The modern cultivated strawberry (Fragaria x ananassa) originates from interspecific hybridization between two octoploid wild species: F. virginiana and F. chiloensis. However, the differences in centromere characteristics and evolutionary patterns between wild and cultivated octoploids have remained poorly understood.

In a study published in Genome Biology, a research team led by Prof. ZHU Andan from the Kunming Institute of Botany (KIB) of the Chinese Academy of Sciences examined centromere divergence and evolutionary patterns in octoploid strawberries. They achieved this by generating a strawberry CENH3-specific antibody and employing advanced genome assembly techniques.

The researchers evaluated various genome phasing strategies and found that the Trio-binning approach facilitated global phasing with moderate contiguity, while the Hi-C-based method provided local phasing with superior contiguity. By integrating the strengths of both methods, they developed a novel "two-step" phasing assembly pipeline, allowing them to construct a globally phased genome for the octoploid strawberry cultivar "EA78."

Notably, the high-quality genome assembly of "EA78" revealed centromere turnover, with six chromosomes showing a loss of the canonical 147-bp centromeric satellite sequence—an observation confirmed by fluorescence in situ hybridization (FISH) assays.

To further investigate this phenomenon, the researchers used their CENH3-specific antibody to identify six neocentromeres and three new types of centromeric satellites in "EA78." Sequence similarity density analysis between canonical centromeres and neocentromeres indicated a bimodal distribution pattern, suggesting substantial genetic divergence between these two types of centromeres.

Comparative analyses demonstrated that centromere length and satellite abundance significantly expanded in both wild and cultivated octoploids compared to their diploid ancestor, F. vesca. This indicates that hybridization events and domestication processes may collectively drive centromere expansion.

This study provides new insights into the rapid evolution of centromeres in octoploid strawberries, highlighting the dynamic interplay between hybridization, domestication, and centromere plasticity.

The octoploid “EA78” genome assembly and the turnover of centromeric satellites. (Image by KIB)