Evidence map›Paper›PMID 38077089›Full record

ArticlebioRxiv : the preprint server for biology2023

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 and 73 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed, 24 citations in OpenAlex.

  1. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

83 authors at 20 institutions in 5 countries.

Kateryna D MakovaPenn State University, University Park, PA, USA.
Brandon D PickettNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0001-8235-4440
Robert S HarrisPenn State University, University Park, PA, USA.
Gabrielle A HartleyUniversity of Connecticut, Storrs, CT, USA.ORCID 0000-0002-5672-2171
Monika CechovaUniversity of California Santa Cruz, Santa Cruz, CA, USA.ORCID 0000-0002-7420-2663
Karol PalPenn State University, University Park, PA, USA.
Sergey NurkNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
DongAhn YooUniversity of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0003-0033-3721
Qiuhui LiJohns Hopkins University, Baltimore, MD, USA.ORCID 0009-0004-6740-8040
Prajna HebbarUniversity of California Santa Cruz, Santa Cruz, CA, USA.
Barbara C McGrathPenn State University, University Park, PA, USA.
Francesca AntonacciUniversità degli Studi di Bari Aldo Moro, Italy.
Margaux AubelUniversity of Münster, Münster, Germany.ORCID 0000-0003-1653-9441
Arjun BiddandaJohns Hopkins University, Baltimore, MD, USA.ORCID 0000-0003-1861-1523
Matthew BorchersStowers Institute, Kansas City, MO, USA.
Erich BombergUniversity of Münster, Münster, Germany.ORCID 0000-0002-1826-3576
Gerard G BouffardNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Shelise Y BrooksNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Lucia CarboneOregon Health & Science University, Portland, OR, USA.ORCID 0000-0002-2118-107X
Laura CarrelPenn State University School of Medicine, Hershey, PA, USA.
Andrew CarrollGoogle, Mountain View, CA, USA.ORCID 0000-0002-4824-6689
Pi-Chuan ChangGoogle, Mountain View, CA, USA.ORCID 0000-0003-3021-6446
Chen-Shan ChinFoundation of Biological Data Sciences, Belmont, CA, USA.
Daniel E CookGoogle, Mountain View, CA, USA.ORCID 0000-0003-3347-562X
Sarah J C CraigPenn State University, University Park, PA, USA.
Luciana de GennaroUniversità degli Studi di Bari Aldo Moro, Italy.ORCID 0009-0007-9572-7630
Mark DiekhansUniversity of California Santa Cruz, Santa Cruz, CA, USA.
Amalia DutraNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Gage H GarciaUniversity of Washington School of Medicine, Seattle, WA, USA.ORCID 0009-0005-2383-722X
Patrick G S GradyUniversity of Connecticut, Storrs, CT, USA.
Richard E GreenUniversity of California Santa Cruz, Santa Cruz, CA, USA.ORCID 0000-0003-0516-5827
Diana HaddadNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Pille HallastThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0002-0588-3987
William T HarveyUniversity of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0003-0646-7528
Glenn HickeyUniversity of California Santa Cruz, Santa Cruz, CA, USA.
David A HillisUniversity of California Santa Barbara, Santa Barbara, CA, USA.ORCID 0000-0001-7062-7376
Savannah J HoytUniversity of Connecticut, Storrs, CT, USA.ORCID 0000-0001-7804-3236
Hyeonsoo JeongUniversity of Washington School of Medicine, Seattle, WA, USA.
Kaivan KamaliPenn State University, University Park, PA, USA.
Sergei L Kosakovsky PondTemple University, Philadelphia, PA, USA.
Troy M LaPolicePenn State University, University Park, PA, USA.ORCID 0000-0003-3537-6633
Charles LeeThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0001-7317-6662
Alexandra P LewisUniversity of Washington School of Medicine, Seattle, WA, USA.
Yong-Hwee E LohUniversity of California Santa Barbara, Santa Barbara, CA, USA.ORCID 0000-0002-6185-9279
Patrick MastersonNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Rajiv C McCoyJohns Hopkins University, Baltimore, MD, USA.ORCID 0000-0003-0615-146X
Paul MedvedevPenn State University, University Park, PA, USA.
Karen H MigaUniversity of California Santa Cruz, Santa Cruz, CA, USA.
Katherine M MunsonUniversity of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0001-8413-6498
Evgenia PakNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Benedict PatenUniversity of California Santa Cruz, Santa Cruz, CA, USA.
Brendan J PintoArizona State University, Tempe, AZ, USA.ORCID 0000-0002-4243-5788
Tamara PotapovaStowers Institute, Kansas City, MO, USA.
Arang RhieNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-9809-8127
Joana L RochaUniversity of California Berkeley, Berkeley, CA, USA.
Fedor RyabovMasters Program in National Research University Higher School of Economics, Moscow, Russia.ORCID 0000-0001-8728-9465
Oliver A RyderSan Diego Zoological Society, San Diego, CA, USA.
Samuel SaccoUniversity of California Santa Cruz, Santa Cruz, CA, USA.ORCID 0000-0003-1227-8934
Kishwar ShafinGoogle, Mountain View, CA, USA.ORCID 0000-0001-5252-3434
Valery A ShepelevInstitute of Molecular Genetics, Moscow, Russia.
Viviane SlonTel Aviv University, Israel.ORCID 0000-0001-6485-7159
Steven J SolarNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-3051-9009
Jessica M StorerUniversity of Connecticut, Storrs, CT, USA.
Peter H SudmantUniversity of California Berkeley, Berkeley, CA, USA.ORCID 0000-0002-9573-8248
SweetalanaPenn State University, University Park, PA, USA.ORCID 0009-0000-5450-5934
Alex SweetenNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Michael G TassiaJohns Hopkins University, Baltimore, MD, USA.ORCID 0000-0002-5485-8155
Françoise Thibaud-NissenNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Mario VenturaUniversità degli Studi di Bari Aldo Moro, Italy.ORCID 0000-0001-7762-8777
Melissa A WilsonArizona State University, Tempe, AZ, USA.ORCID 0000-0002-2614-0285
Alice C YoungNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Huiqing ZengPenn State University, University Park, PA, USA.
Xinru ZhangPenn State University, University Park, PA, USA.ORCID 0000-0002-0633-2888
Zachary A SzpiechPenn State University, University Park, PA, USA.ORCID 0000-0001-6372-8224
Christian D HuberPenn State University, University Park, PA, USA.ORCID 0000-0002-2267-2604
Jennifer L GertonStowers Institute, Kansas City, MO, USA.
Soojin V YiUniversity of California Santa Barbara, Santa Barbara, CA, USA.ORCID 0000-0003-1497-1871
Michael C SchatzJohns Hopkins University, Baltimore, MD, USA.
Ivan A AlexandrovTel Aviv University, Israel.ORCID 0000-0003-4342-2003
Sergey KorenNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-1472-8962
Rachel J O'NeillUniversity of Connecticut, Storrs, CT, USA.ORCID 0000-0002-1525-6821
Evan EichlerUniversity of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0002-8246-4014
Adam M PhillippyNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-2983-8934
National Institutes of Health · USPennsylvania State University · USUniversity of California, Santa Cruz · USUniversity of Washington · USJohns Hopkins University · USUniversity of Connecticut · USGoogle (United States) · USStowers Institute for Medical Research · USUniversity of Bari Aldo Moro · ITUniversity of California, Santa Barbara · USArizona State University · USJackson Laboratory · USTel Aviv University · ILUniversity of California, Berkeley · USUniversity of Münster · DEHoward Hughes Medical Institute · USInstitute of Molecular Genetics · RUNational Research University Higher School of Economics · RUOregon National Primate Research Center · USTemple University · US

Funding

Implementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)U24HG010263 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI Enis Afgan, VINCENT JAMES CAREY · 2018 to 2026
$23.8M
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
Sequence and Assembly of Segmental DuplicationsR01HG002385 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2001 to 2026
$13.3M
An Integrative Analysis of Structural Variation for the 1000 Genomes ProjectU41HG007497 · NHGRI · JACKSON LABORATORY · PI LEE, CHARLES · 2013 to 2017
$13.0M
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
Telomere-to-telomere assemblies of human genomesR01HG011274 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Karen Hayden Miga · 2020 to 2026
$4.5M
Population dynamics and medical consequences of sex chromosome evolutionR35GM124827 · NIGMS · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI WILSON, MELISSA A · 2017 to 2024
$2.7M
Computation, Bioinformatics, and Statistics (CBIOS) Training ProgramT32GM102057 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI CHIAROMONTE, FRANCESCA, GIRIRAJAN, SANTHOSH · 2013 to 2022
$2.7M
Non-B DNA and Genome EvolutionR35GM151945 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI KATERYNA MAKOVA · 2024 to 2026
$2.6M
The evolution and diversity of mutation, molecular fidelity, and genome structureR35GM142916 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Peter Heshedahl Sudmant · 2021 to 2026
$2.5M
Comparative Epigenomics of Primate BrainsR01HG011641 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI KONOPKA, GENEVIEVE, SHERWOOD, CHESTER · 2021 to 2024
$2.4M
NCI NIH HHS R01 CA266339NCI NIH HHS U01 CA253481NHGRI NIH HHS R01 HG002385NHGRI NIH HHS R01 HG010169NHGRI NIH HHS R01 HG011274NHGRI NIH HHS R01 HG011641NHGRI NIH HHS U24 HG007497NHGRI NIH HHS U24 HG010263NHGRI NIH HHS U24 HG011853NHGRI NIH HHS U41 HG007497NIGMS NIH HHS R01 GM123312NIGMS NIH HHS R01 GM130691NIGMS NIH HHS R01 GM136684NIGMS NIH HHS R01 GM146462NIGMS NIH HHS R35 GM124827NIGMS NIH HHS R35 GM142916NIGMS NIH HHS R35 GM146886NIGMS NIH HHS R35 GM146926NIGMS NIH HHS R35 GM151945NIGMS NIH HHS T32 GM102057
6 · The paper itself

Abstract

Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.

Identifiers

PMID38077089
PMCPMC10705393
OpenAlexW4389235076

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.