Fig. 6

Comparison of 45S rDNA units and clusters between strains and species. a Comparison of 45S rDNA units between C. elegans and C. briggsae. b Dot plot showing the alignment of the 45S rDNA unit sequences between two species. c Pairwise sequence alignment of the 45S rDNA unit between two species. The 18S, 5.8S, and 26S RNA gene regions are shaded in grey. Conservation scores are shown at the bottom. d Schematics of the 45S rDNA cluster of C. elegans N2a and CB4856 annotated by ONT reads. In the N2a, the cluster left and right boundaries are flanked by partial 26S rRNA sequences and a partial ETS, respectively. In the 45S rDNA-containing region in C. elegans CB4856, the 45S rDNA cluster is located at the right end of chromosome I while fragmented 45S rDNA sequences along with other sequences are located at the left end. The estimated copy number of the unit is shown. Note that both the chromosome left and right ends are flanked by a ~ 11.6 kb fragment derived from the left end of chromosome IV (pink, see Fig. S8), which is interrupted by some no homologous sequences (white box). A pSX1 cluster is also found adjacent to 45S rDNA. e Schematics of the C. briggsae AF16 genomic regions containing the 45S rDNA annotated by ONT reads in this study. Reconstructed 45S rDNA cluster is located at the left end of chromosome V containing about 85 copies of the 45 rDNA unit. Bottom: A misassembled contig containing partial 26S rRNA gene sequences and 5 protein coding genes was assigned to chromosome I in CB4