Coding sequence divergence between two closely related plant species: Arabidopsis thaliana and Brassica rapa ssp. pekinensis

To characterize the coding-sequence divergence of closely related genomes, we compared DNA sequence divergence between sequences from a Brassica rapa ssp. pekinensis EST library isolated from flower buds and genomic sequences from Arabidopsis thaliana. The specific objectives were (i) to determine the distribution of and relationship between K_a and K_s, (ii) to identify genes with the lowest and highest K_a:K_s values, and (iii) to evaluate how codon usage has diverged between two closely related species. We found that the distribution of K_a:K_s was unimodal, and that substitution rates were more variable at nonsynonymous than synonymous sites, and detected no evidence that K_a and K_s were positively correlated. Several genes had K_a:K_s values equal to or near zero, as expected for genes that have evolved under strong selective constraint. In contrast, there were no genes with K_a:K_s > 1 and thus we found no strong evidence that any of the 218 sequences we analyzed have evolved in response to positive selection. We detected a stronger codon bias but a lower frequency of GC at synonymous sites in A. thaliana than B. rapa. Moreover, there has been a shift in the profile of most commonly used synonymous codons since these two species diverged from one another. This shift in codon usage may have been caused by stronger selection acting on codon usage or by a shift in the direction of mutational bias in the B. rapa phylogenetic lineage.