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Updated: Jan 14, 2026
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Identifying Mutations by High Resolution Melting in a TILLING Population of Rice
Published on: September 2, 2019
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Genetic diversity and evolution of rice centromeres
Lingjuan Xie1, Yujie Huang1, Wei Huang2
1Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, China.
Nature Genetics
|October 21, 2025
Summary
Rice centromere evolution is driven by structural variations and retrotransposon insertions, not just satellite array changes. Retrotransposons may cause satellite array decline and centromere repositioning.
Area of Science:
- Genetics
- Evolutionary Biology
- Genomics
Background:
- Centromere dynamics are key to eukaryotic evolution and speciation.
- Understanding rice centromere structure and evolution provides insights into plant genome complexity.
Purpose of the Study:
- To investigate the driving forces behind centromere evolution in rice.
- To analyze the structure and dynamics of centromeric satellite arrays in the Oryza AA group.
Main Methods:
- Assembled 67 rice genomes from the Oryza AA group.
- Analyzed over 800 centromeres using de novo annotation of CEN155 sequences.
- Employed a progressive compression strategy to quantify satellite array structures.
- Utilized chromatin immunoprecipitation sequencing for CENH3 enrichment analysis.
Main Results:
- Genetic innovations in rice centromeres stem from structural variations and retrotransposon insertions.
- Rice centromeres exhibit lower single-base substitution rates compared to chromosome arms.
- CEN155 arrays, retrotransposons, and functional centromeres show dynamic yet correlated interactions.
- Evidence suggests retrotransposon invasion may lead to satellite array decline and centromere repositioning.
Conclusions:
- Rice centromere evolution is shaped by a complex interplay of structural variations and retrotransposon activity.
- Retrotransposon invasion is proposed as a mechanism driving centromere repositioning, challenging existing models.
- This study offers a new perspective on the evolutionary dynamics of plant centromeres.
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