RRC ID 19671
Author Satou Y, Shin-i T, Kohara Y, Satoh N, Chiba S.
Title A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis.
Journal BMC Genomics
Abstract 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.
Volume 13
Pages 208
Published 2012-5-30
DOI 10.1186/1471-2164-13-208
PII 1471-2164-13-208
PMID 22646724
PMC PMC3424144
MeSH Amino Acid Substitution / genetics Animals Base Sequence Chromosomes / genetics Ciona intestinalis / genetics* Databases, Genetic Gene Deletion Genetic Variation* Genome / genetics* INDEL Mutation / genetics Mutagenesis, Insertional / genetics Polymorphism, Single Nucleotide / genetics Reference Standards Reproducibility of Results
IF 3.73
Times Cited 9
WOS Category BIOTECHNOLOGY & APPLIED MICROBIOLOGY GENETICS & HEREDITY
Resource
C.intestinalis / (O.japonicus) Wild C. int