Ensembl C.intestinalis

Karyotype

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About the Ciona intestinalis genome

Assembly

Ciona intestinalis version 2.0 [details] is a whole genome shotgun assembly released by the JGI. The Ciona intestinalis genome is the smallest of any experimentally manipulable chordate, and thus provides a good system for exploring vertebrate evolutionary origins. This Ensembl website presents the sequence data provided by the JGI, with additional Ensembl genebuild (see below).

The assembly release version 2.0 of the whole genome shotgun reads was constructed with the JAZZ assembly, using paired end sequencing reads. Starting with a coverage of 11x, additional data--including BAC and FISH markers--were used to map scaffolds to chromosome arms. The current size of the assembly which includes unmapped scaffolds is 173Mb with 94Mb of the assembly mapped to chromosome arms.

Annotation

The standard Ensembl mammalian pipeline was modified for annotation of the Ciona genome, owing to the lack of genomic information from closely-related species. Thus, in addition to aligning known Ciona proteins to the sequence (as per the standard pipeline), we aligned the large quantities of Ciona-specific cDNA and EST sequences against the genome, and then used protein data from other species to build additional gene models.

Photo: www.ascidians.com

What's New in Ensembl 39

Ciona intestinalis News

There is no Ciona intestinalis-specific news this release.

General News

• Bug fixes
  In order to fix some problems with the store() method in Gene and Transcript, DBEntryAdaptor and AttributeAdaptor now require a gene/transcript/translation dbID rather than object as one of their arguments (please see POD for details).
• Multiple versions of genes
  The schema and API have been changed to allow multiple versions of genes, transcripts and exons, for better integration with Otter (the Ensembl-based database schema used as a backend for Havana).
  Read more...
• New MLAGAN groups
  A new 3-way MLAGAN Primate group has been created, containing Human, Chimp and macaque.
  Read more...
• Compara - whole genome alignments, syntenies and families
  

  Whome Genome Alignments.
  Read more...

• Gene Homology Trees
  

  Orthologues/paralogues are now based on gene trees, which has required a number of changes in the compara schema and API.

  3 new tables have been added.
  Read more...

More news...

Statistics

Assembly:	JGI2, Mar 2005
Genebuild:	Ensembl, Jan 2006
Database version:	39.2b
Known genes:	666
Novel genes:	13,612
RNA genes:	248
Genscan gene predictions:	14,192
Genefinder gene predictions:	12,384
Gene exons:	134,008
Gene transcripts:	20,000
Base Pairs:	173,499,994
Golden Path Length:	173,460,342
Most common InterPro domains:	Top 40 Top 500