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Open Access Open Badges Research article

A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis

Yutaka Satou1*, Tadasu Shin-i2, Yuji Kohara2, Nori Satoh3 and Shota Chiba1

Author Affiliations

1 Department of Zoology, Graduate School of Science, Kyoto University, Sakyo Kyoto 606-8502, Japan

2 National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan

3 Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan

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BMC Genomics 2012, 13:208  doi:10.1186/1471-2164-13-208

Published: 30 May 2012



Although 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.


Here, 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.


Our 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.

Ciona intestinalis; Short genetic variations; Single nucleotide polymorphisms (SNPs); Ascidian