The two dikaryotic nuclear haplotypes of Pst104E harbor distinct rDNA subtypes. (A) Schematic view of the rDNA tandem repeat array located on Pst104E Chr 13. (B) Diagram of a single canonical rDNA unit of Pst104E containing the transcription start site in the 5′ external transcribed spacer, the catalytic rRNA genes (18S, 5.8S, 25S, and 5S), two internal transcribed spacers (ITS1 and ITS2), and two intergenic spacers (IGS1 and IGS2). The alignment shows two dominant rDNA subtypes (1 and 2), which differ by SNPs and structural variations in both IGS. (C) Estimated copy number of rDNA subtypes 1 and 2 based on ONT duplex and Illumina read data sets. (D) Workflow of our rDNA Hi-C analysis designed to determine the physical location of the two dominant rDNA subtypes in each nuclear haplotype. (E) Mapping quality (MAPQ) distributions of Hi-C reads whose paired mates contained rDNA subtype-specific or non-subtype-specific 31-mers, categorized by the nuclear haplotype they mapped against.