Analysis of codon usage in the mitochondrion genome of Spirodela polyrhiza

•Spirodela polyrhiza, an early branching species of monocot, has the most compact monocot mitochondrial genome among flowering plants.•Codon usage of the mitochondrion genome, including context-dependent mutation, has been analyzed.•Correspondence analysis and optimal codons have been analyzed extensively and intensively.•It is useful to understanding the molecular evolution mode of mitochondrion of monocots in a certain scope and degree. In this study, investigation into the characteristics of codon bias and factors in shaping the codon usage pattern of the mitochondrial genome of Spirodela polyrhiza L. Schleid (strain 7498) was performed. S. polyrhiza had a very high GC content of 45.7% in the mitochondrial genome. Compared with other monocots whose mitochondrial genomes have been sequenced, the GC contents of mitochondrial genome of monocots seem to have a decreasing trend as the molecular evolution, and then finally trend to stable at about 44%. The mitochondrion of S. polyrhiz had extremely narrow GC3s distributions from 0.212 to 0.433, if taking no account of SpMatR (0.559) which was the only protein-coding genes with G/C-biased codon usages. The neutrality plot (GC12 vs. GC3s) indicated that there was no correlation between GC12 and GC3s, suggesting there was little directional mutation pressure on the mitochondrial genome of S. polyrhiza. The ENC-plot (ENC vs. GC3s) showed that there were only a small number of genes lying on the expected curve, but a majority of the points with low ENC values lied well below the expected curve. According to the frequency distributions of the ENC ratio, the dataset displayed a single peak, and the most of genes located into a narrow region of ENC ratios between 0–0.1. Context-dependent mutation was analyzed by Chi square test for contingency tables at the four fold degenerate (FFD) sites, suggesting that the frequencies of N3-position bases were definitely not independent of the N2-position bases. Correspondence analysis (COA) of relative synonymous codon usage (RSCU) yielded a first axis which accounted for only13.23% of the total variation. These results suggested that although other factors might play a role in the mitochondrion evolution of S. polyrhiza, mutation press still was the major factor in shaping the codon usage. Meantime, six codons including UUA(Leu), CAU(His), CGU(Arg), AUU(Ile), GCU(Ala) and GAA(Glu) were determined as the “optimal codons” (p