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Notes for NCBI chimpanzee build 2.1

Assembly

NCBI's build 2.1 of the chimpanzee genome consists of a reference assembly for the whole genome plus alternate assemblies for some parts of the genome. The reference assembly contains genomic DNA sequence released by the Washington University Genome Sequencing Center in March, 2006 as Pan_troglodytes-2.1 and WGS accession AACZ00000000. The reference assembly contains chromosomes 1-22, X, Y, unplaced contigs, and the reference sequence for the mitochondrial genome.

The sequence assembly ICC22Cv1 (The International Chimpanzee Chromosome 22 Consortium assembly version 1), which was included in build 1.1 as an alternate assembly, is included in the build 2.1 reference assembly as chromosome 21 (chromosome 22 of old naming system) and replaces the corresponding WGS sequence of 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).

Errors in the AGPs for chromosome 8 and chromosome 20 of the Pan_troglodytes-2.1 assembly that were imperfectly corrected resulted in the lengths of two gaps in each chromosome being off by 2 or 3 bases. The NCBI RefSeq and Washington University Genome Sequencing Center (WUGSC) sequences for these chromosomes are identical when gaps are ignored, however, there is a coordinate offset discrepancy for one segment on each chromosome when comparing the NCBI & WUGSC data. Chromosome 8: bases 53973874 to 53996884 in the WUGSC sequence are identical to bases 53973877 to 53996887 in NC_006475.2. Chromosome 20: bases 61022460 to 61024512 in the WUGSC sequence are identical to bases 61022462 to 61024514 in NC_006487.2. Therefore, subtract 3 from any feature between 53973877 and 53996887 on NC_006475.2 to obtain the coordinates of the feature on the WUGSC chromosome 8 sequence and subtract 2 from any feature between 61022462 and 61024514 on NC_006487.2 to obtain the coordinates of the feature on the WUGSC chromosome 20 sequence.

Alternate assembly chr6_hla_hap1 contains genomic DNA sequence that aligns better to an alternate haplotype of the human HLA region than to the human chromosome 6 reference assembly sequence. Alternate assembly CCYSCv1 contains Pan troglodytes verus chromosome Y sequence produced by the Chimpanzee Chromosome Y Sequencing Consortium (see BA000047.1).

Annotation

• Masking: As in the previous build, the NCBI program RepeatMasker was used to mask repetitive genomic sequences before making BLAST hits.
  
  
• Transcript and Protein Alignments: A new program developed at NCBI, ProSplign, is used to generate optimized protein-to-genomic alignments that account for splice site location. ProSplign alignments are now used in the prediction of new gene and pseudogene models, complementing those predicted by Splign. The proteins used consisted of the proteins annotated on human and chimpanzee mRNAs from the RefSeq collection and proteins annotated on human and chimpanzee cDNAs available in GenBank.
  
  
• Predicting Gene Models: In generating gene models, we used human and chimpanzee mRNAs and ESTs.
  
  
• Predicting Splice Variants: Gnomon, NCBI's computational gene annotation program, now predicts splice variants based on both transcript and protein alignments. Splice variant predictions are available in the Ab initio map and a subset that are supported by transcript or protein alignments are instantiated as new models (with XM_ or XR_ accessions) for genes that are not represented by a curated RefSeq (accession prefixes NR_, NM_, or NG_).
  
  
• Alternate Assemblies: Both the reference assembly and the alternate assemblies were annotated using the same process flow and parameters.
  
  
• Sources: Annotations on this build were done using sequences in GenBank and RefSeq databases available on July 20, 2006 (including sequences from the Pan troglodytes subspecies schweinfurthii, troglodytes, vellerosus, and verus).
  
  

Map Viewer

• New Maps: Maps added in build 2.1 include Hs_RNA and Hs_UniGene maps.
  
  

Notes for NCBI chimpanzee build 1.1

This is the initial release of the Chimpanzee genome assembly. It became public at NCBI on Tuesday, November 23, 2004. This version defines the initial assembly and Map Viewer data as of this date.

Annotation

The initial chimpanzee genome build is a composite of whole genome shotgun sequences from clones isolated from Yerkes chimp pedigree #C0471 (Clint). Funding for the sequencing project was provided by NHGRI. The assembly was made public and subsequently aligned to the human genome on December 10, 2003, as announced by NHGRI.

Two groups submitted different assemblies for the same whole genome shotgun (WGS) sequencing project: The Washington University School of Medicine in St. Louis and The Broad Institute. The Washington University (WGS) project has project accession AACZ00000000 and is comprised of accessions AACZ01000001-AACZ01435593. The Broad Institute (WGS) project has project accession AADA00000000 and is comprised of accessions AADA01000001-AADA01361864.

The assembly currently displayed and annotated in Map Viewer is from The Broad Institute.

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 sequence of chimpanzee chromosome 22. Their sequence assembly, ICC22Cv1 (The International Chimpanzee Chromosome 22 Consortium chromosome 21 assembly version 1), was included in build 1 as an alternate assembly. It can be visualized in our chromosome 21 MapViewer window by adding in the assembly. Sequences associated with the publication, per Supplementary Table 1, include AL954200-256, AL954258-59, and BS000001-245.

Map Viewer

We have adopted the NEW chimpanzee chromosome naming system as proposed by McConkey, 2004 and endorsed by the International Chimpanzee Genome Consortium. 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 compared to the human chromosome and original chimpanzee chromosome names can be seen in this table.

The maps availible for the initial release include:

• Ab initio
• Component
• Contig
• CpG Island
• GenBank DNA
• Genes Sequence
• Repeats
• STS
• RNA