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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.
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
Canonical transcripts have been defined for all genes in the core databases.
Read more...
| Assembly: | JGI 2, Mar 2005 |
| Genebuild: | Ensembl, Feb 2006 |
| Database version: | 50.2j |
| Known protein-coding genes: | 666 |
| Novel protein-coding genes: | 13,514 |
| RNA genes: | 282 |
| Genscan gene predictions: | 14,192 |
| Genefinder gene predictions: | 12,384 |
| Gene exons: | 133,519 |
| Gene transcripts: | 19,858 |
| Base Pairs: | 173,499,994 |
| Golden Path Length: | 173,499,994 |
| Most common InterPro domains: | Top 40 Top 500 |
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