Differences in the Protein Evolutionary Rates of Arabidopsis Species and Codon Usage Biases in the Tissues of Drosophila melanogaster

Abstract

Protein evolution in an organism or population is determined by a host of phenomena that affect the overall rate of change in the genome. Selection is thought to have a decreased effect in self-fertilizing plants due to decreased effective population size. Arabidopsis thaliana transitioned to self-fertilization while its congeners A. lyrata and A. halleri have retained obligatory out-crossing. The rate of protein change, measured as the nonsynonymous to synonymous divergence ratio (dN/dS), showed an increase in evolutionary rate in A. thaliana compared to A. lyrata and A. halleri, likely due to self-fertilization. Preferential codon usage is affected by translational selection, decreasing the rate of synonymous substitution. Preferred codons tend to correspond to the most abundant tRNAs. Codon usage biases differ amongst species and can be different among the tissues of an organism if relative tRNA abundances differ between the different tissues. Previous studies have found that the differences in codon usage biases may also be attributed to GC content and not only to differences in tissue specific protein expression. In the genome of Drosophila melanogaster, I have found that patterns of codon usage are different amongst proteins expressed in different tissues. Using randomized datasets, I show that these differences are always explained by which tissue these genes are expressed in, and are not due to other confounding properties of these proteins, such as GC content, protein length, or protein expression levels.