Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa

Abstract

Polyploids arise from whole-genome duplication (WGD) events, which have played important roles in genome evolution across eukaryotes. WGD can increase genome complexity, yield phenotypic novelty, and influence adaptation. Neo-polyploids have been reported to often show seemingly stochastic epigenetic and transcriptional changes, but this leaves open the question whether these changes persist in evolved polyploids. A powerful approach to address this is to compare diploids, neo-polyploids, and evolved polyploids of the same species. Arabidopsis arenosa is a species that allows us to do this-natural diploid and autotetraploid populations exist, while neo-tetraploids can be artificially generated. Here, we use ATAC-seq to assay local chromatin accessibility, and RNA-seq to study gene expression on matched leaf and petal samples from diploid, neo-tetraploid and evolved tetraploid A. arenosa. We found over 8,000 differentially accessible chromatin regions across all samples. These are largely tissue specific and show distinct trends across cytotypes, with roughly 70% arising upon WGD. Interestingly, only a small proportion is associated with expression changes in nearby genes. However, accessibility variation across cytotypes associates strongly with the number of nearby transposable elements. Relatively few genes were differentially expressed upon genome duplication, and ∼60% of these reverted to near-diploid levels in the evolved tetraploid, suggesting that most initial perturbations do not last. Our results provide new insights into how epigenomic and transcriptional mechanisms jointly respond to genome duplication and subsequent evolution of autopolyploids, and importantly, show that one cannot be directly predicted from the other.

Keywords: Arabidopsis arenosa; chromatin; epigenome; gene expression; polyploids.

Fig. 1.

dACRs identified in rosette leaf and petal samples. a) Geographical origins of the diploid and autotetraploid populations used in this study. b) Cartoon demonstrating the generation of neo-tetraploids (“neo-4X” lines) from the F1 generation (the progeny of two colchicine-treated plants). c) Libraries prepared and tissues used in this study. d) Heatmap of z-scaled accessibility scores (measure of standard deviations above or below the mean) across dACRs for rosette samples of SNO (2X), neo-4X, and TBG (Est-4X). The dACRs are split into groups based on k-means clustering of accessibility trends across genotypes. The adjacent heatmap on the left shows the mean accessibility value for each dACR. e) Trends in mean accessibility for each k-group indicated in d). Error bars represent the standard error between three biological replicates for every genotype. f, g) Metaplots showing mean accessibility in proximity to genes f) and TEs and repeat regions g), for each k-group in d) and e). For f) TSS and TES represent transcription start site and transcription end site and for g) transposable element/repeat region start site and transposable element/repeat region end site, respectively. Panels h), i), j), k) represent Petal dACRs and are similar to d), e), f), g) respectively. CPM, counts per million.

Fig. 2.

Transcriptome differences across cytotypes. a) Schematic of comparisons between SNO (2X), neo-4X, and TBG (Est-4X). b) Venn diagrams denoting the number of DEGs identified in pairwise comparisons of cytotypes in rosette leaf and petal tissues. c) Heatmap representing union DEGs of rosette leaf samples, split by four groups. Trendline plots for every group indicate mean expression changes across cytotypes. Error bars represent the standard deviation between three biological replicates for every genotype. d) Heatmap similar to c) for petal union DEGs.

Fig. 3.

dACR and DEG associations. a, b) Trendline plots showing chromatin accessibility patterns across cytotypes (dark lines, y axis on the left) and expression patterns across cytotypes (lighter lines, y axis on the right) of dACRs and cis DEGs, split by k-groups for rosette leaf a) and petal b) samples, respectively. Numbers in the triangles represent the percentage of dACR-DEG pairs with positive/negative/inconsistent associations compared with all dACR-DEG pairs. c, d) Venn diagrams representing overlaps between all dACRs and all DEGs in rosette leaf c) and petal d) samples, respectively. e) Heatmap of fold enrichment values for 25 TF-binding motifs at dACRs. Fold enrichment values represent the ratio of TF-binding motifs in dACRs compared with randomly sampled control regions of the same length. TFs which are also identified as DEGs, are marked in green (rosette leaf DEGs) and pink (petal DEGs). Columns representing fold enrichment of TFs at all rosette leaf dACRs and all petal dACRs are highlighted with a black dotted line. f) Proportion of target genes for each motif in e) which are classified as rosette leaf DEGs or non-DEGs (heatmap on the left) and petal DEGs or non-DEGs (heatmap on the right). CPM, counts per million.

Fig. 4.

Cis features of dACRs are associated with accessibility variation across cytotypes. a) Number of rosette leaf and petal dACRs with various combinations (as indicated in the heatmap on the left) of cis features—TEs/repeats, DEGs, non-DEGs. Heatmaps to the right of the bar plots represent the fraction of cis features occurring in proximity to dACRs. b) Stacked barplots showing distribution of various TE sequence ontologies (annotated in the 2X reference genome) across dACRs, randomly sampled control regions, and all TEs/repeats in the 2X reference genome. Solid outlines demarcate three TIR TE sequences that are enriched in dACRs, while dotted lines demarcate TE sequences that show high accessibility changes across cytotypes. c, d) Accessibility dynamics across a varying number of TE/repeat regions, for various k-groups of rosette leaf c) and petal d) dACRs. CV refers to the coefficient of variation in mean accessibility across cytotypes, as a measure of accessibility dynamics. e, f) Accessibility dynamics of rosette leaf e) and petal f) dACRs with a single cis TE, for various TE sequence ontologies. For e, f), boxplots on the right of the dotted line indicate the accessibility CV distribution for dACRs without cis TEs. dACRs with cis TE sequences not denoted by “ns” show significantly different (P < 0.05) mean accessibility CV than dACRs without any cis TEs (far right). For c, d), asterisks indicate statistical significance for pairwise Wilcoxon tests.

Fig. 5.

TEs exhibit the largest changes in accessibility across cytotypes. a) Accessibility dynamics of rosette leaf and petal dACRs with different combinations of cis features. Accessibility dynamics are represented by CV in mean accessibility across cytotypes. P-values of significance are indicated for pairwise comparisons between dACRs with no cis features (“-”) and dACRs with various combinations of cis features, with significance levels provided to the right of a). “ns” refers to non-significant. b) Genome Browser screenshot showing large accessibility changes at two dACRs surrounded by Gypsy (LTR) TEs in a locus on Chromosome 4 for rosette leaf samples. The dACR region is indicated with gray shading across the tracks and marked in red at the locus. Each track represents a distinct sample with accessibility represented in fold enrichment values from [0 to 3] calculated from the respective ATAC-seq and control libraries (using the MACS2 bdgcmp function).