This site presents the 6X whole genome shotgun assembly from a female Sumatran orangutan (Pongo pygmaeus abelii) named Susie, housed at the Gladys Porter Zoo (Brownsville, TX). The primary donor-derived reads were assembled using PCAP (Huang, 2006) using stringent parameters; by aligning the orangutan genome against the human genome, it was possible to identify interchromosomal cross-overs and thus eliminate global mis-assemblies larger than 50kb.
Of the 3.09Gb of total sequence, 3.08Gb are ordered and oriented along the chromosomes. Gap sizes between supercontigs were estimated based on their size in human, with a maximum allowed gap size of 30kb.
Due to the high sequence similarity to the human genome, the Orangutan genebuild was based on a projection of human gene structures. The projections were made through chained whole genome BLASTz alignments. These projected genes were combined with orangutan-specific proteins, and additional human genes were added using exonerate where the projection was unable to make satisfactory gene models. UTRs were added using orangutan-specific ESTs and cDNAs as well as human cDNAs.
General information about this species can be found in Wikipedia.
|Assembly||PPYG2, Sep 2007|
|Golden Path Length||3,446,771,396|
|Annotation method||Projection build|
|Genebuild started||Oct 2007|
|Genebuild released||Mar 2008|
|Genebuild last updated/patched||Aug 2012|
|Non coding genes||6,996|
|Small non coding genes||5,796|
|Misc non coding genes||1,200|
|Genscan gene predictions||53,999|