Genomic asymmetry of the Brassica napus seed: epigenetic contributions of DNA methylation and small RNAs to subgenome bias

Abstract

SUMMARYPolyploidy is a persistent phenomenon in angiosperm genome evolution that is hypothesized to have contributed to the diversity of extant flowering plants. Brassica napus, one of the world's most important angiosperm oilseed species, originated from the interspecific hybridization of Brassica rapa (An) and Brassica oleracea (Cn). While the trends of genome dominance in transcriptomics are beginning to emerge, less is known about the epigenetic and small RNA landscapes in polyploids during reproductive development. The seed is the pivotal developmental transition into the new sporophytic generation, and experiences substantial epigenetic modifications over time. Here, we investigated the prevalence of bias in the contexts of DNA methylation and small interfering (si)RNA profiles in both subgenomes (An and Cn), as well as the ancestral fractionated genomes across B. napus seed development. We report ubiquitous Cn subgenome bias of siRNA expression and cytosine methylation, with DNA methylation being particularly abundant on gene promoters in the Cn subgenome. Further, we provide evidence that siRNA transcriptional patterns were conserved within the ancestral triplicated subgenomes of B. napus, but not across the An and Cn subgenomes. We discuss how methylation patterns in the B. napus seed relate to genes, promoter regions, siRNA loci and transposable elements through the lens of genome fractionation and polyploidization. Taken together we provide evidence for epigenetic regulation selectively silencing the Cn subgenome during seed development, and explore the impact of genome fractionation on the epigenetic components of the B. napus seed.