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Bonobo assembly and gene annotation

The bonobo (Pan paniscus), formerly called the pygmy chimpanzee, is an endangered great ape found in the Congo Basin. Along with the common chimpanzee, the bonobo is the closest extant relative to humans.


The panpan1.1 assembly was submitted by Max-Planck Institute for Evolutionary Anthropology on 2015/08/18 . The assembly is on the Chromosome level, consisting of 121,356 assembled into 10,984 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 66,676 while the scaffold N50 is 8,197,324.

Gene annotation

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments. Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.



Assemblypanpan1.1, INSDC Assembly GCA_000258655.2, Aug 2015
Base Pairs3,286,643,896
Golden Path Length3,286,643,896
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2017
Genebuild releasedDec 2017
Genebuild last updated/patchedMar 2020
Database version104.1

Gene counts

Coding genes21,210
Non coding genes8,499
Small non coding genes4,998
Long non coding genes1,497
Misc non coding genes2,004
Gene transcripts53,360


Genscan gene predictions44,965

About this species