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This is the first release of the Stickleback genome (Gasterosteus
aculeatus). The genome sequencing and assembly are provided by the
Broad Institute, with
cDNAs and ESTs being provided by the Stanford Human Genome Center.
The assembly has been sequenced by whole-genome shotgun
sequencing with a base coverage of approximately 11x. The stickleback
genome is approximately 460 Mb in length and comprises 22 pairs of
chromosomes (groups) including a mitochondrial chromosome and an
additional 1,822 unplaced supercontigs.
The gene set for stickleback was built using a modified version of the standard Ensembl genebuild pipeline. The majority of gene models are based on genewise alignments of proteins from species genetically distant from stickleback. To improve accuracy, genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. cDNA and EST sequences were used to add UTR to genes with 3' and 5' ESTs from the same clone being paired where possible.
The quality of the gene models was assessed by generating sets of potential orthologs to genes from other species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs and used to improve the gene models. 2,208 cDNAs from Stanford Human Genome Center were used to further assess quality before being incorporated into the final gene set.
There is no Gasterosteus aculeatus-specific news this release.
Only minor changes to the database schema this release:
| Assembly: | BROAD S1, Feb 2006 |
| Genebuild: | Ensembl, Jun 2006 |
| Database version: | 44.1b |
| Known genes: | 71 |
| Novel genes: | 20,808 |
| Pseudogenes: | 52 |
| RNA genes: | 1,265 |
| Genscan gene predictions: | 44,884 |
| Gene exons: | 246,105 |
| Gene transcripts: | 27,723 |
| Base Pairs*: | 446,627,861 |
| Golden Path Length**: | 461,533,448 |
* Total number of base pairs = sum of lengths of DNA table
** Reference assembly (Golden path) length = sum of non-redundant top level seq regions
© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
