Fig. 1

Structure of the C. elegans (N2a) 5S rDNA cluster. a INDELs identified with Nanopore reads within the 5S rDNA unit. Shown are normalized INDEL occurrences along with GC content. Deletion and insertion identified with Nanopore raw reads are shown in red and blue, respectively. Cross-validated INDELs used in the subsequent analysis are indicated with black circles (see Methods). Two large indels are indicated. b SNPs in the 5S rDNA are identified with existing NGS data. SNPs present or absent in new rDNA variants are colored in red and black, respectively. c Structure of the 5S rDNA-containing regions on the chromosome V in the current C. elegans N2 reference genome (WBcel235). d Structure of the 5S rDNA cluster assembled by ONT reads, which carries a total of at least 167 partial or complete units. The cluster is divided into 5 regions (R1-5) based on the SNPs and INDELs present in each unit or the position relative to Repeat 1a. Newly identified rDNA units or unique repeats are differentially color coded (see Table 2). Variation in rDNA copy number is indicated with a dash line. Note that three copies of Repeat 1a are inserted into the 5S rDNA unit at the same position within R5