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  • Comprehensive Sequencing of Great Ape Sex Chromosomes Yields Insights into Evolution and Genetic Variability

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    Newly generated, complete genomes for the sex chromosomes of six primate species — produced by an international collaboration led by researchers at Penn State and the National Human Genome Research Institute — reveal rapid evolution on the Y chromosome among apes. These results may inform conservation of these endangered species and shed light on sex-related genetic diseases in both humans and our closest living relatives. (Image Credit: Design: Bob Harris; Photography: San Diego Zoo and Tulsa Zoo)


    An international collaborative team led by researchers at Penn State, the National Human Genome Research Institute, and the University of Washington has successfully generated complete reference genomes for the sex chromosomes of five great ape species and one lesser ape species. This groundbreaking research, published in the journal Nature on May 29, reveals significant variability in the Y chromosome among these species, offering new perspectives on sex chromosome evolution and the genetic basis of related diseases.

    Advanced Sequencing Techniques Overcome Previous Limitations
    The team produced complete sequences for the sex chromosomes of chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. These sequences provide a comprehensive map of genes and other chromosomal regions, serving as vital references for future genetic studies. “Researchers sequenced the human genome in 2001, but it wasn’t actually complete,” explained Kateryna Makova, the Verne M. Willaman Chair of Life Sciences and professor of biology at Penn State. “The technology available at the time meant that certain gaps weren’t filled in until a renewed effort led by the Telomere-to-Telomere, or T2T, Consortium in 2022-23.”

    By leveraging the experimental and computational methods developed by the Human T2T Consortium, the researchers addressed the challenges of sequencing the Y chromosome, which contains many repetitive regions. “T2T methods use long-read sequencing technologies that overcome this challenge,” said Karol Pál, Postdoctoral Researcher at Penn State and co-first author of the study. “Combined with advances in computational analysis, on which we collaborated with Adam Phillippy’s group at the NHGRI, 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.”

    High Variability in the Y Chromosome
    The study revealed that the Y chromosome exhibits remarkable variability across the six ape species in size and sequence composition. For instance, the size of the Y chromosome ranges from 30 million DNA letters in siamang to 68 million bases in Sumatran orangutan. In contrast, the X chromosome shows less variability, ranging from 154 million bases in chimpanzees and humans to 178 million bases in gorillas. Additionally, the amount of DNA sequence shared between species is more variable on the Y chromosome. While about 98% of the X chromosome aligns between humans and chimpanzees, only about a third of the Y aligns between them.

    The percentage of the chromosome occupied by repetitive elements also varies significantly on the Y chromosome. Depending on the species, 71% to 85% of the Y chromosomes are composed of repetitive elements, compared to 62% to 66% of the X chromosomes. These percentages are higher than those found in other chromosomes in the human genome.

    Mechanisms Preserving the Y Chromosome
    Despite the Y chromosome’s tendency to shrink, accumulate mutations, and lose genes, it has not disappeared. “We found that the Y chromosome still has a number of genes evolving under purifying selection,” said Makova. “Many of these genes are important for spermatogenesis. This means that the Y chromosome is unlikely to disappear any time soon.”

    The research identified two key strategies that help the Y chromosome preserve its genetic integrity. The first strategy involves genetic redundancy, where multiple copies of the same gene on the chromosome allow intact copies to compensate for those with mutations. The second strategy leverages palindromes, sequences of DNA that read the same forward and backward, enabling self-correction of mutations We found that the Y chromosome can exchange genetic information with itself between the repeated sequences of the two palindrome arms, which fold so that the inverted sequences align,” Pál noted. “This can compensate for the Y’s lack of genetic information exchange with the other chromosomes.”

    Insights from Comparative Genomics
    The researchers uncovered new details about their evolution by comparing the X and Y chromosomes among species and to the previously generated human T2T sequences. The study also collaborated with Michael Schatz’s team at Johns Hopkins University to analyze the sex chromosomes of 129 individual gorillas and chimpanzees. This analysis provided further evidence of purifying selection acting on the Y chromosome.

    “We obtained substantial new information from previously studied gorilla and chimpanzee individuals by aligning their sex chromosome sequencing reads to our new reference sequences,” said Zachary Szpiech, assistant professor of biology at Penn State. “While increasing the sample size in the future will be very helpful to improve our ability to detect signatures of different evolutionary forces, this can be ethically and logistically challenging when working with endangered species, so it is critical that we can get the most out of the data we do have.”

    Future Implications
    The comprehensive sequencing and analysis of ape sex chromosomes not only enhance our understanding of sex chromosome evolution but also provide critical resources for future research. “The powerful combination of bioinformatic techniques and evolutionary analyses that we used allows us to better explain the evolutionary processes acting on sex chromosomes in our closest living relatives, great apes,” said Christian Huber, assistant professor of biology at Penn State. “Additionally, the reference genomes we produced will be instrumental for future studies of primate evolution and human diseases.”

    Publication Details
    Makova, K.D., Pickett, B.D., Harris, R.S. et al. The complete sequence and comparative analysis of ape sex chromosomes. Nature (2024). https://doi.org/10.1038/s41586-024-07473-2

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