What causes the variations in evolutionary rates is fundamental to molecular evolution. However, in plants, the causes of within-gene evolutionary rate variations remain underexplored. Here we use the principal component regression to examine the contributions of eleven exon features to the within-gene variations in nonsynonymous substitution rate (dN), synonymous substitution rate (dS), and the dN/dS ratio in Arabidopsis species. We demonstrate that exon features related to protein structural-functional constraints and mRNA splicing account for the largest proportions of within-gene variations in dN/dS and dN. Meanwhile, for dS, a combination of expression level, exon length, and structural-functional features explains the largest proportion of within-gene variances. Our results suggest that the determinants of within-gene variations differ from those of between-gene variations in evolutionary rates. Furthermore, the relative importance of different exon features also differs between plants and animals. Our study thus may shed a new light on the evolution of plant genes.
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