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

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.