HUSSAIN, Sofia ; LIVINGSTON, Brian T; University of South Florida; University of South Florida: Codon Usage in a Gene Containing Unusual Repeats within the Coding Region

Repetitive DNA sequences often undergo concerted evolution leading to homogenization though unequal crossover and gene conversion. However base substitution can limit unequal crossing over thereby diversifying each repeat. When the repetitive sequences are found within the coding region of a gene, these processes are also constrained by the need to produce a functional protein. Even so, variation does occur and can lead to disorders characterised by an expansion of repeated area such as Huntington’s disease and spinobulbar muscular atrophy. Here we examine the codon usage in a sea urchin skeletal matrix gene that contains a series of imperfect repeats. Analysis of the repeated region of this gene in a number of different species shows clear evidence of concerted evolution coupled with varying amounts of base substitution. We compare codon usage of the repeat region to both the non-repeat region of the gene and the genome, then among different sea urchin species. Not all sites within the repeats share the same synonymous verses non-synonymous rates of. Biases in codon usage illustrate both where concerted evolution occurred and the effects of base substitution. One group of sea urchins within the genus Strongylocentrotus contains a truncated repeat interspersed within the longer repeats. Although there is base substitution in the areas surrounding this truncated repeat the codon usage is invariant, both within a species and between species that share this type of repeat. This suggests codon usage is important, perhaps for proper translation of the mRNA into protein.