Abstract
BackgroundAlthough the Ciona intestinalis genome contains many allelic polymorphisms, there is only limited data analyzed systematically. Establishing a dense map of genetic variations in C. intestinalis 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.ResultsHere, we identified over three million candidate short genomic variations within a 110 Mb euchromatin region among five C. intestinalis 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.ConclusionsOur results provide a framework for studying evolution of the animal genome, as well as a useful resource for a wide range of C. intestinalis researchers.
Highlights
The Ciona intestinalis genome contains many allelic polymorphisms, there is only limited data analyzed systematically
Identification of short genetic variations In the present study, we used only high quality regions of raw shotgun reads from three different sets of genomic DNAs, which we used for determining the draft genome sequence of C. intestinalis [1]
If we obtain more sequence data from different individuals in future, more variations would turn out to be shared between the two populations. These data suggest that C. intestinalis possesses a large gene pool, because we found genetic variations taking ~3.3% of the genome from only the five animals of the two populations
Summary
The Ciona intestinalis genome contains many allelic polymorphisms, there is only limited data analyzed systematically. Based on the frequency of allelic polymorphisms of this single animal, the difference between two haplotypes was estimated at 1.2%. Millions of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) have been reported. Allelic polymorphisms within a single individual comprise 0.4% of the genome [5,6]. Higher heterozygosity within individuals has been reported in several invertebrate deuterostomes, including sea urchin (4−5%) [7], amphioxus (4.0%) [8] and two other tunicates (4.5% in Ciona savignyi and 2.2% in Oikopleura dioica) [9,10,11,12,13]
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