Fig. 2: Repetitive sequences of 32 de novo genomes.

a Number and percentage of core, variable, and rare transposable element (TE) families. b Classification of 780 pan-TE families. c Distribution of TE types in core, variable, and rare TE families. d TE length identified in different A. thaliana genomes. e Composition of different TE types in A. thaliana genomes. Blue rectangles display relict ecotypes while red rectangles display non-relict ecotypes. f Comparison of peak intact long terminal repeat-retrotransposons (LTR) insertion times of relict ecotypes (n = 6) and non-relict (n = 26) ecotypes. Significance was determined using a two tailed Wilcoxon test with p = 2.2e-3 < 0.05. g Comparison of the expression levels between genes with (n = 97,922) and without (n = 789,801) TE insertion. Significance was determined using a two tailed Wilcoxon test with p = 0 < 0.05. The upper and lower edges of the boxes represent the 75% and 25% quartiles, the central line denotes the median, and the whiskers extend to 1.5× inter-quartile range (IQR), and the outliers are removed in (f) and (g). h The two haplotypes of CCR1 are determined by the presence or absence of DNA/MULE-MuDR insertion (red bar) in the fourth intron. HiFi and RNA-seq read mapping supports the gene structure annotation. i The distributions of the two CCR1 haplotypes in relict and non-relict ecotypes. j Relative CCR1 mRNA levels assessed by quantitative RT-PCR. Data are mean ± SD from independent biological replicates (n = 3). Significance was determined using a two tailed t-test with p = 6.1e-5 < 0.05. k Schematic diagram of reporters of transient dual-luciferase assay. l Transient dual-luciferase assay in N. benthamiana. LUC: Firefly Luciferase; REN: Renilla Luciferase; NOS: NOS terminator. Data are mean ± SD from independent biological replicates (n = 3). Significance was determined using a two tailed t-test with p = 8.0e-3 < 0.05. Source data are provided as a Source Data file.