J Integr Plant Biol. ›› 2010, Vol. 52 ›› Issue (12): 1100-1108.DOI: 10.1111/j.1744-7909.2010.00998.x

• Molecular Ecology and Evolution • Previous Articles     Next Articles

Complex Mutation and Weak Selection together Determined the Codon Usage Bias in Bryophyte Mitochondrial Genomes

Bin Wang, Jing Liu, Liang Jin, Xue-Ying Feng and Jian-Qun Chen   

  1. State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
  • Received:2010-06-30 Accepted:2010-09-17 Published:2010-12-01
  • About author:
    *Corresponding author Tel: +86 25 8359 2733; Fax: +86 25 8663 3057; Email:chenjq@nju.edu.cn
    These authors contributed equally to this paper.

Abstract:

Mutation and selection are two major forces causing codon usage biases. How these two forces influence the codon usages in green plant mitochondrial genomes has not been well investigated. In the present study, we surveyed five bryophyte mitochondrial genomes to reveal their codon usage patterns as well as the determining forces. Three interesting findings were made. First, comparing to Chara vulgaris, an algal species sister to all extant land plants, bryophytes have more G, C-ending codon usages in their mitochondrial genes. This is consistent with the generally higher genomic GC content in bryophyte mitochondria, suggesting an increased mutational pressure toward GC. Second, as indicated by Wright's Nc-GC3s plot, mutation, not selection, is the major force affecting codon usages of bryophyte mitochondrial genes. However, the real mutational dynamics seem very complex. Context-dependent analysis indicated that nucleotide at the 2nd codon position would slightly affect synonymous codon choices. Finally, in bryophyte mitochondria, tRNA genes would apply a weak selection force to fine-tune the synonymous codon frequencies, as revealed by data of Ser4-Pro-Thr-Val families. In summary, complex mutation and weak selection together determined the codon usages in bryophyte mitochondrial genomes.

Wang B, Liu J, Jin L, Feng XY, Chen JQ (2010) Complex mutation and weak selection together determined the codon usage bias in bryophyte mitochondrial genomes. J. Integr. Plant Biol. 52(12), 1100–1108.

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