Extended Data Fig. 5: Cannabis centromere and telomere analysis shows higher order repeat structure.

A-B) The AceHigh3 (AH3M) chromosomal features of nine pairs of autosomes and one pair of sex chromosomes (X and Y). One million base pair rectangular windows extend outward from each pair of haplotypes at a width proportional to the absence of the CpG motif. Each rectangular window is colored by gene density with warm colors indicating high gene density and cool colors indicating low gene density. Each pair of haplotypes is connected by polygons indicating structural arrangement, with gray for syntenic regions and orange connecting inversions. Rectangles along each haplotype indicate select loci, including 45S (26S, 5.8S, 18S) rDNA arrays (firebrick red), 5S RNA arrays (black), 237 bp centromere repeat (blue), 370 bp CS-1 sub-telomeric repeat (pink) and cannabinoid synthases (forest green; CBCAS, CBDAS, THCAS, and OAC). Chromosomal plots for all 78 haplotype-resolved, chromosome-scale genomes show similar trends (see Ideos.pdf at https://doi.org/10.25452/figshare.plus.28405079.v1). C) The centromere arrays identified in the AH3M genome (as an exemplar for the pangenome) with Tandem Repeat Finder (TRF). Two high copy number arrays were identified with base repeats of 237 and 370 bp, along with their higher order repeats (HOR). The 237 bp array is sparsely found in the genome (blue, panel A), although usually proximal to the high “CpG” sites. The 370 bp repeat is the same sequence as the sub-telomeric repeat CS-1¹⁰⁶ and found on the ends of the chromosomes (pink, panel A). D) A subset of the genomes were sequenced on Oxford Nanopore Technologies to estimate the telomere length in cannabis genomes¹⁰³. The N50 ONT read length is plotted as a function of the max telomere repeat identified using the TeloNum software¹⁰³.