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Holocentromeres can consist of merely a few megabase-sized satellite arrays

Author

Listed:
  • Yi-Tzu Kuo

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Amanda Souza Câmara

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Veit Schubert

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Pavel Neumann

    (Czech Academy of Sciences, Institute of Plant Molecular Biology)

  • Jiří Macas

    (Czech Academy of Sciences, Institute of Plant Molecular Biology)

  • Michael Melzer

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Jianyong Chen

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Jörg Fuchs

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Simone Abel

    (Julius Kühn-Institute (JKI), Institute for Breeding Research on Horticultural Crops)

  • Evelyn Klocke

    (Julius Kühn-Institute (JKI), Institute for Breeding Research on Horticultural Crops)

  • Bruno Huettel

    (Max Planck Institute for Plant Breeding Research)

  • Axel Himmelbach

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Dmitri Demidov

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Frank Dunemann

    (Julius Kühn-Institute (JKI), Institute for Breeding Research on Horticultural Crops)

  • Martin Mascher

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Takayoshi Ishii

    (Tottori University)

  • André Marques

    (Max Planck Institute for Plant Breeding Research)

  • Andreas Houben

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

Abstract

The centromere is the chromosome region where microtubules attach during cell division. In contrast to monocentric chromosomes with one centromere, holocentric species usually distribute hundreds of centromere units along the entire chromatid. We assembled the chromosome-scale reference genome and analyzed the holocentromere and (epi)genome organization of the lilioid Chionographis japonica. Remarkably, each of its holocentric chromatids consists of only 7 to 11 evenly spaced megabase-sized centromere-specific histone H3-positive units. These units contain satellite arrays of 23 and 28 bp-long monomers capable of forming palindromic structures. Like monocentric species, C. japonica forms clustered centromeres in chromocenters at interphase. In addition, the large-scale eu- and heterochromatin arrangement differs between C. japonica and other known holocentric species. Finally, using polymer simulations, we model the formation of prometaphase line-like holocentromeres from interphase centromere clusters. Our findings broaden the knowledge about centromere diversity, showing that holocentricity is not restricted to species with numerous and small centromere units.

Suggested Citation

  • Yi-Tzu Kuo & Amanda Souza Câmara & Veit Schubert & Pavel Neumann & Jiří Macas & Michael Melzer & Jianyong Chen & Jörg Fuchs & Simone Abel & Evelyn Klocke & Bruno Huettel & Axel Himmelbach & Dmitri Dem, 2023. "Holocentromeres can consist of merely a few megabase-sized satellite arrays," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38922-7
    DOI: 10.1038/s41467-023-38922-7
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    References listed on IDEAS

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    1. Peter Eastman & Jason Swails & John D Chodera & Robert T McGibbon & Yutong Zhao & Kyle A Beauchamp & Lee-Ping Wang & Andrew C Simmonett & Matthew P Harrigan & Chaya D Stern & Rafal P Wiewiora & Bernar, 2017. "OpenMM 7: Rapid development of high performance algorithms for molecular dynamics," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-17, July.
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    Cited by:

    1. Yennifer Mata-Sucre & Marie Krátká & Ludmila Oliveira & Pavel Neumann & Jiří Macas & Veit Schubert & Bruno Huettel & Eduard Kejnovský & Andreas Houben & Andrea Pedrosa-Harand & Gustavo Souza & André M, 2024. "Repeat-based holocentromeres of the woodrush Luzula sylvatica reveal insights into the evolutionary transition to holocentricity," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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