Features of DNA methylome in Capsicum spp

DNA methylation is a most heritable epigenetic modification. Being a major vegetable crop, pepper (Capsicum spp.) possesses an over 3 Gb genome populated with TEs. This indicates a rich reservoir of epigenetic regulatory mechanisms. However, this large and complex genome renders the study of DNA methylation unaffordable and technically challenging. In this study, we analyzed DNA methylome in Capsicum spp., with a focus on C. annuum ST-8. We found that the genomes of Capsicum spp. are heavily methylated, particularly in the non-CG contexts. This is true when comparing to wheat, whose genome is over 16 Gb, containing over 80% TEs and repeats. Interestingly, we observed genic non-CG methylation and found that it is likely maintained by the CMTs, instead of RdDM. Overall, there is a negative relationship between gene expression and H3K9me2, and a positive relationship between genic non-CG methylation and H3K9me2, despite that genes without genic CHH methylation also possess some H3K9me2. Finally, we performed salt stress treatment with and without priming, and profiled active chromatin features as well as transcriptomes. We found that regardless of the environmental stimuli and developmental stages, the overall negative relationship between transcription and H3K9me2 is stably maintained. Altogether, our study revealed features of DNA methylation in ST-8 and we suggest that these features are likely common in Capsicum spp.