Pongo pygmaeus abelii Photo courtesy of NHGRI (press photos)

UCSC Genome Browser assembly ID: ponAbe2
Sequencing/Assembly provider ID: WUSTL Pongo_abelii-2.0.2
Assembly date: Jul. 2007
NCBI Genome ID: 325 (Pongo abelii)
NCBI Assembly ID: 6678 (P_pygmaeus_2.0.2)
NCBI BioProject ID: 20869

Search the assembly:

• By position or search term: Use the "position or search term" box to find areas of the genome associated with many different attributes, such as a specific chromosomal coordinate range; mRNA, EST, or STS marker names; or keywords from the GenBank description of an mRNA. More information, including sample queries.
• By gene name: Type a gene name into the "search term" box, choose your gene from the drop-down list, then press "submit" to go directly to the assembly location associated with that gene. More information.
• By track type: Click the "track search" button to find Genome Browser tracks that match specific selection criteria. More information.

Download sequence and annotation data:

• Using rsync (recommended)
• Using FTP
• Using HTTP
• Data use conditions and restrictions
• Acknowledgments

Assembly details

The Pongo pygmaeus abelii assembly (6X coverage) consists of whole genome shotgun data from primary donor-derived reads obtained from "Susie", a female Sumatran orangutan housed at the Gladys Porter Zoo in Brownsville, TX. The combined sequence reads were assembled using the PCAP software (Huang, 2003) and filtered for all known non-orangutan sequence contaminants using stringent parameters derived by eliminating detectable global mis-assemblies larger than 50 kb. Mis-assemblies (interchromosomal cross-overs) were determined by aligning the orangutan genome against the human genome. Sequences were obtained from plasmids, fosmids, and BAC-end sequences from CHORI-276, also obtained from "Susie". A fingerprint map with a target of 12X clone coverage is currently in progress.

The assembly data were aligned against the human genome at UCSC (B. Raney) using BLASTZ (Schwartz, 2003) to align and score non-repetitive orangutan regions against repeat-masked human sequence. The alignment chains differentiated between orthologous and paralogous alignments (Kent, 2003), and only "reciprocal best" alignments were retained in the final alignment set. The orangutan AGP files were generated from these alignments in a manner similar to that already described (The Chimpanzee Genome Sequencing and Analysis Consortium, 2005). Documented inversions based primarily on FISH data (Rocchi, personal communication) as well as inversions suggested by the assembly and supported by additional mapping data (e.g. fosmid end sequences against the human assembly, (Chen and Eichler, personal communication)) were introduced. The alignments to human chromosome 2 were separated into organutan chromosomes 2A and 2B. Finally, 78 finished BAC (CHORI-273) clones were integrated into the final chromosomal sequences.

Of the 3.09 Gb of total sequence, 3.08 Gb are ordered and oriented along the chromosomes. Gap sizes between supercontigs were estimated based on their size in human, with a maximum gap size of 30 kb allowed. Click the "Sequences" link above for a list of the chromosomes available in this assembly. The mitochondrial sequence is also available as the virtual chromosome "chrM". For more information about this assembly, see the WUSTL Pongo abelii web page.

GenBank pipeline details

References

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al. Comparative and demographic analysis of orang-utan genomes. Nature. 2011 Jan 27;469(7331):529-33. PMID: 20010809