Fig. 3: Structural variation at Ea-IR in Arabidopsis natural accessions affects chromatin architecture and EFR expression.

a, Ea-IR variation, as deduced from a published short-read based variant atlas in 216 natural accessions from the 1001 Genomes Project. b, Multiple=sequence alignment of EFR and Xl-k region in genomes assembled from long reads. Each line represents one genome. Single-nucleotide polymorphisms are indicated by short, vertical colored lines, relatively small deletions are indicated as horizontal black lines and large deletions are indicated as white spaces. LIMPET1 and Ea-IR are highlighted with blue and orange lines. The genomes are ordered according to the presence or absence of the Ea-IR as mapped to the Col-0 reference genome. c, Expression of EFR and XI-k in 216 accessions, as measured by RNA-seq from⁸⁵. Each dot represents the normalized expression value for accessions with or without Ea-IR. P values were calculated with a two-tailed unpaired t-test with Welch’s correction. d, Chromatin contacts from CaptureC in the EFR and Xl-k region in Col-0, Ba-1 and Hod accessions. Loop^EFR, which includes Ea-IR, is marked in cyan, Loop^Xl-k is marked in green and all other interactions are marked in purple. The region targeted by CaptureC is indicated, with all potential restriction fragments below. Fragments diagnostic for the Ea-IR region are indicated in cyan. e, The 24-nt siRNAs mapping uniquely over Ea-IR in Col-0, Ba-1 and Hod accessions. Three individual sRNA-seq replicates are plotted separately and shown with different color tones. f, Left, cytosine methylation in the CG, CHG and CG contexts at Ea-IR (demarcated by vertical black lines) and flanking regions (700 bp) in Col-0, Br-0 and Hod accessions. The average of three individual BS-seq replicates is plotted for each genotype. Data are presented as the mean values ± s.d. Right, the average percentage of cytosine methylation in the CG, CHG and CG for each region and the same genotypes. The absence of the Ea-IR in Hod and Br-0 rendered no informative reads (not determined, N/D) over the IR-encoding region for these specific genotypes.

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