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Higher order repeat structures reflect diverging evolutionary paths in maize centromeres and knobs.

Rebecca D Piri1, Mingyu Wang1, M Cinta Romay2

  • 1Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.

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|February 14, 2026
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Summary
This summary is machine-generated.

Higher-order repeats (HORs) are common in maize satellite DNA. While not linked to centromere function, conserved HOR patterns in knobs may drive meiotic drive, impacting genome evolution.

Keywords:
ArabidopsisCentromereHORKnobsMaizeMeiotic driveSatellite DNA

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Area of Science:

  • Genomics
  • Molecular Biology
  • Plant Science

Background:

  • Satellite DNA, characterized by repetitive tandem arrays, is concentrated in low-recombination genomic areas like centromeres.
  • These satellite arrays can feature complex structures known as higher-order repeats (HORs), potentially influencing their function.
  • Maize exhibits unique satellite DNA distribution in both centromeres (interacting with kinetochore proteins) and knobs (involved in meiotic drive).

Purpose of the Study:

  • To investigate the presence and characteristics of higher-order repeats (HORs) in maize centromeres and knobs.
  • To determine if specific HOR patterns are associated with the functions of maize centromeres and knobs.
  • To understand the potential role of HORs in maize genome evolution and meiotic drive.

Main Methods:

  • Generation of 13 repeat-sensitive genome assemblies for maize and teosinte.
  • Development and application of a novel graph-based pipeline (HiReNET) for HOR classification.
  • Analysis of HOR distribution in centromeric and knob regions using genome assemblies and functional markers.

Main Results:

  • HORs are widespread in maize satellite DNA but typically appear as low-frequency, small patterns, unlike large blocks in human centromeres.
  • Approximately 38% of centromeric CentC monomers are part of HORs, with no single HOR class dominating functional centromeres.
  • Maize knobs display a more organized HOR distribution, with large knobs containing megabase-scale similarity blocks and repeated HOR patterns potentially driving meiotic drive.

Conclusions:

  • Higher-order repeats (HORs) are present across all major maize satellite arrays.
  • No specific HORs are linked to centromere function; however, conserved HOR patterns within knob similarity blocks may facilitate meiotic drive.