Evidence map›Paper›PMID 42282846›Full record

ArticlebioRxiv : the preprint server for biology2026

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.

Pille Hallast, Arang Rhie, Mark Loftus, Mariateresa Mazzetto, Peter Ebert, Shenghan Gao, Gianni V Martino, Peter A Audano, Hufsah Ashraf, Karol Pal and 39 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

49 authors.

Pille HallastThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0002-0588-3987
Arang RhieGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-9809-8127
Mark LoftusThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0002-6279-6855
Mariateresa MazzettoFaculty of Informatics, Masaryk University, Brno, Czech Republic.ORCID 0009-0003-4281-7270
Peter EbertCore Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0001-7441-532X
Shenghan GaoDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Gianni V MartinoClemson University, Department of Genetics & Biochemistry, Clemson, SC, USA.ORCID 0009-0005-4143-7465
Peter A AudanoThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0002-5187-0415
Hufsah AshrafCenter for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0001-7760-0627
Karol PalDepartment of Biology, Penn State University, University Park, PA, USA.ORCID 0000-0002-7726-4691
Rebecca SifordComparative Genomics and Reproductive Health Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-9786-1338
Jana EblerCenter for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0002-0382-3702
Sergey KorenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-1472-8962
DongAhn YooUniversity of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA.ORCID 0000-0003-0033-3721
Kwondo KimThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0001-8254-528X
Yunzhe JiangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID 0000-0001-8768-0050
Nancy F HansenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-0950-0699
Prajna HebbarUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID 0009-0008-9817-5330
Tomoya KannoDepartment of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, PA, USA.
Oliver PurnochFaculty of Informatics, Masaryk University, Brno, Czech Republic.ORCID 0009-0004-7333-2505
Caroline MontañoDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Jiadong LinUniversity of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA.
Keisuke K OshimaDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Luyao RenUniversity of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA.
Andrea GuarracinoBioinnovation and Genome Sciences, Translational Genomics Research Institute (TGen), part of City of Hope, Phoenix, AZ, USA.ORCID 0000-0001-9744-131X
Matthew JensenDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID 0000-0002-5153-8543
Brendan J PintoComparative Genomics and Reproductive Health Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-4243-5788
David PorubskyUniversity of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA.ORCID 0000-0001-8414-8966
Samuel KuzielFaculty of Informatics, Masaryk University, Brno, Czech Republic.ORCID 0009-0001-9867-9992
Lingbin NiUniversity of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA.
Jiaqi LiDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Parithi BalachandranThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0003-3256-1403
Feyza YilmazThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0001-8795-5800
Human Genome Structural Variation Consortium (HGSVC)
Human Pangenome Reference Consortium (HPRC)
Jan O KorbelEuropean Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID 0000-0001-8863-3539
Mark GersteinDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID 0000-0002-9746-3719
Kateryna D MakovaDepartment of Biology, Penn State University, University Park, PA, USA.ORCID 0000-0002-6212-9526
Xinghua ShiDepartment of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, PA, USA.ORCID 0000-0003-4662-3177
Evan E EichlerUniversity of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA.ORCID 0000-0002-8246-4014
Christine R BeckThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0001-7821-8489
Melissa A WilsonComparative Genomics and Reproductive Health Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-2614-0285
Miriam K KonkelClemson University, Department of Genetics & Biochemistry, Clemson, SC, USA.ORCID 0000-0002-3190-1667
Tobias MarschallCenter for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0002-9376-1030
Monika CechovaFaculty of Informatics, Masaryk University, Brno, Czech Republic.ORCID 0000-0002-7420-2663
Glennis A LogsdonDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID 0000-0003-2396-0656
Adam M PhillippyGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-2983-8934
Charles LeeThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0001-7317-6662

Funding

The AnVIL Data Ecosystem DACReS SupplementU24HG010262 · NHGRI · BROAD INSTITUTE, INC. · PI Robert J Carroll, Jonathan Lawson · 2018 to 2026
$40.5M
Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human GenomesU24HG007497 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Evan Eichler, Jan Oliver Korbel · 2019 to 2026
$17.2M
Single-molecule sequence assembly and analysisZIAHG200398 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI PHILLIPPY, ADAM · 2016 to 2025
$15.9M
Sequence and Assembly of Segmental DuplicationsR01HG002385 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2001 to 2026
$13.3M
Statistical Methods for Gene Regulatory Analysis From Single Cell Genomics DataP20GM139769 · NIGMS · CLEMSON UNIVERSITY · PI MACKAY, TRUDY F. · 2021 to 2025
$10.8M
NRSA Training CoreTL1TR001880 · NCATS · UNIVERSITY OF PENNSYLVANIA · PI MEAGHER, EMMA ANNE · 2016 to 2025
$10.0M
Dockstore: The Community Platform for Reproducible Biomedical Workflows and ApplicationsU24HG011853 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Jonathan Lawson, Benedict Paten · 2021 to 2026
$5.7M
Sequence-resolved structural variation of human genomesR01HG010169 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2018 to 2026
$4.5M
Comprehensive, Flexible and FAIR Tools for the HuBMAP HIVEOT2OD026682 · OD · CARNEGIE-MELLON UNIVERSITY · PI PATEN, BENEDICT, RUFFALO, MATTHEW · 2018 to 2021
$3.4M
The construction and utility of reference pan-genome graphsU01HG010961 · NHGRI · DANA-FARBER CANCER INST · PI LI, HENG, PATEN, BENEDICT · 2020 to 2023
$3.2M
Repetitive sequences drive genome variation and plasticityR35GM133600 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Christine R Beck · 2019 to 2026
$3.0M
Non-B DNA and Genome EvolutionR35GM151945 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI KATERYNA MAKOVA · 2024 to 2026
$2.6M
Intramural NIH HHS ZIA HG200398NCATS NIH HHS TL1 TR001880NHGRI NIH HHS R01 HG002385NHGRI NIH HHS R01 HG010169NHGRI NIH HHS R01 HG014490NHGRI NIH HHS R03 HG014804NHGRI NIH HHS U01 HG010961NHGRI NIH HHS U01 HG013748NHGRI NIH HHS U24 HG007497NHGRI NIH HHS U24 HG010262NHGRI NIH HHS U24 HG011853NIGMS NIH HHS P20 GM139769NIGMS NIH HHS R00 GM147352NIGMS NIH HHS R35 GM133600NIGMS NIH HHS R35 GM151945NIH HHS OT2 OD026682
6 · The paper itself

Abstract

The human Y chromosome is among the most structurally dynamic chromosomes in the human genome, yet much of its diversity remains unresolved because of extensive palindromes, ampliconic gene families, satellite-rich heterochromatin and large segmental duplications. What remained unclear was how these diverse forms of variation fit together across the full chromosome, how often similar structures recur in different lineages, and which aspects of organization remain constrained despite rapid sequence turnover. Here, we generated and analyzed 142 nearly complete human Y chromosome assemblies from 17 major haplogroups spanning approximately 180,000 years of evolution, creating a population-scale resource for studying Y chromosome biology and diversity. These assemblies show that structural change on the Y chromosome is recurrent but constrained, even in its most repetitive regions. In the fertility-associated azoospermia factor c (

Identifiers

PMID42282846
PMCPMC13252187

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