Organism Data in GenBank
In January 2010, the Broad Institute and the Washington University Genome Sequencing Center released an updated assembly of the Pan troglodytes (chimpanzee) genome - Pan_troglodytes-2.1.4. In comparison to Pan_troglodytes-2.1, this assembly has an additional 300,000 finishing reads and 640 finished BACs as well as approximately 49,000 sequence merges. The DNA for the whole genome shotgun data came from "Clint" - a captive-born descendant of chimpanzees from the West African subspecies Pan troglodytes verus. The DNA for some BAC sequences came from a different male captive-born chimpanzee (Donald). NCBI's build 3.2 includes the Pan_troglodytes-2.1.4 genome assembly, the alternate chromosome Y sequence and assembly CCYSCv1, annotation of these two assemblies, and a complete mitochondrial genome that was derived from a different chimpanzee.
Contigs were assembled using the human genome as a guide, and are therefore "humanized" in their construction. This is an important distinction, as some sequences, such as insertions, deletions, and gene duplications, may not be accurately represented by the current chimpanzee assembly.
Watanabe et al., 2004 published the finished sequence of chimpanzee chromosome 22 (chromosome 21 in the new chromosome naming system). The sequence assembly, ICC22Cv1 (The International Chimpanzee Chromosome 22 Consortium assembly version 1), is included in the reference assembly as chromosome 21 and replaces the corresponding WGS sequences.
A 5-Mb region of chromosome 7 was finished by the Washington University Genome Sequencing Center in collaboration with David Page's group at the Whitehead Institute. This finished 5-Mb region replaces the corresponding WGS sequence of chromosome 7.
The chromosome Y sequence of the Pan_troglodytes-2.1.4 assembly was finished at the Washington University Genome Sequencing Center with detailed mapping and extensive collaboration with David Page's group at the Whitehead Institute. Kuroki et al., 2006 published the sequence of an alternate chromosome Y that came from a single male chimpanzee (Gon) of the subspecies Pan troglodytes verus. This alternate chromosome Y sequence is available as assembly unit CCYSCv1 (the Chimpanzee Chromosome Y Sequencing Consortium assembly version 1).
We have adopted the chimpanzee chromosome naming system proposed by McConkey, 2004. This system renames the chimpanzee chromosomes to correspond to their syntenic human chromosomes. A comparison of the current and former chimpanzee chromosome names and the orthologous human chromosomes can be viewed in this table.
The NCBI Map Viewer provides graphical displays of features on the Pan_troglodytes-2.1.4 assembly. Map features that can be seen along the sequence includes NCBI contigs (the 'Contig' map), WGS sequences (the 'Component' map), and the location of genes, CpG islands, Gnomon predicted gene models, repeats, GenBank sequences, STSs, ESTs, and RefSeq transcripts.
You can find genes or markers of interest by submitting a query against the whole genome, or one chromosome at a time. Results are indicated both graphically, as tick marks on the chromosome, or in a tabular format. The results table includes links to a chromosome graphical view where the gene or marker can be seen in the context of additional data. For genes, a particularly useful display includes Gene and "Model transcripts" (e.g., the Gnomon predicted models). You can also browse a chromosome by clicking on a chromosome link in the ideogram above. Use the "Maps & Options" window, available on individual chromosome displays, to configure your display.
Please note that other genomes can also be viewed in the NCBI Map Viewer resource. The Map Viewer Home Page provides a current list of available genomes. Consider also reviewing the resources listed on the Genomic Biology site.
Last modified: Jun 9 2013