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 41

Gasterosteus aculeatus News

• Compara - whole genome alignments and syntenies
  

  Whole Genome Alignments

  Chimp (Pan troglodytes)

  Owing to the new Chimp assembly and genebuild, there is a new MLAGAN primate 3-way alignment of human, chimp and macaque.
  Read more...

• RNA updates
  

  Ensembl RNA data has been updated as follows:

  • New ncRNAs for Zebrafish, Chimp, Medaka, Elephant, Rabbit, Armadillo and Tenrec
  • Updated miRNAs for all chordates.

General News

• New animated tutorials
  A selection of Ensembl tutorials are now available online as Flash-animated presentations (with popup notes instead of a soundtrack).
  Read more...
• Compara updates
  

  Homologies

  Gene trees have been updated to include the 2X genomes and use a multifurcating species tree, and homologues added based on gene trees.
  Read more...

• Minor schema changes
  

  analysis_description

  Now has a 'displayable' flag to control whether or not it is usually displayed in the web pages

  xref

  One column has been changed and one added

  • the info_type column has addition ENUM values to give more details about xref provenance
  • A new column 'priority' supports the fetching of xrefs of the same type

  The API has of course been updated to reflect these changes

  .
  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