Ensembl Stickleback

Karyotype

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About the Gasterosteus aculeatus genome

Assembly

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.

Annotation

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.

What's New in Ensembl 46

Gasterosteus aculeatus News

There is no Gasterosteus aculeatus-specific news this release.

General News

• Functional genomics
  eFG will contribute the second version of the regulatory build with focus on CD4 T-cells comprising more than 20 different epigenetic factors.
• API changes
  

  The following changes have been made to the Ensembl API.
  Read more...

• ncRNA updates
  ncRNAs have been updated for all chordate species, using models from the new version of Infernal.
• miRNA update
  miRNAs have been updated to be consistent with miRBase 9.2.
• Projections
  

  More species are now in name projections.
  Read more...

More news...

Statistics

* Total number of base pairs = sum of lengths of DNA table

** Reference assembly (Golden path) length = sum of non-redundant top level seq regions