In December 2003, the Broad Institute and the Genome Sequencing Center at the Washington University School of Medicine released a 4X whole genome shotgun (WGS) draft of the Pan troglodytes (chimpanzee) genome (build 1.1). In March 2006, the Chimpanzee Sequencing and Analysis Consortium produced a 6X WGS draft assembly (build 2.1). This assembly includes sequence from the initial 4X chimpanzee WGS assembly along with an additional 2X WGS plasmid reads generated by the Genome Sequencing Center at the Washington University School of Medicine.

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.

We have adopted the NEW chimpanzee chromosome naming system as proposed by McConkey, 2004. This new system renames the chimpanzee chromosomes to correspond to their syntenic human chromosomes. The new system will make comparisons between chimpanzee and human genomes easier to understand.

The NEW chimpanzee chromosome naming system compared to the human chromosome and original chimpanzee chromosome names can be reviewed in this table.

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), was included in build 1 as an alternate assembly. In build 2 it is included in the reference assembly as chromosome 21 and replaces the corresponding WGS sequences of the previous assembly (build 1.1). A 5-Mb region of chromosome 7 was finished by the Genome Sequencing Center at the Washington University School of Medicine in collaboration with David Page's group at the Whitehead Institute. This finished region replaces the corresponding WGS sequences of the previous assembly (build 1.1).

Kuroki et al., 2006 published the sequence of chimpanzee chromosome Y. The assembly of this sequence, CCYSCv1 (The Chimpanzee Chromosome Y Sequencing Consortium assembly version 1), was included in build 2 as an alternate assembly. This chromosome Y alternate assembly sequence came from a single male chimpanzee (Gon) of the subspecies Pan troglodytes verus while the chromosome Y reference assembly sequence came from a single male captive-born chimpanzee (Clint) of the species Pan troglodytes.

chr6_hla_hap1 is an alternate assembly of the chimpanzee chromosome 6 HLA region that aligns better to an alternate haplotype of the human chromosome 6 HLA region than to the HLA region of the human reference assembly.

The NCBI Map Viewer provides graphical displays of features on the chimpanzee genomic sequence data. Current maps display NCBI contigs (the 'Contig' map), WGS sequences (the 'Component' map), genes, CpG islands, Gnomon models, repeats, GenBank sequences, STSs, and RefSeq transcripts. Additional maps will be introduced over time, including chimpanzee ESTs, UniGene, and links to an ideogram, as data becomes available.

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 Ab initio (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.

Available Documentation:

• NCBI Handbook: Map Viewer chapter - resource description
• NCBI Handbook: Map Viewer Exercises - tutorials and examples
• Map Viewer Help - details about navigation and customizing your display
• Genome Assembly - description of genome assembly and annotation process
• Gnomon - description of NCBI's Hidden Markov Model (HMM) ab initio prediction program

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