Divergence of cis-regulatory sequences and subgenome dominance in octoploid strawberry

Cultivated strawberry (Fragaria x ananassa) is an allo-octoploid that contains a complete set of homoeologous chromosomes from all four progenitors. Among the four subgenomes (A, B, C, D), the A subgenome, which was derived Fragaria vesca, retains more genes and exhibits higher levels of gene expression than the B/C/D subgenomes. Therefore, strawberry provides a great model system to study subgenome dominance. We developed a genome-wide map of accessible chromatin regions (ACRs) using MNase-hypersensitivity sequencing (MH-seq) in cultivated strawberry. ACRs are known to contain active cis-regulatory DNA sequences (CRSs). The strawberry ACR data were used to investigate subgenome dominance at the transcriptional level. We demonstrate that the dynamics of the ACRs, including sequence variation and mutation, loss of ACRs, and TE interruptions, play an important role in subgenome dominance in strawberry.