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Book Summary:
We use the ascidians, Ciona savignyi and Ciona intestinalis, as model systems to investigate current issues in comparative genomics. First, we develop genomics resources for Ciona savignyi , including a genome sequencing effort. We then characterize the relationship between noncoding sequence constraint and function. We find that the high level of sequence divergence, coupled with virtually identical embryology, makes noncoding sequence comparisons between the Ciona species uniquely sensitive. We then use computational and functional methods to characterize the Ciona muscle-specific regulatory module. We find that conserved clusters of muscle-specific motifs are sensitive predictors of function. We search the C. savignyi genome for conserved motif clusters and find new enhancers with complex expression patterns. Finally, we use five exemplary gene families to examine evolutionary trends of 5′ regions and their corresponding proteins (paralogues and orthologues). We find that constraint in 5′ regions and proteins sequences are highly correlated. This work demonstrates that Ciona has strong potential to solve problems that are of interest to the greater genomics community. |
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