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

Polyploidy 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 (A(n)) and Brassica oleracea (C-n). 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 (A(n) and C-n), as well as the ancestral fractionated genomes across B. napus seed development. We report ubiquitous C-n subgenome bias of siRNA expression and cytosine methylation, with DNA methylation being particularly abundant on gene promoters in the C-n subgenome. Further, we provide evidence that siRNA transcriptional patterns were conserved within the ancestral triplicated subgenomes of B. napus, but not across the A(n) and C-n 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 C-n subgenome during seed development, and explore the impact of genome fractionation on the epigenetic components of the B. napus seed.

Automated summary

This study investigated the DNA methylation and small RNA expression patterns during seed development in Brassica napus, and found the biased expression and methylation in the C-n subgenome. The results also showed conserved transcription patterns of small RNAs in the ancestral triplicated subgenomes of B. napus, but not in the A(n) and C-n subgenomes. The study discussed the relationship between methylation patterns and genes, promoter regions, small RNA loci, and transposable elements, as well as the impact of genome fractionation and polyploidization on the epigenetic components of the B. napus seed.