The near-complete genome assembly of allotetraploid 'Purple' reveals the genetic and epigenetic landscape of centromeres.
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| Format: | Artículo científico |
| Language: | en |
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Horticulture research
2026
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| _version_ | 1868266079685443584 |
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| author | Huang, Yongji Lin, Jinbin Xu, Jun Lin, Xinyi Deng, Zuhu Zhong, Xiaoxian Zuo, Sheng Zhang, Zhiliang |
| author_facet | Huang, Yongji Lin, Jinbin Xu, Jun Lin, Xinyi Deng, Zuhu Zhong, Xiaoxian Zuo, Sheng Zhang, Zhiliang Huang, Yongji Lin, Jinbin Xu, Jun Lin, Xinyi Deng, Zuhu Zhong, Xiaoxian Zuo, Sheng Zhang, Zhiliang |
| collection | PubMed - marine biology |
| contents | The near-complete genome assembly of allotetraploid 'Purple' reveals the genetic and epigenetic landscape of centromeres. Huang, Yongji Lin, Jinbin Xu, Jun Lin, Xinyi Deng, Zuhu Zhong, Xiaoxian Zuo, Sheng Zhang, Zhiliang Drastic karyotype changes are a major evolutionary force, potentially involving centromere position, number, distribution, or strength alterations. Yet, the genetic and epigenetic landscape of centromeres, especially in allopolyploid plants during subgenome reshuffling, remains poorly understood. Here, we present a near-complete chromosome-scale genome assembly of the allotetraploid 'Purple', resolving all 14 centromeres. We find that subgenome-biased expansion of six LTR retrotransposons drives architectural divergence between subgenomes. Centromeric satellite repeats (CentPs) show rapid sequence divergence across subgenomes and chromosomes, with CENH3 preferentially binding conserved higher order repeats. Intriguingly, centromeric retrotransposons in (CRPs) are evolutionarily younger compared to their noncentromeric counterparts, coupled with marked subgenome B-biased amplification. Notably, CRP insertions flanking CentP satellites correlate with elevated satellite DNA polymorphism, supporting a model wherein CentP homogenization processes actively purge retrotransposons from centromeric arrays. Despite rapid sequence diversification of centromeric repeats, the epigenetic landscapes remain evolutionarily conserved in the centromeres of two subgenomes. Additionally, comparative analyses across species demonstrate rapid species- and chromosome-level turnover of CentPs and CRPs. Overall, our study illuminates the genetic and epigenetic plasticity of centromeres in allopolyploids, revealing how centromeric repeats adapt post-subgenome reshuffling. |
| format | Artículo científico |
| id | pubmed_41756045 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | Horticulture research |
| record_format | pubmed |
| spellingShingle | The near-complete genome assembly of allotetraploid 'Purple' reveals the genetic and epigenetic landscape of centromeres. Huang, Yongji Lin, Jinbin Xu, Jun Lin, Xinyi Deng, Zuhu Zhong, Xiaoxian Zuo, Sheng Zhang, Zhiliang The near-complete genome assembly of allotetraploid 'Purple' reveals the genetic and epigenetic landscape of centromeres. Huang, Yongji Lin, Jinbin Xu, Jun Lin, Xinyi Deng, Zuhu Zhong, Xiaoxian Zuo, Sheng Zhang, Zhiliang Drastic karyotype changes are a major evolutionary force, potentially involving centromere position, number, distribution, or strength alterations. Yet, the genetic and epigenetic landscape of centromeres, especially in allopolyploid plants during subgenome reshuffling, remains poorly understood. Here, we present a near-complete chromosome-scale genome assembly of the allotetraploid 'Purple', resolving all 14 centromeres. We find that subgenome-biased expansion of six LTR retrotransposons drives architectural divergence between subgenomes. Centromeric satellite repeats (CentPs) show rapid sequence divergence across subgenomes and chromosomes, with CENH3 preferentially binding conserved higher order repeats. Intriguingly, centromeric retrotransposons in (CRPs) are evolutionarily younger compared to their noncentromeric counterparts, coupled with marked subgenome B-biased amplification. Notably, CRP insertions flanking CentP satellites correlate with elevated satellite DNA polymorphism, supporting a model wherein CentP homogenization processes actively purge retrotransposons from centromeric arrays. Despite rapid sequence diversification of centromeric repeats, the epigenetic landscapes remain evolutionarily conserved in the centromeres of two subgenomes. Additionally, comparative analyses across species demonstrate rapid species- and chromosome-level turnover of CentPs and CRPs. Overall, our study illuminates the genetic and epigenetic plasticity of centromeres in allopolyploids, revealing how centromeric repeats adapt post-subgenome reshuffling. |
| title | The near-complete genome assembly of allotetraploid 'Purple' reveals the genetic and epigenetic landscape of centromeres. |
| url | https://pubmed.ncbi.nlm.nih.gov/41756045/ |