The genome of the Western lowland gorilla (Gorilla gorilla ssp. gorilla) has been sequenced at a high level of quality beginning to approach that of the human genome, says a team of scientists led by Prof. Evan Eichler from the University of Washington.
The Western lowland gorilla (Gorilla gorilla ssp. gorilla). Image credit: Jack Hynes / CC BY-SA 3.0.
The first Western lowland gorilla genome was sequenced in 2012.
However, the original genome was highly fragmented, containing 433,861 gaps with missing sequence, and was constructed using the human genome as a guiding reference.
“These gaps are not random, but are clustered at sites of repeats,” Prof. Eichler said.
“If geneticists can’t capture these repeats and determine structural differences in genomes, they have problems understanding the organization of genes and comparing genetic variation within and across species.”
The new assembly, which was carried out de novo (i.e. without any reference information), represents a remarkable decrease in assembly fragmentation.
Prof. Eichler and his colleagues used long-read sequencing technology, along with a unique combination of algorithms, to reconstruct a much more accurate genome, using DNA isolated from a Western lowland gorilla named Susie at the Lincoln Park Zoo in Chicago.
Compared with the old genome, this new assembly has a 96% reduction in contigs, short sequences that may lack information of their location within the genome.
As well, the scientists have closed 94% of the 433,861 sequence gaps that were in the old genome.
They used information from six additional Western lowland gorilla genomes to create a pan-reference genome for use by the scientific community.
“Our results demonstrate the utility of long-read sequence technology to generate high-quality working draft genomes of complex vertebrate genomes without guidance from preexisting reference genomes,” Prof. Eichler and co-authors said.
“The genome assembly that results from using the long-read data provides a more complete picture of gene content, structural variation and repeat biology, as well as allows us to refine population genetic and evolutionary inferences.”
Comparison of Western lowland gorilla and human genome assemblies revealed a total of 117,512 insertions and deletions and 697 inversion variants. More than 86% of these events were previously unidentified.
These results provide a better understanding of genetic variation between our species and our non-human cousins, but also demonstrate ways to sequence other mammalian genomes with better accuracy.
The results were published in the April 1, 2016 issue of the journal Science.
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David Gordon et al. 2016. Long-read sequence assembly of the gorilla genome. Science, vol. 352, no. 6281; doi: 10.1126/science.aae0344
