Fig. 2: TEs shape the cannabis pangenome.
From: Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome
a, Percentage of genome covered by TEs, using 78 chromosome-level, haplotype-resolved genomes, grouped by population. The y axis shows the Gaussian kernel density estimation. b, Across the pangenome, the age distribution of fragmented TEs, with inset showing their distribution within the past 100,000 years. In the inset, the highest density occurs since 10 thousand years ago (ka). c, Age distribution of intact TEs, with inset showing distribution within the last 100,000 years. In the inset, the highest density occurs within 10 kya. d, Average solo:intact ratio for Ty1-LTR elements in 78 chromosome-level, haplotype-resolved genomes, grouped by chromosome. For all box plots, the green dashed line is the mean and the orange solid line is the median. The lower and upper edges of the box correspond to the lower and upper quartiles. The vertical lines (whiskers) extending from the box reflect the minimum and maximum values in the dataset. Each scatter point represents an individual genome. e, Average solo:intact ratio for Ty3-LTR elements. f, Average solo:intact ratio for Ty1-LTR elements in the sex chromosomes grouped according to boundary (PAR, X-specific region or SDR). g, Average solo:intact ratio for Ty3-LTR elements in the sex chromosomes grouped according to boundary (PAR, X-specific region or SDR). h, Genomic landscape plot for the AH3Mb Y chromosome, showing density of LTRs, methylation, CpG content and transcripts across the chromosome. i, Genomic landscape plot for the AH3Mb Y chromosome, showing the ratio of solo:intact Ty1-LTRs across the chromosome. j, Visualization of whole-genome alignments between the AH3Ma X and Y chromosomes. The bracketed region with high similarity is the PAR. k, Genomic landscape plot for the AH3Ma X chromosome, showing density of LTRs, methylation, CpG content and transcripts across the length of the chromosome. l, Genomic landscape plot for the AH3Ma X chromosome, showing the ratio of solo:intact Ty1-LTRs across the length of the chromosome.
