rDNA structure and strategy for visualizing rDNA. (A) Structure of rDNA. rDNA is largely divided into the coding 45S rRNA gene (45S rDNA) and the noncoding intergenic spacer (IGS). The IGS has repetitive sequences, such as microsatellite and transposable elements. Here, typical R and Long/Butterfly repeats are shown. (B) rDNA visualization strategy for Nanopore reads containing rDNA. First, the read is split into 300-nt sections, and each split read is mapped to the rDNA reference sequence. The structure is then reconstructed based on the position in the read and the mapped position in the reference. (C) Typical mutations and how they look in the visualization strategy. In this example, the reference sequence has three R and two Long/Butterfly repeats.
