| Summary: | <p>Abstract</p> <p>Background</p> <p>Although the <it>Ciona intestinalis</it> genome contains many allelic polymorphisms, there is only limited data analyzed systematically. Establishing a dense map of genetic variations in <it>C. intestinalis</it> is necessary not only for linkage analysis, but also for other experimental biology including molecular developmental and evolutionary studies, because animals from natural populations are typically used for experiments.</p> <p>Results</p> <p>Here, we identified over three million candidate short genomic variations within a 110 Mb euchromatin region among five <it>C. intestinalis</it> individuals. The average nucleotide diversity was approximately 1.1%. Genetic variations were found at a similar density in intergenic and gene regions. Non-synonymous and nonsense nucleotide substitutions were found in 12,493 and 1,214 genes accounting for 81.9% and 8.0% of the entire gene set, respectively, and over 60% of genes in the single animal encode non-identical proteins between maternal and paternal alleles.</p> <p>Conclusions</p> <p>Our results provide a framework for studying evolution of the animal genome, as well as a useful resource for a wide range of <it>C. intestinalis</it> researchers.</p>
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