Skip to main content

Erratum to: Methylome Evolution in plants

The Original Article was published on 20 December 2016

Erratum

After publication of this article [1] we noticed that the centromere of Chromosome 3 was missing from Fig. 4a, and that the Fig. 4e y-axis should read ‘CG meth. Div. W-Acc.’. The y-axis of the barplot in Fig. 5a should read ‘Number of cytosines’. The corrected Figs. 4 and 5 are shown below.

Fig. 4
figure 1

a Gene (light gray) and transposable element (TE) (dark gray) densities along the A. thaliana genome (Columbia reference). A schematic representation of the five chromosomes is shown above (circle, centromere; dark gray, pericentromeric region; light gray, arm). b Annotation-specific CG epimutations produce distinct methylome diversity (CG meth. div.) patterns among mutation accumulation lines (MA-lines) that have diverged for merely 30 generations (average diversity was calculated in 1 Mb sliding windows, step size 100 kb). These diversity patterns can be predicted from annotation-specific estimates of epimutation rate and the density distribution of annotation units along the genome (red theoretical line). c CG methylome diversity (CG meth. div.) patterns among 13 North American accessions (N-Acc.) (after around 200 generations of divergence). d Methylome diversity patterns among 138 worldwide accessions (W-Acc.) (after several hundred thousand years of divergence). e CG methylome diversity patterns are significantly correlated between the MA-lines and the W-Acc., both in pericentromeric (peri) regions (dark gray dots) as well as in euchromatic chromosome arms (light gray dots). f These correlations are even stronger when MA-lines are compared to the N-Acc., suggesting that the accumulation of DNA sequence polymorphism has perturbed epimutation-induced methylome diversity patterns over time

Fig. 5
figure 2

a Simplification of the reconstruction of a methylation site frequency spectrum (mSFS). In this example, we consider a sample size of five accessions (Acc.), and eight sites among which two (in gray) are monomorphic and thus discarded for the mSFS. For each cytosine, each accession might exhibit a methylated (M) or an unmethylated (U) state. For the mSFS, counts are taken of the number of accessions that are unmethylated for that cytosine. These counts define discrete epiallelic classes (number of unmethylated alleles). b The observed frequencies of each epiallelic class is determined, in this case, from genic CG sites of 92 A. thaliana worldwide natural accessions (red bars), along with the maximum likelihood estimate based on the theoretical result of Charlesworth and Jain [123] (pink bars). The theoretical model (see Box 1) provides an accurate fit to the observed genic CG methylation diversity patterns, suggesting that CG epimutations are a major factor in shaping methylome diversity in natural populations of A. thaliana over evolutionary timescales

Reference

  1. Vidalis A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F. Methylome evolution in plants. Genome Biol. 2016;17:264.

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Aurélien Tellier or Frank Johannes.

Additional information

The online version of the original article can be found under doi:10.1186/s13059-016-1127-5.

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Vidalis, A., Živković, D., Wardenaar, R. et al. Erratum to: Methylome Evolution in plants. Genome Biol 18, 41 (2017). https://doi.org/10.1186/s13059-017-1176-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s13059-017-1176-4