Evidence map›Paper›PMID 41315353›Full record

ArticleNature communications2025

Insights into natural neocentromere evolution from a cattle T2T X chromosome.

Paulene S Pineda, Callum MacPhillamy, Yan Ren, Tong Chen, Luan Zhong, David L Adelson, Carey Dessaix, Jose Perez-Silva, Leanne Haggerty, Fergal J Martin and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. 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.

  1. Article
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

15 authors.

Paulene S Pineda *Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia.
Callum MacPhillamy *Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia.
Yan Ren *Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia.
Tong ChenDavies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia.ORCID http://orcid.org/0000-0002-7681-9632
Luan ZhongSchool of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
David L AdelsonSchool of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.ORCID http://orcid.org/0000-0003-2404-5636
Carey DessaixSchool of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
Jose Perez-SilvaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0003-4421-3676
Leanne HaggertyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Fergal J MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Cynthia D K BottemaDavies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia.
Wayne S PitchfordDavies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia.
Benjamin D RosenAnimal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD, USA.ORCID http://orcid.org/0000-0001-9395-8346
Timothy P L SmithUS Meat Animal Research Center, ARS USDA, Clay Center, NE, USA.ORCID http://orcid.org/0000-0003-1611-6828
Wai Y LowDavies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia. wai.low@adelaide.edu.au.ORCID http://orcid.org/0000-0002-0749-765X

Funding

Wellcome Trust
6 · The paper itself

Abstract

The cattle genome is crucial for understanding ruminant biology, but it remains incomplete. Here we present a telomere-to-telomere haplotype-resolved X chromosome and four autosomes of cattle in a near-complete assembly that is 431 Mb (16%) longer than the current reference genome. Using this assembly (UOA_Wagyu_1) we identify 738 new protein-coding genes and support the characterization of centromeric repeats, identification of transposable elements, and enabled the detection of 2397 more structural variants from 20 Wagyu animals than using ARS-UCD2.0. We find that the cattle X centromere is a natural neocentromere with highly identical inverted repeats, no bovine satellite repeats, low CENP-A signal, low methylation, and low CpG content, in contrast to the autosomal centromeres that are comprised of typical bovine satellite repeats and epigenetic features. Our results suggest it likely formed from transposable element expansion and CpG deamination, suggesting dynamic evolution. We find eighteen X-pseudoautosomal region genes have conserved testes expression between cattle and apes. We also find all cattle X neocentromere protein-coding genes are expressed in testes, which suggests they potentially play a role in reproduction.

Indexed as

CentromereEvolution, MolecularX ChromosomeAnimalsCattleCpG IslandsDNA MethylationDNA Transposable ElementsHaplotypesMaleTelomereDNA Transposable Elements

Identifiers

PMID41315353
PMCPMC12663436

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.