A test of concerted evolution models using ribosomal RNA genes from the Caenorhabditis elegans genome
LE3 .A278 2013
Bachelor of Science
The eukaryotic genome exhibits extensive evidence of gene duplication events. Typically these duplicated genes share similarity in sequence but have different functions. Being made up of hundreds of identical, tandemly arranged copies, the ribosomal RNA (rRNA) genes are a rare contradiction to the classical model of ‘gene duplication followed by divergence in function’. The maintenance in function and copy number of rRNA genes indicates a type of dependent evolution that is referred to as ‘concerted evolution’. Unequal crossing-over and gene conversion are two known genetic mechanisms that could explain this type of evolution, however, most of the support for these mechanisms is still theoretical. Our hypothesis is that if these mechanisms are operating, the central regions of clusters are more likely to remain identical than cluster edges; therefore sequence degradation near edges should be present. We use the genome of the nematode worm Caenorhabditis elegans as a study tool as its genome sequence is complete and well annotated. Our objectives were to: (1) locate sequence that is adjacent to rRNA gene clusters in the genome using a genome search strategy, (2) find ribosomal DNA-like regions (RDLR) and (3) analyze the positioning, percentage of base-pair matches, and frequencies of RDLR. The program BLAST was used to align published rRNA gene sequence first to the C. elegans genome (in order to find a cluster of rDNA units) then to published genomic sequence adjacent to the cluster (to locate RDLRs). Results indicate that RDLR showing sequence degradation are present next to the cluster, and occur in diminishing frequency and size with distance away from the cluster. This observed gene degradation branching out from the rRNA gene clusters supports the role of unequal crossing-over in rRNA gene evolution and fewer homogenizing events at cluster edges.
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