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Cell. 2016 Jul 14;166(2):492-505. doi: 10.1016/j.cell.2016.06.044.

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Author information

1
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.
2
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.
3
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria.
4
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA.
5
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
6
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.
7
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
8
Human Biology, J. Craig Venter Institute, La Jolla, CA 92037, USA.
9
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.

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.

PMID:
27419873
PMCID:
PMC5172462
DOI:
10.1016/j.cell.2016.06.044
[Indexed for MEDLINE]
Free PMC Article

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