Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures
Abstract
The human Y chromosome remains underrepresented in genomic resources because its repetitive architecture is difficult to resolve and poorly represented by any single reference. Here, we present 142 curated near-complete de novo Y chromosome assemblies spanning 98 terminal-marker-defined lineages across 17 haplogroup clades and 180,000 years of evolution, establishing a population-scale sequence and annotation resource for the chromosome. Across 100 quality-filtered AZFc intervals, recurrent inversions, deletions and complex rearrangements resolve into 12 structural haplotypes, while DAZ, RBMY and TSPY families show distinct paralogue- and array-specific evolution. Complete centromere and Yq12 sequences reveal extensive lineage-specific change within comparatively stable higher-order architectures, and haplotype-resolved methylomes show distinct epigenetic states among similar repeat copies. The reference panel reduces analytical bias: in testis Iso-Seq data, the best-matching assembly increased median DAZ transcript alignment identity from 91.7% to 99.9% and improved isoform annotation. Together, this resource enables analysis of Y-chromosome structural, evolutionary and reproductive variation.
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BibTeX
@misc{hallast2026populationscale,
title = {{Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures}},
author = {P. Hallast and A. Rhie and M. Loftus and M. Mazzetto and P. Ebert and S. Gao and G. V. Martino and P. A. Audano and H. Ashraf and K. Pal and R. Siford and J. Ebler and S. Koren and D. Yoo and K. Kim and Y. Jiang and N. F. Hansen and P. Hebbar and T. Kanno and O. Purnoch and C. Montano and J. Lin and K. K. Oshima and L. Ren and A. Guarracino and M. Jensen and B. J. Pinto and D. Porubsky and S. Kuziel and L. Ni and J. Li and P. Balachandran and F. Yilmaz and Human Genome Structural Variation Consortium (HGSVC) and Human Pangenome Reference Consortium (HPRC) and J. O. Korbel and B. Paten and M. Gerstein and K. D. Makova and X. Shi and E. Eichler and C. R. Beck and M. Wilson},
howpublished = {bioRxiv},
year = {2026},
month = jun,
doi = {10.64898/2026.06.03.729890},
url = {https://www.biorxiv.org/content/10.64898/2026.06.03.729890v2},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures
AU - P. Hallast
AU - A. Rhie
AU - M. Loftus
AU - M. Mazzetto
AU - P. Ebert
AU - S. Gao
AU - G. V. Martino
AU - P. A. Audano
AU - H. Ashraf
AU - K. Pal
AU - R. Siford
AU - J. Ebler
AU - S. Koren
AU - D. Yoo
AU - K. Kim
AU - Y. Jiang
AU - N. F. Hansen
AU - P. Hebbar
AU - T. Kanno
AU - O. Purnoch
AU - C. Montano
AU - J. Lin
AU - K. K. Oshima
AU - L. Ren
AU - A. Guarracino
AU - M. Jensen
AU - B. J. Pinto
AU - D. Porubsky
AU - S. Kuziel
AU - L. Ni
AU - J. Li
AU - P. Balachandran
AU - F. Yilmaz
AU - Human Genome Structural Variation Consortium (HGSVC)
AU - Human Pangenome Reference Consortium (HPRC)
AU - J. O. Korbel
AU - B. Paten
AU - M. Gerstein
AU - K. D. Makova
AU - X. Shi
AU - E. Eichler
AU - C. R. Beck
AU - M. Wilson
PY - 2026
DA - 2026/06/03
PB - bioRxiv
DO - 10.64898/2026.06.03.729890
UR - https://www.biorxiv.org/content/10.64898/2026.06.03.729890v2
AB - The human Y chromosome remains underrepresented in genomic resources because its repetitive architecture is difficult to resolve and poorly represented by any single reference. Here, we present 142 curated near-complete de novo Y chromosome assemblies spanning 98 terminal-marker-defined lineages across 17 haplogroup clades and 180,000 years of evolution, establishing a population-scale sequence and annotation resource for the chromosome. Across 100 quality-filtered AZFc intervals, recurrent inversions, deletions and complex rearrangements resolve into 12 structural haplotypes, while DAZ, RBMY and TSPY families show distinct paralogue- and array-specific evolution. Complete centromere and Yq12 sequences reveal extensive lineage-specific change within comparatively stable higher-order architectures, and haplotype-resolved methylomes show distinct epigenetic states among similar repeat copies. The reference panel reduces analytical bias: in testis Iso-Seq data, the best-matching assembly increased median DAZ transcript alignment identity from 91.7% to 99.9% and improved isoform annotation. Together, this resource enables analysis of Y-chromosome structural, evolutionary and reproductive variation.
ER -