Synonymous and nonsynonymous substitutions in genes from Gramineae: Intragenic correlations

In this work, we have investigated the relationships between synonymous and nonsynonymous rates and base composition in coding sequences from Graminea e to analyze the factors underlying the variation in substitutional rates. We have shown that in these genes the rates of nucleotide divergence, both synonymous and nonsynonymous, are, to some extent, dependent on each other and on the base composition. In the first place, the variation in nonsynony mous rate is related to the GC level at the second codon position (the high er the GC(2) level, the higher the amino acid replacement rate). The correl ation is especially strong with T-2, the coefficients being significant in the three data sets analyzed. This correlation between nonsynonymous rate a nd base composition at the second codon position is also detectable at the intragenic level, which implies that the factors that tend to increase the intergenic Variance in nonsynonymous rates also affect the intragenic varia nce. On the other hand, we have shown that: the synonymous rate is strongly correlated with the GC, level. This correlation is observed both across ge nes and at the intragenic level. Similarly, the nonsynonymous rate is also affected at the intragenic level by CC, level, like the silent rate. In fac t, synonymous and nonsynonymous rates exhibit a parallel behavior in relati on to CC, level, indicating that the intragenic patterns of both silent and amino acid divergence rates are influenced in a similar way by the intrage nic variation of GC,. This result,taken together with the fact that the num ber of genes displaying intragenic correlation coefficients between synonym ous and nonsynonymous rates is not very high, but higher than random expect ation (in the three data sets analyzed), strongly suggests that the process es of silent and amino acid replacement divergence are, at least in part, d riven by common evolutionary forces in genes from Gramineae.