PICKLE RELATED 2 is a neofunctionalised gene duplicate under positive Darwinian selection with antagonistic effects to the ancestral PICKLE gene on the seed transcriptome

The evolution and diversification of proteins capable of remodelling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodelling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologues have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast-evolving under positive selection, while PKL is evolving under purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein’s intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis of gene expression in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights on gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants. To investigate the relative evolution and changing roles of the chromatin remodelers PKR2 and PKL, we analyzed the transcriptome of developing seeds (3 DAP) from simple mutants pkl-1 and pkr2-2 as well as from the double mutant pkl-10;pkr2-2. All transcriptomic data was compared to the Wild-type Col-0.