title: DNA methylome of the 20-gigabase Norway spruce genome.
abstract: 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 genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.
authors.affiliation: Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Israel
authors.initials: I
authors.lastname: Ausin
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095.|Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095.
authors.forename: Suhua
authors.initials: S
authors.lastname: Feng
authors.affiliation: State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Chaowei
authors.initials: C
authors.lastname: Yu
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095.|Molecular Biology Institute, University of California, Los Angeles, CA 90095.
authors.forename: Wanlu
authors.initials: W
authors.lastname: Liu
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095.
authors.forename: Hsuan Yu
authors.initials: HY
authors.lastname: Kuo
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095.
authors.forename: Elise L
authors.initials: EL
authors.lastname: Jacobsen
authors.affiliation: Department of Biology, South University of Science and Technology, Shenzhen 518055, China.
authors.forename: Jixian
authors.initials: J
authors.lastname: Zhai
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095.
authors.forename: Javier
authors.initials: J
authors.lastname: Gallego-Bartolome
authors.affiliation: State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Wang
authors.affiliation: Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea SE-901 84, Sweden.
authors.forename: Ulrika
authors.initials: U
authors.lastname: Egertsdotter
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umea SE-901 87, Sweden.
authors.forename: Nathaniel R
authors.initials: NR
authors.lastname: Street
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095; jacobsen@ucla.edu haifengwang@fafu.edu.cn.|Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095.|Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
authors.affiliation: Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; jacobsen@ucla.edu haifengwang@fafu.edu.cn.|State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Wang
mesh_terms: D001483:Base Sequence; D002478:Cells, Cultured; D017124:Conserved Sequence; D032462:Cycadopsida / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism*; D018745:Genome, Plant; D010802:Phylogeny; D028222:Picea / Q000196:embryology / Q000235:genetics* / Q000378:metabolism*; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism
chemical_list: D018744:DNA, Plant
keywords: DNA methylation; Norway spruce; genome size; gymnosperms; small RNA