC values were lying below the expected curve, a few genes lied on the expected curve. Correspondence analysis of relative synonymous codon usage yielded a first axis that explained only a partial amount of variation of codon usage. These findings suggest that natural selection is likely to be playing a large role in codon usage bias in plant mitochondrial genomes, but not only natural selection but also other several factors are likely to be involved in determining the selective constraints on codon bias in plant mitochondrial genomes. Meantime, 1 codon (P. patens), 6 codons (Z. mays), 9 codons (T. aestivum), 15 codons (A. thaliana), 15 codons (M. polymorpha) and 15 codons (N. tabacum) were defined as the preferred codons of the six plant mitochondrial genomes.


Codon usage GC content Preferred codon Mitochondrial genome 



This work was supported in part by the National High Tech Development Project of China, the 863 Program (Grant Nos. 2007AA02Z329) and the National Natural Science Foundation of China (Grant Nos. 20060213024).


  1. 1.
    Grantham R, Gautier C, Gouy M (1980) Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res 8:1893–1912CrossRefPubMedGoogle Scholar
  2. 2.
    Angellotti MC, Bhuiyan SB, Chen G et al (2007) CodonO: codon usage bias analysis within and across genomes. Nucleic Acids Res 35:132–136CrossRefGoogle Scholar
  3. 3.
    John F (1999) Analysis of codon usage. The University of Nottingham for the Degree of Doctor of Philosophy, AugustGoogle Scholar
  4. 4.
    Gouy M, Gautier C (1982) Codon usage in bacteria, correlation with gene expressivity. Nucleic Acids Res 10:7055–7074CrossRefPubMedGoogle Scholar
  5. 5.
    Stenico M, Lloyd AT, Sharp PM (1994) Codon usage in Caenorhabditis elegans, delineation of translational selection and mutational biases. Nucleic Acids Res 22:2437–2446CrossRefPubMedGoogle Scholar
  6. 6.
    Sharp PM, Bailes E, Grocock RJ et al (2005) Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res 33:1141–1153CrossRefPubMedGoogle Scholar
  7. 7.
    Sharp PM, Stenico M, Peden JF et al (1993) Codon usage, mutational bias, translational selection, or both? Biochem Soc Trans 21:835–841PubMedGoogle Scholar
  8. 8.
    Karlin S, Mrázek J (1996) What drives codon choices in human genes? J Mol Biol 262:459–472CrossRefPubMedGoogle Scholar
  9. 9.
    Francino HP, Ochman H (1999) Isochores result from mutation not selection. Nature 400:30–31CrossRefPubMedGoogle Scholar
  10. 10.
    Powell JR, Moriyama EN (1997) Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA 94:7784–7790CrossRefPubMedGoogle Scholar
  11. 11.
    Wang HC, Hickey DA (2007) Rapid divergence of codon usage patterns within the rice genome. BMC Evol Biol 7(suppl 1):S6CrossRefPubMedGoogle Scholar
  12. 12.
    Ingvarsson PK (2007) Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol Biol Evol 24:836–844CrossRefPubMedGoogle Scholar
  13. 13.
    Kawabe A, Miyashita NT (2003) Patterns of codon usage bias in three dicot and four monocot plant species. Genes Genet Syst 78:343–352CrossRefPubMedGoogle Scholar
  14. 14.
    Saccone C, Gissi C, Reyes A et al (2002) Mitochondrial DNA in Metazoa, degree of freedom in a frozen event. Gene 286:3–12CrossRefPubMedGoogle Scholar
  15. 15.
    Le TH, McManus DP, Blair D (2004) Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes. Korean J Parasitol 42:159–167CrossRefPubMedGoogle Scholar
  16. 16.
    Jia W, Higgs PG (2008) Codon usage in mitochondrial genomes, distinguishing context-dependent mutation from translational selection. Mol Biol Evol 25:339–351CrossRefPubMedGoogle Scholar
  17. 17.
    Wright F (1990) The ‘effective number of codons’ used in a gene. Gene 87:23–29CrossRefPubMedGoogle Scholar
  18. 18.
    Chiapello H, Fisacek F, Caboche M et al (1998) Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene 209:1–38CrossRefGoogle Scholar
  19. 19.
    Wright SI, Yau CBK, Looseley M (2004) Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol 21:1719–1726CrossRefPubMedGoogle Scholar
  20. 20.
    Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA 85:2653–2657CrossRefPubMedGoogle Scholar
  21. 21.
    Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2:13–34PubMedGoogle Scholar
  22. 22.
    Sueoka N (1999) Translation-coupled violation of parity rule 2 in human genes is not the case of heterogeneity of the DNA G + C content of third codon position. Gene 238:53–58CrossRefPubMedGoogle Scholar
  23. 23.
    Sharp PM, Cowe E, Higgins DG et al (1988) Codon usage in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res 16:8207–8711CrossRefPubMedGoogle Scholar
  24. 24.
    Sueoka N, Kawanishi Y (2000) DNA G + C content of the third codon position and codon usage biases of human genes. Gene 261:53–62CrossRefPubMedGoogle Scholar
  25. 25.
    Blake WJ, Kaern M, Cantor CR et al (2003) Noise in eukaryotic gene expression. Nature 422:633–637CrossRefPubMedGoogle Scholar
  26. 26.
    Wan XF, Xu D, Kleinhofs A et al (2004) Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol Biol 4:19CrossRefPubMedGoogle Scholar
  27. 27.
    Lu H, Zhao WM, Zheng Y et al (2005) Analysis of synonymous codon usage bias in Chlamydia. Acta Biochim Biophys Sin 37:1–10PubMedCrossRefGoogle Scholar
  28. 28.
    Bonitz SG, Berlani R, Coruzzi G et al (1980) Codon recognition rules in yeast mitochondria. Proc Natl Acad Sci USA 77:3167–3170CrossRefPubMedGoogle Scholar
  29. 29.
    Pfitzinger H, Guillemaut P, Weil JH et al (1987) Adjustment of the tRNA population to the codon usage of chloroplasts. Nucleic Acids Res 15:137CrossRefGoogle Scholar
  30. 30.
    Xia X (1998) How optimized is the translational machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae? Genetics 149:37–44PubMedGoogle Scholar
  31. 31.
    Lynn DJ, Singer GA, Hickey DA (2002) Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 30:4272–4277CrossRefPubMedGoogle Scholar
  32. 32.
    Liu QP, Xue QZ (2005) Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. J Genet 84:55–62CrossRefPubMedGoogle Scholar
  33. 33.
    Liu Q, Feng Y, Xue Q (2004) Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa. Mitochondrion 4:313–320CrossRefPubMedGoogle Scholar
  34. 34.
    Morton BR (1998) Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages. J Mol Evol 46:449–459CrossRefPubMedGoogle Scholar
  35. 35.
    Morton BR (1999) Strand asymmetry and codon usage bias in the chloroplast genome of Euglena gracilis. Proc Natl Acad Sci USA 96:5123–5128CrossRefPubMedGoogle Scholar
  36. 36.
    Morton BR, So BG (2000) Codon usage in plastid genes is correlated with context, position within the gene, and amino acid content. J Mol Evol 50:184–193PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Department of BioinformaticsHarbin Medical UniversityHarbinChina

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