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
Database version76.1
Base Pairs446,627,861
Golden Path Length461,533,448
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedJun 2006
Genebuild releasedAug 2006
Genebuild last updated/patchedMay 2010

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

20,787
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, tRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

1,617
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

52
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.29,245

Other

Genscan gene predictions44,884