241: Wagyu T2T reveals a cattle X neocentromere

Pineda PS et al., Nature Communications - A telomere-to-telomere Wagyu assembly uncovers a natural neocentromere on the cattle X formed by inverted repeats and transposable element expansion, adds hundreds of new genes, and improves variant discovery. Key terms: cattle genomics, neocentromere, centromere evolution, telomere-to-telomere, structural variants.

Study Highlights:
The UOA_Wagyu_1 haplotype-resolved assembly includes a complete X chromosome and four T2T autosomes, adding 431 Mb relative to the ARS-UCD2.0 reference and annotating 738 new protein-coding genes. The cattle X centromere spans ~12 Mb and is a natural neocentromere composed mainly of highly identical inverted repeats and transposable elements, lacking canonical bovine satellite arrays and showing low CENP-A signal. The BTAX centromere exhibits CpG depletion and elevated TpG consistent with TE expansion followed by methylation and CpG deamination, and all 37 centromeric protein-coding genes are expressed in testes. Using UOA_Wagyu_1_Y increased mapping rates for Wagyu reads and enabled discovery of 49,610 structural variants from 20 animals, revealing Wagyu-specific SV and PAV hotspots overlapping genes enriched for olfactory transduction.

Conclusion:
A breed-specific T2T cattle genome reveals a dynamic, TE-rich X neocentromere with testis-expressed genes and substantially improves structural variant discovery for Wagyu populations

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Insights into natural neocentromere evolution from a cattle T2T X chromosome

First author:
Pineda PS

Journal:
Nature Communications

DOI:
10.1038/s41467-025-65778-w

Reference:
Pineda PS, MacPhillamy C, Ren Y, Chen T, Zhong L, Adelson DL, Dessaix C, Perez-Silva J, Haggerty L, Martin FJ, Bottema CDK, Pitchford WS, Rosen BD, Smith TPL, Low WY. Insights into natural neocentromere evolution from a cattle T2T X chromosome. Nature Communications. 2025;16:10745. https://doi.org/10.1038/s41467-025-65778-w

License:
CC BY 4.0 International License

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/wagyu-t2t-x-neocentromere

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-27.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript's core scientific claims as presented in the article, focusing on BTAX assembly, centromere architecture, epigenetics, neocentromere formation, gene content within BTAX, X-Y PAR, and improvements in SV discovery and mapping.
- transcript topics: BTAX assembly and haplotype-resolved X chromosome (UOA_Wagyu_1_Y); BTAX centromere structure: inverted repeats and TE content; absence of bovine satellites; Epigenetic features: CENP-A signal, methylation, CpG/TpG dynamics; Two-step model for neocentromere formation: TE expansion followed by CpG deamination; BTAX centromere gene content: 37 centromere genes, 24 newly identified; testes expression; Wagyu SV discovery and improved mapping rates using the Wagyu reference

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- BTAX centromere is a natural neocentromere located on the cattle X chromosome
- BTAX centromere consists primarily of highly identical inverted repeats and transposable elements
- BTAX centromere lacks bovine satellite repeats
- BTAX centromere exhibits low CENP-A signal and CpG depletion with low methylation relative to TpG dinucleotides
- Two-step model for neocentromere formation: TE expansion followed by CpG deamination
- BTAX contains 37 centromere genes; 24 of these are newly identified; all centromere genes are expressed in testes

QC result: Pass.