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Stickleback assembly and gene annotation

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 Kingsley Lab at Stanford University School of Medicine. 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.

Gene 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.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyBROAD S1, Feb 2006
Base Pairs446,627,861
Golden Path Length461,533,448
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJun 2006
Genebuild releasedAug 2006
Genebuild last updated/patchedMay 2010
Database version94.1

Gene counts

Coding genes20,787
Non coding genes1,617
Small non coding genes1,607
Misc non coding genes10
Pseudogenes52
Gene transcripts29,245

Other

Genscan gene predictions44,884

About this species