Abstract
BACKGROUND: Highly repetitive tandem repeat arrays, known as satellite DNAs, are enriched in low-recombination regions such as centromeres. Satellite arrays often contain complex internal structures called higher-order repeats (HORs), which may have functional significance. Maize is unusual in that its satellites occur in two distinct genomic contexts: centromeres, which interact with kinetochore proteins, and knobs, which undergo meiotic drive in the presence of Abnormal chromosome 10. Whether maize centromeres or knobs contain HOR patterns, and how such patterns relate to function, remains unclear. RESULTS: Here, we generate 13 repeat-sensitive genome assemblies of maize and its recent ancestor, teosinte. We develop a new graph-based pipeline, HiReNET, to classify HORs and demonstrate its utility in both Arabidopsis and maize. We find that HORs are ubiquitous in maize satellites but are typically low-frequency with small patterns, unlike the large, continuous HOR blocks characteristic of human centromeres. Approximately 38% of centromeric CentC monomers occur in HORs; however, no specific HOR class dominates any functional centromere as marked by centromeric histone H3. Arabidopsis centromeres have a similar HOR landscape. In contrast, maize knobs exhibit a more structured HOR distribution. Large knobs contain megabase-scale similarity blocks with repeated HOR patterns. These repeat units likely promote unequal crossing over, enabling rapid knob expansion, and may harbor motifs recognized by trans-acting factors involved in meiotic drive. CONCLUSIONS: HORs occur in all major maize satellite arrays. Specific HORs are not associated with centromere function, but knobs contain conserved HOR patterns within similarity blocks that may facilitate meiotic drive.
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Claims 10
Claim · model-written summary
Thirteen repeat-sensitive genome assemblies of maize and its recent ancestor teosinte were generated.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“maize”
e0“we generate 13 repeat-sensitive genome assemblies of maize and its recent ancestor, teosinte”
Claim · model-written summary
A new graph-based pipeline, HiReNET, was developed to classify higher-order repeats and was shown to work in Arabidopsis and maize.
- Taxon
- Arabidopsis and maize
Arabidopsis
Zea mayse0 - Outcome
- classify HORse0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We develop a new graph-based pipeline, HiReNET, to classify HORs and demonstrate its utility in both Arabidopsis and maize”
Claim · model-written summary
Higher-order repeats are ubiquitous in maize satellites but are typically low-frequency with small patterns.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“HORs are ubiquitous in maize satellites but are typically low-frequency with small patterns”
Claim · model-written summary
About 38% of centromeric CentC monomers in maize occur in higher-order repeats.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“maize”
e0“Approximately 38% of centromeric CentC monomers occur in HORs”
Claim · model-written summary
No specific HOR class dominates any functional centromere (marked by centromeric histone H3) in maize.
- Outcome
- no specific HOR class dominates any functional centromeree0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“maize”
e0“no specific HOR class dominates any functional centromere”
Claim · model-written summary
Arabidopsis centromeres have a similar HOR landscape to maize centromeres.
- Taxon
- ArabidopsisArabidopsise0
- Outcome
- similar HOR landscapee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Arabidopsis centromeres have a similar HOR landscape”
Claim · model-written summary
Maize knobs exhibit a more structured HOR distribution than centromeres.
- Outcome
- more structured HOR distributione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“maize knobs exhibit a more structured HOR distribution”
Claim · model-written summary
Large maize knobs contain megabase-scale similarity blocks with repeated HOR patterns.
- Outcome
- megabase-scale similarity blocks with repeated HOR patternse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“maize”
e0“Large knobs contain megabase-scale similarity blocks with repeated HOR patterns”
Claim · model-written summary
The repeat units in knobs likely promote unequal crossing over, enabling rapid knob expansion.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“maize”
e0“These repeat units likely promote unequal crossing over, enabling rapid knob expansion”
Claim · model-written summary
The repeat units may harbor motifs recognized by trans-acting factors involved in meiotic drive.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“maize”
e0“may harbor motifs recognized by trans-acting factors involved in meiotic drive”