Analysis of gene-targeted DNA methylation patterns through the annual cycle in clonal epitypes of Norway spruce

Main goal of the study is to distinguish stable DNA methylation differences from dynamic changes during the annual cycle in different epitypes. We examined whether the extant epigenetic marks created during embryogenesis under EpI-temperature conditions are maintained in the resulting epitype trees. We used unique well-defined clonal epitypes with a stable epigenetic memory of the temperature sum experienced during embryogenesis impacting bud phenology. Due to the massive size of the Norway spruce genome (Nystedt et al., 2013), we used a targeted approach to address the DNA methylation status at a single-base resolution in specific target gene regions of selected genes involved in the epigenetic machinery and adaptive traits formation. From these we have characterized DNA methylation patterns in apical buds for 10 time points throughout the year to observe the differences between epitypes and its dynamics through the annual cycle of development. Overall design: 60 pooled captured bisulfite-converted DNA libraries were sequenced at the BGI Genomics (Hong Kong, China) using DNBSEQ (G-400) sequencing platform with 150PE with 40% in lane control sequencing.