Evidence of selectively driven codon usage in rice: Implications for GC content evolution of Gramineae genes

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Abstract
Two gene classes characterized by high and low GC content have been found in rice and other cereals, but not dicot genomes. We used paralogs with high and low GC contents in rice and found: (a) a greater increase in GC content at exonic fourfold‐redundant sites than at flanking introns; (b) with reference to their orthologs in Arabidopsis, most substitution sites between the two kinds of paralogs are found at 2‐ and 4‐degenerate sites with a T → C mode, while A → C and A → G play major roles at 0‐degenerate sites; and (c) high‐GC genes have greater bias and codon usage is skewed toward codons that are preferred in highly expressed genes. We believe this is strong evidence for selectively driven codon usage in rice. Another cereal, maize, also showed the same trend as in rice. This represents a potential evolutionary process for the origin of genes with a high GC content in rice and other cereals.