The complete sequence and comparative analysis of ape sex chromosomes

Kateryna D. Makova (), Brandon D. Pickett, Robert S. Harris, Gabrielle A. Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C. McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G. Bouffard, Shelise Y. Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E. Cook, Sarah J. C. Craig, Luciana Gennaro, Mark Diekhans, Amalia Dutra, Gage H. Garcia, Patrick G. S. Grady, Richard E. Green, Diana Haddad, Pille Hallast, William T. Harvey, Glenn Hickey, David A. Hillis, Savannah J. Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L. Kosakovsky Pond, Troy M. LaPolice, Charles Lee, Alexandra P. Lewis, Yong-Hwee E. Loh, Patrick Masterson, Kelly M. McGarvey, Rajiv C. McCoy, Paul Medvedev, Karen H. Miga, Katherine M. Munson, Evgenia Pak, Benedict Paten, Brendan J. Pinto, Tamara Potapova, Arang Rhie, Joana L. Rocha, Fedor Ryabov, Oliver A. Ryder, Samuel Sacco, Kishwar Shafin, Valery A. Shepelev, Viviane Slon, Steven J. Solar, Jessica M. Storer, Peter H. Sudmant, Sweetalana, Alex Sweeten, Michael G. Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A. Wilson, Alice C. Young, Huiqing Zeng, Xinru Zhang, Zachary A. Szpiech, Christian D. Huber, Jennifer L. Gerton, Soojin V. Yi, Michael C. Schatz, Ivan A. Alexandrov, Sergey Koren, Rachel J. O’Neill, Evan E. Eichler () and Adam M. Phillippy ()
Additional contact information
Kateryna D. Makova: Penn State University
Brandon D. Pickett: National Institutes of Health
Robert S. Harris: Penn State University
Gabrielle A. Hartley: University of Connecticut
Monika Cechova: University of California Santa Cruz
Karol Pal: Penn State University
Sergey Nurk: National Institutes of Health
DongAhn Yoo: University of Washington School of Medicine
Qiuhui Li: Johns Hopkins University
Prajna Hebbar: University of California Santa Cruz
Barbara C. McGrath: Penn State University
Francesca Antonacci: Università degli Studi di Bari Aldo Moro
Margaux Aubel: University of Münster
Arjun Biddanda: Johns Hopkins University
Matthew Borchers: Stowers Institute
Erich Bornberg-Bauer: University of Münster
Gerard G. Bouffard: National Institutes of Health
Shelise Y. Brooks: National Institutes of Health
Lucia Carbone: Oregon Health and Science University
Laura Carrel: Penn State University School of Medicine
Andrew Carroll: Google
Pi-Chuan Chang: Google
Chen-Shan Chin: Foundation of Biological Data Sciences
Daniel E. Cook: Google
Sarah J. C. Craig: Penn State University
Luciana Gennaro: Università degli Studi di Bari Aldo Moro
Mark Diekhans: University of California Santa Cruz
Amalia Dutra: National Institutes of Health
Gage H. Garcia: University of Washington School of Medicine
Patrick G. S. Grady: University of Connecticut
Richard E. Green: University of California Santa Cruz
Diana Haddad: National Institutes of Health
Pille Hallast: The Jackson Laboratory for Genomic Medicine
William T. Harvey: University of Washington School of Medicine
Glenn Hickey: University of California Santa Cruz
David A. Hillis: University of California Santa Barbara
Savannah J. Hoyt: University of Connecticut
Hyeonsoo Jeong: University of Washington School of Medicine
Kaivan Kamali: Penn State University
Sergei L. Kosakovsky Pond: Temple University
Troy M. LaPolice: Penn State University
Charles Lee: The Jackson Laboratory for Genomic Medicine
Alexandra P. Lewis: University of Washington School of Medicine
Yong-Hwee E. Loh: University of California Santa Barbara
Patrick Masterson: National Institutes of Health
Kelly M. McGarvey: National Institutes of Health
Rajiv C. McCoy: Johns Hopkins University
Paul Medvedev: Penn State University
Karen H. Miga: University of California Santa Cruz
Katherine M. Munson: University of Washington School of Medicine
Evgenia Pak: National Institutes of Health
Benedict Paten: University of California Santa Cruz
Brendan J. Pinto: Arizona State University
Tamara Potapova: Stowers Institute
Arang Rhie: National Institutes of Health
Joana L. Rocha: University of California Berkeley
Fedor Ryabov: Masters Program in National Research, University Higher School of Economics
Oliver A. Ryder: San Diego Zoological Society
Samuel Sacco: University of California Santa Cruz
Kishwar Shafin: Google
Valery A. Shepelev: Institute of Molecular Genetics
Viviane Slon: Tel Aviv University
Steven J. Solar: National Institutes of Health
Jessica M. Storer: University of Connecticut
Peter H. Sudmant: University of California Berkeley
Sweetalana: Penn State University
Alex Sweeten: National Institutes of Health
Michael G. Tassia: Johns Hopkins University
Françoise Thibaud-Nissen: National Institutes of Health
Mario Ventura: Università degli Studi di Bari Aldo Moro
Melissa A. Wilson: Arizona State University
Alice C. Young: National Institutes of Health
Huiqing Zeng: Penn State University
Xinru Zhang: Penn State University
Zachary A. Szpiech: Penn State University
Christian D. Huber: Penn State University
Jennifer L. Gerton: Stowers Institute
Soojin V. Yi: University of California Santa Barbara
Michael C. Schatz: Johns Hopkins University
Ivan A. Alexandrov: Tel Aviv University
Sergey Koren: National Institutes of Health
Rachel J. O’Neill: University of Connecticut
Evan E. Eichler: University of Washington School of Medicine
Adam M. Phillippy: National Institutes of Health

Nature, 2024, vol. 630, issue 8016, 401-411

Abstract: Abstract Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility1. The X chromosome is vital for reproduction and cognition2. Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements—owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species.

Date: 2024
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Citations: View citations in EconPapers (3)

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DOI: 10.1038/s41586-024-07473-2

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