Epigenetic Analyses in Brassica oleracea

Domestication of Brassica oleracea has resulted in an array of starkly contrasting phenotypes that are familiar to us all as common vegetable crops.  The tremendous amount of morphological variation present within B. oleracea is testament to both the polyploid origin and flexibility of its gene expression. Numerous layers of information regulate gene expression, including the interaction among promoters, enhancers, repressors and the general transcription machinery.  Superimposed onto these are additional regulatory mechanisms acting through epigenetic pathways involving DNA methylation, histone modifications and non-coding RNA molecules that together control the expression of complex traits. The recent development of a high quality genome sequence for B. oleracea has heralded the beginning of the post-genomics era for this species and it also serves as a model for its close relatives B. napus and B. carinata.  DNA methylation is an important epigenetic mark that regulates gene expression but the information is not encoded in the primary DNA sequence.  This study focuses on the detection of DNA methylation patterns in B. oleracea.  We describe the application of whole genome bisulfite sequencing and RNA-Seq to characterize global DNA methylation and transcript abundance patterns and discuss the bioinformatics challenges of working within an ancient polyploid crop species.