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DNA methylome of the 20-gigabase Norway spruce genome.

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DNA methylome of the 20-gigabase Norway spruce genome.

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dc.contributor.author Ausin, Israel es_ES
dc.contributor.author Feng, Suhua es_ES
dc.contributor.author Yu, Chaowei es_ES
dc.contributor.author Liu, Wanlu es_ES
dc.contributor.author Kuo, Hsuan Yu es_ES
dc.contributor.author Jacobsen, Elise L. es_ES
dc.contributor.author Zhai, Jixian es_ES
dc.contributor.author Gallego Bartolomé, Javier es_ES
dc.contributor.author Wang, Lin es_ES
dc.contributor.author Egertsdotter, Ulrika es_ES
dc.contributor.author Street, Nathaniel R. es_ES
dc.contributor.author Jacobsen, Steven E. es_ES
dc.contributor.author Wang, Haifeng es_ES
dc.date.accessioned 2023-12-22T19:02:27Z
dc.date.available 2023-12-22T19:02:27Z
dc.date.issued 2016-12-13 es_ES
dc.identifier.issn 0027-8424 es_ES
dc.identifier.uri http://hdl.handle.net/10251/201095
dc.description.abstract [EN] 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. es_ES
dc.description.sponsorship We thank members of the S.E.J. laboratory for useful discussions. We are grateful for support from the Umea Plant Science Centre (UPSC) bioinformatics platform. This work was supported by funds from National Natural Science Foundation of China Grant 31501031, Program for Excellent Youth Talents in Fujian Province University, and Fujian-Taiwan Joint Innovative Centre for Germplasm Resources and Cultivation of Crop (Fujian 2011 Program) (to H.W.), the University of California, Los Angeles-Fujian Agriculture and Forestry University Joint Research Center on Plant Proteomics, the Alice Wallenberg Foundation, the Swedish Research Council (VR), the Swedish Governmental Agency for Innovation Systems (Vinnova), the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas), and the Swedish Foundation for Strategic Research, in part through the UPSC Berzelii Centre for Forest Biotechnology. W.L. is supported by a Philip J. Whitcome fellowship from the Molecular Biology Institute of University of California, Los Angeles and a scholarship from the Chinese Scholarship Council. J.Z. is a Life Science Research Foundation Postdoctoral Fellow, sponsored by the Gordon and Betty Moore Foundation. N.R.S. is supported by the Trees and Crops for the Future project. S.E.J. is an Investigator of the Howard Hughes Medical Institute. es_ES
dc.language Inglés es_ES
dc.publisher Proceedings of the National Academy of Sciences es_ES
dc.relation.ispartof Proceedings of the National Academy of Sciences es_ES
dc.rights Reserva de todos los derechos es_ES
dc.subject GymnospermsNorway spruce es_ES
dc.subject DNA methylation es_ES
dc.subject Small RNA es_ES
dc.subject Genome size es_ES
dc.title DNA methylome of the 20-gigabase Norway spruce genome. es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1073/pnas.1618019113 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/NSF//31501031/ es_ES
dc.rights.accessRights Cerrado es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes es_ES
dc.description.bibliographicCitation Ausin, I.; Feng, S.; Yu, C.; Liu, W.; Kuo, HY.; Jacobsen, EL.; Zhai, J.... (2016). DNA methylome of the 20-gigabase Norway spruce genome. Proceedings of the National Academy of Sciences. 113(50):E8106-E8113. https://doi.org/10.1073/pnas.1618019113 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1073/pnas.1618019113 es_ES
dc.description.upvformatpinicio E8106 es_ES
dc.description.upvformatpfin E8113 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 113 es_ES
dc.description.issue 50 es_ES
dc.identifier.pmid 27911846 es_ES
dc.identifier.pmcid PMC5167160 es_ES
dc.relation.pasarela S\505592 es_ES
dc.contributor.funder University of California es_ES
dc.contributor.funder China Scholarship Council es_ES
dc.contributor.funder Trees and Crops for the Future es_ES
dc.contributor.funder Swedish Research Council Formas es_ES
dc.contributor.funder Gordon and Betty Moore Foundation es_ES
dc.contributor.funder Umea Plant Science Centre, Suecia es_ES
dc.contributor.funder National Science Foundation, China es_ES
dc.contributor.funder Knut and Alice Wallenberg Foundation es_ES
dc.contributor.funder Natural Science Foundation of Fujian Province es_ES
dc.contributor.funder Swedish Governmental Agency for Innovation Systems es_ES
dc.contributor.funder Swedish Foundation for Humanities and Social Sciences es_ES
dc.description.references EJ Finnegan, WJ Peacock, ES Dennis, DNA methylation, a key regulator of plant development and other processes. Curr Opin Genet Dev 10, 217–223 (2000). es_ES
dc.description.references SJ Cokus, , Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008). es_ES
dc.description.references S Feng, , Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 107, 8689–8694 (2010). es_ES
dc.description.references R Lister, , Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008). es_ES
dc.description.references MA Matzke, RA Mosher, RNA-directed DNA methylation: An epigenetic pathway of increasing complexity. Nat Rev Genet 15, 394–408 (2014). es_ES
dc.description.references QX Song, , Genome-wide analysis of DNA methylation in soybean. Mol Plant 6, 1961–1974 (2013). es_ES
dc.description.references S Zhong, , Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 31, 154–159 (2013). es_ES
dc.description.references A Zemach, , Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci USA 107, 18729–18734 (2010). es_ES
dc.description.references H Wang, , CG gene body DNA methylation changes and evolution of duplicated genes in cassava. Proc Natl Acad Sci USA 112, 13729–13734 (2015). es_ES
dc.description.references M Regulski, , The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res 23, 1651–1662 (2013). es_ES
dc.description.references CE Niederhuth, , Widespread natural variation of DNA methylation within angiosperms. Genome Biol 17, 194 (2016). es_ES
dc.description.references S Takuno, J-H Ran, BS Gaut, Evolutionary patterns of genic DNA methylation vary across land plants. Nat Plants 2, 15222 (2016). es_ES
dc.description.references EK Lee, , A functional phylogenomic view of the seed plants. PLoS Genet 7, e1002411 (2011). es_ES
dc.description.references Y Huang, , Ancient origin and recent innovations of RNA Polymerase IV and V. Mol Biol Evol 32, 1788–1799 (2015). es_ES
dc.description.references MA Matzke, T Kanno, AJ Matzke, RNA-directed DNA methylation: The evolution of a complex epigenetic pathway in flowering plants. Annu Rev Plant Biol 66, 243–267 (2015). es_ES
dc.description.references L Ma, , Angiosperms are unique among land plant lineages in the occurrence of key genes in the RNA-directed DNA Methylation (RdDM) pathway. Genome Biol Evol 7, 2648–2662 (2015). es_ES
dc.description.references IA Yakovlev, E Carneros, Y Lee, JE Olsen, CG Fossdal, Transcriptional profiling of epigenetic regulators in somatic embryos during temperature induced formation of an epigenetic memory in Norway spruce. Planta 243, 1237–1249 (2016). es_ES
dc.description.references F Krueger, SR Andrews, Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011). es_ES
dc.description.references X Li, , Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics 13, 300 (2012). es_ES
dc.description.references H Stroud, , Plants regenerated from tissue culture contain stable epigenome changes in rice. eLife 2, e00354 (2013). es_ES
dc.description.references SC Stelpflug, SR Eichten, PJ Hermanson, NM Springer, SM Kaeppler, Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize. Genetics 198, 209–218 (2014). es_ES
dc.description.references DK Seymour, D Koenig, J Hagmann, C Becker, D Weigel, Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet 10, e1004785 (2014). es_ES
dc.description.references B Nystedt, , The Norway spruce genome sequence and conifer genome evolution. Nature 497, 579–584 (2013). es_ES
dc.description.references C Vitte, MA Fustier, K Alix, MI Tenaillon, The bright side of transposons in crop evolution. Brief Funct Genomics 13, 276–295 (2014). es_ES
dc.description.references M Lechner, , The correlation of genome size and DNA methylation rate in metazoans. Theory Biosci 132, 47–60 (2013). es_ES
dc.description.references S Jansson, G Meyer-Gauen, R Cerff, W Martin, Nucleotide distribution in gymnosperm nuclear sequences suggests a model for GC-content change in land-plant nuclear genomes. J Mol Evol 39, 34–46 (1994). es_ES
dc.description.references I Birol, , Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics 29, 1492–1497 (2013). es_ES
dc.description.references DB Neale, , Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 15, R59 (2014). es_ES
dc.description.references D Uddenberg, S Akhter, P Ramachandran, JF Sundström, A Carlsbecker, Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology. Front Plant Sci 6, 970 (2015). es_ES
dc.description.references T Ujino-Ihara, , Comparative analysis of expressed sequence tags of conifers and angiosperms reveals sequences specifically conserved in conifers. Plant Mol Biol 59, 895–907 (2005). es_ES
dc.description.references XQ Wang, JH Ran, Evolution and biogeography of gymnosperms. Mol Phylogenet Evol 75, 24–40 (2014). es_ES
dc.description.references A Zemach, IE McDaniel, P Silva, D Zilberman, Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916–919 (2010). es_ES
dc.description.references I Hakman, LC Fowke, S Von Arnold, T Eriksson, The development of somatic embryos in tissue cultures initiated from immature embryos of Picea abies (Norway Spruce). Plant Sci 38, 53–59 (1985). es_ES
dc.description.references SVA Inger Hakman, Plantlet regeneration through somatic embryogenesis in Picea abies (Norway Spruce). J Plant Physiol 121, 149–158 (1985). es_ES
dc.description.references Ø Johnsen, CG Fossdal, N Nagy, J Mølmann, OG Dæhlen, T Skrøppa, Climatic adaptation in Picea abies progenies is affected by the temperature during zygotic embryogenesis and seed maturation. Plant Cell Environ 28, 1090–1102 (2005). es_ES
dc.description.references M Ong-Abdullah, , Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525, 533–537 (2015). es_ES
dc.description.references E Businge, K Brackmann, T Moritz, U Egertsdotter, Metabolite profiling reveals clear metabolic changes during somatic embryo development of Norway spruce (Picea abies). Tree Physiol 32, 232–244 (2012). es_ES
dc.description.references J Du, , Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Mol Cell 55, 495–504 (2014). es_ES
dc.description.references X Cao, SE Jacobsen, Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci USA 99, 16491–16498 (2002). es_ES
dc.description.references H Stroud, MV Greenberg, S Feng, YV Bernatavichute, SE Jacobsen, Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152, 352–364 (2013). es_ES
dc.description.references C Trapnell, L Pachter, SL Salzberg, TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009). es_ES
dc.description.references C Trapnell, , Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562–578 (2012). es_ES
dc.description.references M Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads. Bioinformatics in Action 17, 10–12 (2012). es_ES
dc.description.references B Langmead, C Trapnell, M Pop, SL Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). es_ES


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