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


RESULTS
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.


CONCLUSIONS
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.
Department of Zoology, Graduate School of Science, Kyoto University, Sakyo Kyoto 606-8502, Japan. yutaka@ascidian.zool.kyoto-u.ac.jp
Yutaka
Y
Satou
Tadasu
T
Shin-i
Yuji
Y
Kohara
Nori
N
Satoh
Shota
S
Chiba
D019943:Amino Acid Substitution / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D002875:Chromosomes / Q000235:genetics; D002938:Ciona intestinalis / Q000235:genetics*; D030541:Databases, Genetic; D017353:Gene Deletion; D014644:Genetic Variation; D016678:Genome / Q000235:genetics*; D054643:INDEL Mutation / Q000235:genetics; D016254:Mutagenesis, Insertional / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012015:Reference Standards; D015203:Reproducibility of Results