# The near-complete genome assembly of allotetraploid Pennisetum purpureum ‘Purple’ reveals the genetic and epigenetic landscape of centromeres

## TL;DR

This study provides a detailed genome assembly of a purple Pennisetum plant, revealing how centromeres evolve genetically and epigenetically in polyploid species.

## Contribution

The study presents a near-complete genome assembly of an allotetraploid Pennisetum purpureum and reveals subgenome-specific dynamics of centromeric repeats and epigenetic conservation.

## Key findings

- Subgenome-biased expansion of six LTR retrotransposons drives architectural divergence between subgenomes.
- Centromeric satellite repeats (CentPs) show rapid sequence divergence, while CENH3 binds conserved higher order repeats.
- Centromeric retrotransposons (CRPs) are younger and subgenome B-biased, with insertions linked to satellite DNA polymorphism.

## Abstract

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 Pennisetum purpureum ‘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 Pennisetum (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 Pennisetum 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.