X and Y chromosome sequences of endangered great apes determined

Geneticists have completed the first “end-to-end” genetic sequencing of the sex chromosomes of 5 species of great ape.

The analyses provide insights into the evolution of the Y chromosome, which is typically present in males, and the X chromosome which is present in both males and females.

The researchers found that more than 90% of the ape X chromosome sequences align to the human X chromosome, which indicates the stable chromosome regions have stayed relatively the same over the course of evolution.

In comparison, the Y chromosome varies greatly across ape species and harbors many species-specific sequences. Only 14% to 27% of the ape Y chromosome aligns to the human Y.

“The extent of the differences between the Y chromosomes of these species was very surprising,” says Kateryna Makova, a biologist at Pennsylvania State University in the US and leader of the study published in Nature.

“Some of these species diverged from the human lineage only seven million years ago, which is not a lot of time in terms of evolution. This shows that the Y chromosomes are evolving very fast.

“Sex chromosomes started like any other chromosome pair, but the Y has been unique in accumulating many deletions, other mutations and repetitive elements because it does not exchange genetic information with other chromosomes over most of its length.”

The team generated the sequences for one individual of each of the species – bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus), and Sumatran orangutan (Pongo abelii). A lesser ape, the siamang gibbon (Symphalangus syndactylus), was studied as an outgroup.

Previous sex chromosome sequences for these species were incomplete or, for the Bornean orangutan and siamang, did not exist. The resulting reference genomes will act as a map to help scientists sequence and assemble genomes of other individuals of the species.

“The Y chromosome has been challenging to sequence because it contains many repetitive regions, and, because traditional technology decodes sequences in short bursts, it is difficult to put the resulting segments in the correct order,” says Karol Pál, a postdoctoral researcher at Penn State and a co-first author of the study.

The researchers used experimental and computational methods developed for the Telomere-to-Telomere (T2T) Consortium, which generated the first complete assembly of a whole human genome.

 “T2T methods use long-read sequencing technologies that overcome this challenge,” says Pál.

“Combined with advances in computational analysis, this allowed us to completely resolve repetitive regions that were previously difficult to sequence and assemble.

“By comparing the X and Y chromosomes to each other and among species, including to the previously generated human T2T sequences of the X and the Y, we learned many new things about their evolution.”

The researchers are currently working to describe the entire genomes of these ape species. But as the closest living relatives to humans, even the X and Y sequences alone can help inform understanding of diseases related to sex chromosomes in both apes and humans.

“The Y chromosome is important for human fertility, and the X chromosome harbours genes critical for reproduction, cognition and immunity,” says Makova.

“Our study opens doors for investigations of sex chromosomes, how they evolved, and diseases associated with them.

“The living non-human great ape species we studied are all endangered. The availability of their complete sex chromosome sequences will facilitate studies of their sex-specific dispersal in the wild and of their genes important for reproduction and fertility.”

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