On Jan 21, 2010 this sequence version replaced gi:89888069.
The Pan troglodytes whole genome shotgun (WGS) project has the project accession AACZ00000000. This version of the project (03) has the accession number AACZ03000000, and consists of sequences AACZ03000001-AACZ03192898.
This assembly, version 2.1.4, has an updated chromosome Y compared to version 2.1.3. Assembly 2.1.3 represented an improvement on the 2.1 chimp assembly by adding in over 300,000 finishing reads, and merging in 640 finished BACS. There were approximately 49,000 additional merges made in that assembly as compared to the 2.1 assembly.
Sequencing/Assembly: The whole genome shotgun sequence data were assembled and organized by the Washington University Genome Center. The underlying whole genome shotgun data were generated at the Washington University School of Medicine and the Broad Institute. A 5 megabase region of chromosome 7 was finished at the Washington University Genome Sequencing Center (chr7:84674857-89461887). The chromosome Y sequence was finished at the Washington University Genome Sequencing Center with detailed mapping and extensive collaboration with David Page's group at the Whitehead Institute (The DNA Sequence of Chimpanzee Chromosome Y, unpublished; Hughes et al., Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature, 2005 437:100-3; PMID:16136134). The chromosome 21 sequence data was kindly provided by Todd Taylor and the Riken Genome Sciences Center (Watanabe et al., DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature. 2004 May27;429(6990):382-8. PMID: 15164055).
This assembly covers about 97 percent of the genome and is based on 6X sequence coverage. It is composed of 192,898 contigs with an N50 length of 44kb, and 33,990 supercontigs with an N50 length of 8.4 Mb.
The whole genome shotgun data from primary donor-derived reads (Clint, a captive-born male chimpanzee from the Yerkes Primate Research Center (Atlanta, USA)) were assembled using PCAP (Huang 2006) using stringent parameters derived by eliminating detectable global mis-assemblies (interchromosomal cross-overs determined by alignment of the chimpanzee genome against the human genome) larger than 50kb.
The assembly data were aligned against the human genome at UCSC (B. Raney) utilizing BLASTZ (Schwartz 2003) to align and score non-repetitive chimpanzee regions against repeat-masked human sequence. Alignment chains differentiated between orthologous and paralogous alignments (Kent 2003) and only 'reciprocal best' alignments were retained in the alignment set. The chimpanzee AGP files were generated from these alignments in a manner similar to that already described (The Chimpanzee Genome Sequencing Consortium 2005). Centromeres were introduced into the chimp sequence at the positions of the centromeres in the human chromosomes. Ten documented/known human inversions (Yunis 1982) supported by the assembly were introduced into the ordering as was the separation of alignments to human chromosome 2 into chimpanzee chromosomes 2A and 2B. We removed the contigs from the WGS project that corresponded to the finished chromosome 21 and chromosome Y sequences as well as the contig corresponding to chromosome 7 because they are represented by the corresponding finished sequences. The chromosome 21 sequence is GenBank Accession Number BA000046 and the chromosome Y sequence is GenBank Accession Number DP000054.
The Nov. 2010 version of chromosome 7, CM000321.3, is assembled from BACs plus contigs of the previous version of the WGS project, AACZ02000000. With the release of CM000321.3, nearly 700 unlocalized chromosome 7 scaffolds that were redundant with the new chr7 were suppressed and some AACZ03000000 contigs are not part of assembly Pan_troglodytes-2.1.3 or Pan_troglodytes-2.1.4.
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