Researchers have generated a new bonobo genome assembly, helping to pinpoint specific variants that distinguish chimpanzee and bonobo lineages.
Closest living species
Chimpanzees and bonobos are among the most-recently diverged ape species (around 1.7 million years ago). They both represent the closest living species to humans. As a result, they offer the potential to identify genetic changes that are specific to humans.
Researchers generated the first bonobo sequence using short-read whole-genome sequencing in 2012. There were over 108,000 gaps, most of which were segmental duplications. In addition, very few structural variants were identified. With the advent of long-read sequencing technologies, our ability to generate contagious, high-quality genomes has improved.
Constructing a bonobo genome assembly
In a recent study, published in Nature, researchers harnessed the power of various sequencing platforms to produce a highly contiguous, accurate bonobo reference genome.
The team generated a bonobo genome assembly of which over 98% of genes were completely annotated and 99% of the gaps were closed. This included the resolution of about half of the segmental duplications and also almost all of the full-length mobile elements.
The researchers compared the bonobo genome to those of other great apes. Here, they identified more than 5,569 fixed structural variants that set the bonobo and chimpanzee lineages apart. The team were particularly interested in exploring incomplete lineage sorting. This refers to when ancestral gene copies fail to come together into a common ancestral copy. Analyses of incomplete lineage sorting can provide insights into gene evolution and also genetic relationships. Using the bonobo assembly, the researchers specifically produced a high-resolution map of incomplete lineage sorting. They estimated that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo genomes and that over 36.5% of the genome shows incomplete lineage sorting. This proportion of incomplete lineage sorting was nearly double previous estimates (3.3%).
Image credit: By USO – canva