Data for: The role of repetitive DNA in re-patterning of major rDNA clusters in Lepidoptera

Genes for major ribosomal RNAs (rDNA) are present in multiple copies organized in tandem arrays. Number and position of rDNA loci can change dynamically and their re-patterning is presumably driven by repetitive sequences. We explored a peculiar rDNA organization in several representatives of Lepidoptera with either extremely large or numerous rDNA clusters. We combined molecular cytogenetics with analyses of second and third generation sequencing data to show that rDNA spreads as a transcription unit and reveal association between rDNA and various repeats. Furthermore, we performed comparative long read analyses between the species with derived rDNA distribution and moths with a single rDNA locus, which is considered ancestral. Our results suggest that satellite arrays, rather than mobile elements, facilitate homology-mediated spread of rDNA via either integration of extrachromosomal rDNA circles or ectopic recombination. The latter arguably better explains preferential spread of rDNA ..., Repeat Explorer analysis
For analysis of repetitive DNA content, whole gDNA was sequenced on the Illumina platform generating either 150 bp pair-end reads from library with mean insert size 450 bp (Novogene Co., Ltd., Beijing, China) or 250 bp PE reads with the mean insert size 700 bp in case of C. ohridella (Genomics Core Facility, EMBL Heidelberg, Germany). The raw reads were quality filtered and trimmed to uniform length of 120 bp (230 bp for C. ohridella) by Trimmomatic 3.2 (Bolger et al., 2014). Random sample of two million (one million for C. ohridella) trimmed PE reads was analysed by RE pipeline (version cerit-v0.3.1-2706) implemented in Galaxy environment (https://repeatexplorer-elixir.cerit-sc.cz/galaxy/) with automatic annotation via blastn and blastx using the Metazoan 3 Repeat Explorer database. The resulting html files were searched for clusters annotated as major rDNA and their connection to other clusters.
Long read sequencing and analysis
High molecular weight DNA from ..., Au_assembly_rDNA.fasta: A. urticae rDNA region assembly
Au_rDNA_reads.fasta: A. urticae PacBio reads containing at least 200 bp rDNA based on blast results
Au_sat_only_reads.fasta: A. urticae PacBio reads containing at least 200 bp AuSat, however, no rDNA or othe IGS parts
Hh_assembly_rDNA.fasta: H. humuli rDNA region assembly
Hh_rDNA_reads.fasta: H. humuli Oxford Nanopore reads containing at least 200 bp rDNA based on blast results
Ii_assembly_rDNA.fasta: I. io rDNA region assembly
Ii_rDNA_reads.fasta: I. io PacBio reads containing at least 200 bp rDNA based on blast results
Ii_sat_only_reads.fasta: I. io PacBio reads containing at least 200 bp IiSat, however, no rDNA or othe IGS parts 
Ld_assembly_rDNA.fasta: L. dispar rDNA region assembly
Ld_rDNA_reads.fasta: L. dispar PacBio reads containing at least 200 bp rDNA based on blast results
Pc_assembly_rDNA.fasta: P. californicus rDNA region assembly
Pc_rDNA_reads.fasta: P. californicus Oxford nanopore reads containing at least 200 bp rDN...