Chimpanzees and bonobos diverged comparatively recently in great ape evolutionary history. They split into different species about 1.7 million years ago. Some of the distinctions between chimpanzee (Pan troglodytes) and bonobo (Pan paniscus) lineages have been made clearer by a recent achievement in hominid genomics.
A new bonobo genome assembly has been constructed with a multiplatform
approach and without relying on reference genomes. According to the researchers
on this project, more than 98% of the genes are now completely annotated and
99% of the gaps are closed.
The high quality of this assembly is allowing scientists to more
accurately compare the bonobo genome to that of other great apes - the gorilla,
orangutan, chimpanzee - as well as to the modern human. All these species, as
well as extinct, ancient, human-like beings, are referred to as hominids.
Because chimpanzee and bonobo are also the closest living species to
modern humans, comparing higher-quality genomes could help uncover genetic
changes that set the human species apart.
In a recently published paper in Nature, researchers explain how they
developed and analyzed the new bonobo assembly, and what juxtaposing it to
other great ape genomes is revealing.
The multi-institutional project was led by Yafei Mao, of the Department
of Genome Sciences at the University of Washington School of Medicine in
Seattle, and Claudia R. Catacchio, of the Department of Biology at the
University of Bari, Italy. The senior scientists were Evan Eichler, professor
of genome sciences at the UW School of Medicine, and Mario Ventura of the
University of Bari. Eichler is also a Howard Hughes Medical Institute
investigator.
By comparing the bonobo genome to that of other great apes, the
researchers found more than 5,571 structural variants that distinguished the
bonobo and chimpanzee lineages.
The researchers explained in the paper, "We focused on genes that
have been lost, changed in structure, or expanded in the last few million years
of bonobo evolution."
The great ape genome comparisons are also enabling researchers to gain
new insights on what happened to the various ape genomes during and after the
divergence or splitting apart into different species from a common ancestor.
They were particularly interested in what is called incomplete lineage
sorting. This is the less-than-perfect passing along of alleles into the
separating populations as species diverge, as well as the loss of alleles or
their genetic drift. Analyses of incomplete lineage sorting can help clarify
gene evolution and the genetic relationships among present-day hominids.
The higher-quality bonobo genome assembly enabled the researchers to
generate a higher resolution map comparing incomplete lineage sorting in
hominids. They identified regions that are inconsistent with the species tree.
In addition, they estimate that 2.52% of the human genome is more closely
related to the bonobo genome than the chimpanzee genome, and 2.55% of the human
genome is more closely related to the chimpanzee genome than the bonobo genome.
The total proportion based on incomplete lineage sorting analysis
(5.07%) is almost double earlier estimates (3.1%).
"We predict a greater fraction of the human genome is genetically
closer to chimpanzees and bonobos compared to previous studies," the
researchers note.
The researchers took their incomplete lineage sorting analysis back 15
million years to include genome data from orangutan and gorilla. This increased
the incomplete lineage sorting estimates for the hominid genomes to more than
36.5%, which is only slightly more than earlier predictions.
Surprisingly, more than a quarter of these regions are distributed non-randomly,
have elevated rates of amino acid replacement, and are enriched for particular
genes with related functions such as immunity. This suggests that incomplete
lineage sorting might work to increase diversity for specific regions.
The new bonobo genome assembly is named for the female great ape whose
DNA was sequenced, Mhudiblu, a current resident of the Wuppertal Zoo in
Germany. The researchers estimate that sequence accuracy of the new assembly is
about 99.97% to 99.99%, and closes about 99.5% of the 108,390 gaps in the
previous bonobo assembly.
The bonobo is one of the last great ape genomes to be sequenced with
more advanced long-read genome sequence technologies, the researchers noted.
"Its sequence will facilitate more systematic comparisons between
human, chimpanzee, gorilla and orangutan without the limitations of
technological differences in sequencing and assembly of the original
reference," according to the researchers.
Source: University of Washington
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