title: Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.
abstract: The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Taiji
authors.initials: T
authors.lastname: Kawakatsu
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Shao-Shan Carol
authors.initials: SC
authors.lastname: Huang
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Florian
authors.initials: F
authors.lastname: Jupe
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria.
authors.forename: Eriko
authors.initials: E
authors.lastname: Sasaki
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schmitz
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Urich
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Rosa
authors.initials: R
authors.lastname: Castanon
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Nery
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Cesar
authors.initials: C
authors.lastname: Barragan
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Yupeng
authors.initials: Y
authors.lastname: He
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Huaming
authors.initials: H
authors.lastname: Chen
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria.
authors.forename: Manu
authors.initials: M
authors.lastname: Dubin
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria.
authors.forename: Cheng-Ruei
authors.initials: CR
authors.lastname: Lee
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, PR China.
authors.forename: Congmao
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Felix
authors.initials: F
authors.lastname: Bemm
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Claude
authors.initials: C
authors.lastname: Becker
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: O'Neil
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Ronan C
authors.initials: RC
authors.lastname: O'Malley
authors.affiliation: Human Biology, J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Danjuma X
authors.initials: DX
authors.lastname: Quarless
authors.affiliation: Human Biology, J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Schork
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria.
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address: ecker@salk.edu.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059467:Transcriptome