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Additional file 1 of Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression

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posted on 07.11.2020, 04:29 by Ulfar Bergthorsson, Caroline J. Sheeba, Anke Konrad, Tony Belicard, Toni Beltran, Vaishali Katju, Peter Sarkies
Figure S1. Quantitative analysis of TE variability across different population sizes. A Mean change in expression relative to the ancestral control across all TEs for each line. B Violin plots showing distribution of changes in TE expression across all TEs for each line. Lines are ordered by increasing mean TE expression change (L to R). C Fano factor of individual TE transcript levels across all lines of the indicated population size. D Fano factor in individual protein-coding gene transcript levels across all lines of the indicated population size. E Fano factor of TE transcript levels in 1000 samples of five N.1 lines, 253 samples of five N.10 lines [the maximum] and all five N.100 lines. F Total variance in transcript level differences between each TE and its corresponding value in the starting population across lines of different population size. G Total variance of transcript level differences between each protein-coding gene and the starting population in lines of the indicated population size. Boxplots for A-D are as in Fig. 1D. H Variance in TE transcript changes relative to starting population compared to the variance in protein-coding gene transcript changes in the same line. Figure S2. Characteristics of C. elegans TEs analysed in this study. A Base pairs covered by TE families for which robust RNA-Seq coverage was obtained in at least one line (analysed in this study), grouped by family and coloured according to type of TE. B Number of elements of each TE family found, coloured according to type of TE. C Distribution of TEs analysed in this study across chromosomes. D Number of TEs analysed in this study targeted by different small RNA pathways. E Number of TEs analysed in this study in different chromatin domains. Figure S3. Further analysis of small RNA mediated TE control in MA lines. A Number of piRNA loci containing a mismatch to the genome of the parental line across different population sizes of MA lines, as assessed by small RNA sequencing. B Total piRNA expression across lines of different population sizes. C 22G-RNAs targeted to TEs targeted by piRNAs across different population sizes. D Scatterplot comparing 22G-RNA levels and mRNA levels for Turmoil2 elements across all lines. E Spearman’s rank correlation coefficient between expression changes and 22G-RNA levels for different TEs across all lines, coloured by HRDE-1 targets. F Spearman’s rank correlation coefficient between expression changes and 22G-RNA levels for different TEs across all lines, coloured by WAGO-1 targets. G Total expression changes of TEs targeted by HRDE-1 across different population sizes. H Total expression changes of TEs targeted by WAGO-1 across different population sizes. Figure S4. TEs on the X chromosome are not upregulated in MA lines. A Expression of TEs located on autosomes across different population sizes. B Expression of TEs located on the X chromosome across different population sizes. See Additional File 1: Fig. S2 for the numbers of TEs on each chromosome. Figure S5. Further analysis of the effect of sequence features on TE desilencing in MA lines. A GC-content does not affect reactivation of TEs in the N.1 lines. Bins with high to low GC-content, left to right. There are no significant (q < 0.1) trends in any category. Regression lines were therefore omitted for clarity. B GC-content does not affect the change in 22G-RNA levels. Bins with high to low-GC content, left to right. There are no significant trends in any category so regression lines were omitted as in A. C No clear difference in the proportion of TEs from different chromatin domains within bins of different PATC content. D Expression of TEs from regulated, heterochromatic and active chromatin regions in the top PATC bin. E Expression of TEs from regulated, heterochromatic and active chromatin regions in the lowest PATC bin. (PDF 2643 kb)

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Medical Research Council Foundation for the National Institutes of Health

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