• Figure 8.
    Download figureOpen in new tabFigure 8. Association scan between TE variants and C-DMR methylation variation.

    (A) Significant correlations between TE insertions and C-DMR DNA methylation level. Points show correlations between individual TE-DMR pairs that were more extreme than all 500 permutations of the DMR data. Top plots show the total number of significant correlations for each TE insertion across the whole genome. (B) As for (A), for TE deletions.

    DOI: http://dx.doi.org/10.7554/eLife.20777.038

  • Table 1.

    Mapping of paired-end reads providing evidence for TE presence/absence variants in the Ler reference genome.

    DOI: http://dx.doi.org/10.7554/eLife.20777.006

    ConcordantDiscordantSplitUnmappedTotal
    Col-0 mapped09939513010,206
    Ler mapped10,0739234710,206
    • Note: Discordant and split read categories are not mutually exclusive, as some discordant reads may have one read in the mate pair split-mapped.

  • Table 2.

    Summary of TE variant classifications.

    DOI: http://dx.doi.org/10.7554/eLife.20777.007

    TEPID callTE classificationCount
    PresenceNA310
    Insertion14,689
    Deletion8
    AbsenceNA1852
    Insertion388
    Deletion5848
  • Table 3.

    Percentage of DMRs within 1 kb of a TE variant.

    DOI: http://dx.doi.org/10.7554/eLife.20777.035

    C-DMRsCG-DMRs
    ObservedExpected95% CIObservedExpected95% CI
    TE deletions17160.00794.1160.0041
    TE insertions28260.00899.1260.0047
    NA calls8.76.20.00531.66.20.0027
    Total54480.0115480.0054
  • The following dataset was generated:

    Stuart T, Eichten SR, Cahn J, Karpievitch Y, Borevitz JO, Lister R, 2016,Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation, http://dx.doi.org/10.5061/dryad.187b3, Available at Dryad Digital Repository under a CC0 Public Domain Dedication

    The following previously published datasets were used:

    Schmitz RJ, Schultz MD, Urich MA , Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR, 2013,Patterns of population epigenomic diversity, http://www.ncbi.nlm.nih.gov/sra?term=SRA012474, Publicly available at the NCBI Short Read Archive (accession no: SRA012474)

    Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR, 2013,Patterns of population epigenomic diversity, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43858, Publicly available at the NCBI Gene Expression Omnibus (accassion no: GSE43858)

    Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR, 2013,Patterns of population epigenomic diversity, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43857, Publicly available at the NCBI Gene Expression Omnibus (accassion no: GSE43857)

    Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, Lanz C, Smith LM, Cao J, Fitz J, Warthmann N, Henz SR, Huson DH, Weigel D, 2011,Reference-guided assembly of four diverse Arabidopsis thaliana genomes, http://1001genomes.org/data/MPI/MPISchneeberger2011/releases/current/Ler-1/Reads/, Available at the 1001 Genomes Project

    Jiang C, Mithani A, Belfield EJ, Mott R, Hurst LD, Harberd NP, 2014,Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations, http://www.ncbi.nlm.nih.gov/sra/?term=SRP045804, Publicly available at the NCBI Short Read Archive (accession no: SRP045804)

    Sullivan A, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan S, Thompson A, Neri FV, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes T, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA, 2014,Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1289359, Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE53322)

    Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M, 2005,Genome-Wide Association Mapping in Arabidopsis Identifies Previously Known Flowering Time and Pathogen Resistance Genes, http://dx.doi.org/10.1371/journal.pgen.0010060.sd002, Available at PLOS