An Integrated Database of the Ascidian, Ciona intestinalis: Towards Functional Genomics

Abstract An integrated genome database is essential for future studies of functional genomics. In this study, we update cDNA and genomic resources of the ascidian, Ciona intestinalis, and provide an integrated database of the genomic and cDNA data by extending a database published previously. The updated resources include over 190,000 ESTs (672,396 in total together with the previous ESTs) and over 1,000 full-insert sequences (6,773 in total). In addition, results of mapping information of the determined scaffolds onto chromosomes, ESTs from a full-length enriched cDNA library for indication of precise 5′-ends of genes, and comparisons of SNPs and indels among different individuals are integrated into this database, all of these results being reported recently. These advances continue to increase the utility of Ciona intestinalis as a model organism whilst the integrated database will be useful for researchers in comparative and evolutionary genomics.

[1]  B. Degnan,et al.  A genomewide survey of developmentally relevant genes in Ciona intestinalis , 2003, Development Genes and Evolution.

[2]  N. Satoh,et al.  A genomewide survey of developmentally relevant genes in Ciona intestinalis , 2003, Development Genes and Evolution.

[3]  Y. Kohara,et al.  Profiles of maternally expressed genes in fertilized eggs of Ciona intestinalis. , 2001, Developmental biology.

[4]  N. Satoh,et al.  Molecular Cytogenetic Characterization of Ciona intestinalis Chromosomes , 2005, Zoological science.

[5]  Y. Kohara,et al.  Gene expression profiles in Ciona intestinalis tailbud embryos. , 2001, Development.

[6]  Y. Kohara,et al.  Gene expression profiles in tadpole larvae of Ciona intestinalis. , 2002, Developmental biology.

[7]  Michael Levine,et al.  Ciona intestinalis: an emerging model for whole-genome analyses. , 2003, Trends in genetics : TIG.

[8]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[9]  Kimberly Van Auken,et al.  WormBase: a comprehensive data resource for Caenorhabditis biology and genomics , 2004, Nucleic Acids Res..

[10]  Takeshi Kawashima,et al.  A cDNA resource from the basal chordate Ciona intestinalis , 2002, Genesis.

[11]  Nori Satoh,et al.  The ascidian tadpole larva: comparative molecular development and genomics , 2003, Nature Reviews Genetics.

[12]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[13]  Yutaka Satou,et al.  Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks , 2004, Development.

[14]  E. Uberbacher,et al.  Discovering and understanding genes in human DNA sequence using GRAIL. , 1996, Methods in enzymology.

[15]  Takeshi Kawashima,et al.  Large scale EST analyses in Ciona intestinalis: its application as Northern blot analyses. , 2003, Development genes and evolution.

[16]  Lior Pachter,et al.  Intraspecies sequence comparisons for annotating genomes. , 2004, Genome research.

[17]  Y. Kohara,et al.  Ciona intestinalis cDNA projects: expressed sequence tag analyses and gene expression profiles during embryogenesis. , 2002, Gene.

[18]  N. Satoh,et al.  A genomewide survey of developmentally relevant genes in Ciona intestinalis , 2003, Development Genes and Evolution.

[19]  Madeline A. Crosby,et al.  FlyBase: genes and gene models , 2004, Nucleic Acids Res..

[20]  Kanako O. Koyanagi,et al.  Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones , 2004, PLoS Biology.

[21]  M. Levine,et al.  A genomewide survey of developmentally relevant genes in Ciona intestinalis , 2003, Development Genes and Evolution.

[22]  N. Satoh,et al.  Fgf genes in the basal chordate Ciona intestinalis , 2002, Development Genes and Evolution.

[23]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.

[24]  N. Satoh.  Genomic resources for ascidians: sequence/expression databases and genome projects. , 2004, Methods in cell biology.

[25]  Y. Kohara,et al.  Gene expression profiles in young adult Ciona intestinalis , 2002, Development Genes and Evolution.

[26]  Paul Richardson,et al.  The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins , 2002, Science.

[27]  B. Degnan,et al.  A genomewide survey of developmentally relevant genes in Ciona intestinalis , 2003, Development Genes and Evolution.

[28]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.