Four near-complete genome assemblies reveal the landscape and evolution of centromeres in Salicaceae

Abstract

Centromeres play a crucial role in maintaining genomic stability during cell division. They are typically composed of large arrays of tandem satellite repeats, which hinder high-quality assembly and complicate our efforts to understand their evolution across species. Here, we use long-read sequencing to generate near-complete genome assemblies for two Populus and two Salix species belonging to the Salicaceae family and characterize the genetic and epigenetic landscapes of their centromeres. The results show that only limited satellite repeats are present as centromeric components in these species, while most of them are located outside the centromere but exhibit a homogenized structure similar to that of the Arabidopsis centromeres. Instead, the Salicaceae centromeres are mainly composed of abundant transposable elements, including CRM and ATHILA, while LINE elements are exclusively discovered in the poplar centromeres. Comparative analysis reveals that these centromeric repeats are extensively expanded and interspersed with satellite arrays in a species-specific and chromosome-specific manner, driving rapid turnover of centromeres both in sequence compositions and genomic locations in the Salicaceae. Our results highlight the dynamic evolution of diverse centromeric landscapes among closely related species mediated by satellite homogenization and widespread invasions of transposable elements and shed further light on the role of centromere in genome evolution and species diversification.