摘要
DNA methylation plays important roles in many biological processes,such as silencing of transposable elements,imprinting and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms(flowering plants). However,few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here,we present the first genome-wide singlebase resolution methylation maps of Norway spruce(Picea abies) from both needles and culture tissues through whole genome bisulfite sequencing. Dense methylation was observed globally across the whole genome,which differed from other plants that only had increased methylation present in their pericentromeric regions. On average,DNA methylation levels of CG and CHG were much higher than most other model plants. Consistent with other plants,CHH methylation was relatively low and at least one copy of Rd DM pathway genes was found in Norway spruce. In comparison to needles,culture tissue showed lower CG and CHG methylation levels but higher CHH methylation,which is inconsistent with other regenerated tissue studies. Similar to other genic DNA methylation studies,global DNA methylation levels were also positively correlated with genome size in plants. Two rounds of GYPSY-type LTR expansions were identified in the history of Norway spruce. This could partly explain the large genome size of the gymnosperms,like Norway spruce,which differ from most of angiosperms in that they have not undergone recent whole genome duplication(WGD). Altogether,the secret of the large genome of Norway spruce could not be explained by reduced DNA methylation levels and reactivation of transposons or whole genome duplication,but it can be partly explained by ancient GYPSY expansions.
DNA methylation plays important roles in many biological processes,such as silencing of transposable elements,imprinting and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms(flowering plants). However,few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here,we present the first genome-wide singlebase resolution methylation maps of Norway spruce(Picea abies) from both needles and culture tissues through whole genome bisulfite sequencing. Dense methylation was observed globally across the whole genome,which differed from other plants that only had increased methylation present in their pericentromeric regions. On average,DNA methylation levels of CG and CHG were much higher than most other model plants. Consistent with other plants,CHH methylation was relatively low and at least one copy of Rd DM pathway genes was found in Norway spruce. In comparison to needles,culture tissue showed lower CG and CHG methylation levels but higher CHH methylation,which is inconsistent with other regenerated tissue studies. Similar to other genic DNA methylation studies,global DNA methylation levels were also positively correlated with genome size in plants. Two rounds of GYPSY-type LTR expansions were identified in the history of Norway spruce. This could partly explain the large genome size of the gymnosperms,like Norway spruce,which differ from most of angiosperms in that they have not undergone recent whole genome duplication(WGD). Altogether,the secret of the large genome of Norway spruce could not be explained by reduced DNA methylation levels and reactivation of transposons or whole genome duplication,but it can be partly explained by ancient GYPSY expansions.
引文
