Relationships of bonobos to humans and other apes can be determined by comparing their genes or whole genomes. While the first bonobo genome was published in 2012, a high-quality reference genome became available only in 2021. The overall nucleotide divergence between chimpanzee and bonobo based on the latter is 0.421 ± 0.086% for autosomes and 0.311 ± 0.060% for the X chromosome. The reference genome predicts 22,366 full-length protein-coding genes and 9,066 noncoding genes, although cDNA sequencing confirmed only 20,478 protein-coding and 36,880 noncoding bonobo genes, similar to the number of genes annotated in the human genome. Overall, 206 and 1,576 protein-coding genes are part of gene families that contracted or expanded in the bonobo genome compared to the human genome, respectively, that is, these genes were lost or gained in the bonobo genome compared to humans.
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