Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Pille Hallast, Peter Ebert, Mark Loftus, Feyza Yilmaz, Peter A. Audano, Glennis A. Logsdon, Marc Jan Bonder, Weichen Zhou, Wolfram Höps, Kwondo Kim, Chong Li, Savannah J. Hoyt, Philip C. Dishuck, David Porubsky, Fotios Tsetsos, Jee Young Kwon, Qihui Zhu, Katherine M. Munson, Patrick Hasenfeld, William T. Harvey, Alexandra P. Lewis, Jennifer Kordosky, Kendra Hoekzema, Rachel J. O’Neill, Jan O. Korbel, Chris Tyler-Smith, Evan E. Eichler, Xinghua Shi, Christine R. Beck, Tobias Marschall, Miriam K. Konkel and Charles Lee ()
Additional contact information
Pille Hallast: The Jackson Laboratory for Genomic Medicine
Peter Ebert: Heinrich Heine University
Mark Loftus: Clemson University
Feyza Yilmaz: The Jackson Laboratory for Genomic Medicine
Peter A. Audano: The Jackson Laboratory for Genomic Medicine
Glennis A. Logsdon: University of Washington School of Medicine
Marc Jan Bonder: German Cancer Research Center (DKFZ)
Weichen Zhou: University of Michigan Medical School
Wolfram Höps: European Molecular Biology Laboratory (EMBL)
Kwondo Kim: The Jackson Laboratory for Genomic Medicine
Chong Li: Temple University
Savannah J. Hoyt: University of Connecticut
Philip C. Dishuck: University of Washington School of Medicine
David Porubsky: University of Washington School of Medicine
Fotios Tsetsos: The Jackson Laboratory for Genomic Medicine
Jee Young Kwon: The Jackson Laboratory for Genomic Medicine
Qihui Zhu: The Jackson Laboratory for Genomic Medicine
Katherine M. Munson: University of Washington School of Medicine
Patrick Hasenfeld: European Molecular Biology Laboratory (EMBL)
William T. Harvey: University of Washington School of Medicine
Alexandra P. Lewis: University of Washington School of Medicine
Jennifer Kordosky: University of Washington School of Medicine
Kendra Hoekzema: University of Washington School of Medicine
Rachel J. O’Neill: University of Connecticut
Jan O. Korbel: European Molecular Biology Laboratory (EMBL)
Chris Tyler-Smith: Wellcome Sanger Institute, Wellcome Genome Campus
Evan E. Eichler: University of Washington School of Medicine
Xinghua Shi: Temple University
Christine R. Beck: The Jackson Laboratory for Genomic Medicine
Tobias Marschall: Heinrich Heine University
Miriam K. Konkel: Clemson University
Charles Lee: The Jackson Laboratory for Genomic Medicine

Nature, 2023, vol. 621, issue 7978, 355-364

Abstract: Abstract The prevalence of highly repetitive sequences within the human Y chromosome has prevented its complete assembly to date1 and led to its systematic omission from genomic analyses. Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure. Half of the male-specific euchromatic region is subject to large inversions with a greater than twofold higher recurrence rate compared with all other chromosomes2. Ampliconic sequences associated with these inversions show differing mutation rates that are sequence context dependent, and some ampliconic genes exhibit evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, Yq12, is composed of alternating repeat arrays that show extensive variation in the number, size and distribution, but retain a 1:1 copy-number ratio. Finally, our data suggest that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kb away from the currently established1 boundary. The availability of fully sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of traits with specific Y-chromosomal variants and garnering insights into the evolution and function of complex regions of the human genome.

Date: 2023
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DOI: 10.1038/s41586-023-06425-6

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