ArticleNature genetics2025
Genetic diversity and evolution of rice centromeres.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Near-complete genomes for nine haplochromine cichlid fishes reveal a novel centromeric satellite structure organised around a pair of inverted elements.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Evolution and domestication-trait associations of ultra-long centromere haplotypes in pepper plants.Nature ecology & evolution · 2026Article
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- A near-complete genome assembly of onion resolves its genomic architecture, origin, and evolution.Plant communications · 2026Article
- Two telomere-to-telomere Nelumbo genome assemblies reveal domestication history and empower precision breeding.Nature communications · 2026Article
- EasyCen: A Lightweight Framework for Centromere Localisation and Repeat-Organisation Profiling in Telomere-to-Telomere Genomes.Molecular ecology resources · 2026Article
- Gapless and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres.Genome biology · 2026Article
- Telomere-to-telomere genome assembly of Oryza australiensis reveals transposon-driven centromere repositioning and shared EE-DD ancestry.Nature communications · 2026Article
- RIFinder reveals widespread adaptive remote introgression in grass genomes.Plant communications · 2026Article
- High-resolution genome assembly reveals retrotransposon-mediated centromere dynamics in rye.Genome biology · 2025Article
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Authors and funding
15 authors.
Funding
Abstract
Understanding the driving force of centromere dynamics is crucial for deciphering the complexity of eukaryotic evolution and speciation. Here we assembled 67 rice genomes from the Oryza AA group and analyzed >800 nearly complete centromeres. Through de novo annotation of centromeric satellite CEN155 sequences and employing a progressive compression strategy, we quantified the local homogenization and multilayer structures of rice satellite arrays. Our results indicate that genetic innovations in rice centromeres primarily arise from structural variations and centrophilic retrotransposon insertions. The single-base substitution rate in rice centromeres appears to be lower relative to that in chromosome arms. Comparisons of CEN155 arrays, retrotransposons and functional centromeres highlight their dynamic but correlated interplay. Contrary to the KARMA model for Arabidopsis centromere evolution, we propose a hypothesis that retrotransposon invasion probably contributes to the decline of progenitor centromeric satellite arrays and promotes centromere repositioning, as evidenced by extended CENH3 chromatin immunoprecipitation sequencing enrichment beyond the native satellite arrays.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.