Abstract
The synonymous codons usage shows a characteristic pattern of preference in each organism. This codon usage bias is thought to have evolved for efficient protein synthesis. Synonymous codon usage was studied in genes of the hexaploid wheat Triticum aestivum (AABBDD) and its progenitor species, Triticum urartu (AA), Aegilops tauschii (DD), and Triticum turgidum (AABB). Triticum aestivum exhibited stronger usage bias for G/C-ending codons than did the three progenitor species, and this bias was especially higher compared to T. turgidum and Ae. tauschii. High GC content is a primary factor influencing codon usage in T. aestivum. Neutrality analysis showed a significant positive correlation (p<0.001) between GC12 and GC3 in the four species with regression line slopes near zero (0.16–0.20), suggesting that the effect of mutation on codon usage was only 16–20%. The GC3s values of genes were associated with gene length and distribution density within chromosomes. tRNA abundance data indicated that codon preference corresponded to the relative abundance of isoaccepting tRNAs in the four species. Both mutation and selection have affected synonymous codon usage in hexaploid wheat and its progenitor species. GO enrichment showed that GC biased genes were commonly enriched in physiological processes such as photosynthesis and response to acid chemical. In some certain gene families with important functions, the codon usage of small parts of genes has changed during the evolution process of T. aestivum.
Highlights
In protein synthesis, triplet codons in the mRNA are translated into amino acids to form polypeptide chains
We analyzed the codon bias patterns in T. aestivum and its progenitor species and found that T. aestivum has similar preference in codon usage with T. urartu and that it differs most from T. turgidum. This phenomenon is mainly explained by the similar genomic GC content in T. aestivum and T. urartu (Supplementary Table 1), which considered to be the strongest determinant of codon usage variation caused by mutational processes across species (Muyle et al, 2011; Plotkin and Kudla, 2011)
Codon usage correlates with the cognate tRNA abundance with highly used codons generally having higher intracellular tRNA concentrations than low-use codons (Zalucki et al, 2009)
Summary
Triplet codons in the mRNA are translated into amino acids to form polypeptide chains. From 2 to 6 synonymous codons can be assigned to a specific amino acid, except for methionine and tryptophan, which are encoded only by AUG and UGG, respectively. Such synonymous codons are not used but are instead biased to some optimal codon (Sirihongthong et al, 2019). Codon usage bias reflects a mutation-selection balance, which can be affected by mutation, translational selection, and genetic drift in a population (Shah and Gilchrist, 2011; Duan et al, 2021). Understanding the codon usage bias can reveal the effects of long-term evolution on plant genomes
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