DOI: 10.5061/dryad.bb249
title: Data from: Silenced rRNA genes are activated and substitute for partially eliminated active homoelogs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

description: To study the relationship between uniparental rDNA (encoding 18S, 5.8S and
 26S ribosomal RNA) silencing (nucleolar dominance) and rRNA gene dosage,
 we studied a recently emerged (within the last 80 years) allotetraploid
 Tragopogon mirus (2n=24), formed from the diploid progenitors T. dubius
 (2n=12, D-genome donor) and T. porrifolius (2n=12, P-genome donor). Here,
 we used molecular, cytogenetic and genomic approaches to analyse rRNA gene
 activity in two sibling T. mirus plants (33A and 33B) with widely
 different rRNA gene dosages. Plant 33B had ~400 rRNA genes at the D-genome
 locus, which is typical for T. mirus, accounting for ~25% of total rDNA.
 We observed characteristic expression dominance of T. dubius-origin genes
 in all organs. Its sister plant 33A harboured a homozygous macrodeletion
 that reduced the number of T. dubius-origin genes to about 70 copies (~4%
 of total rDNA). It showed biparental rDNA expression in root, flower and
 callus, but not in leaf where D-genome rDNA dominance was maintained.
 There was upregulation of minor rDNA variants in some tissues. The RNA
 polymerase I promoters of reactivated T. porrifolius-origin rRNA genes
 showed reduced DNA methylation, mainly at symmetrical CG and CHG
 nucleotide motifs. We hypothesise that active, decondensed rDNA units are
 most likely to be deleted via recombination. The silenced homeologs could
 be used as a ‘first reserve’ to ameliorate mutational damage and
 contribute to evolutionary success of polyploids. Deletion and
 reactivation cycles may lead to bidirectional homogenisation of rRNA
 arrays in the long term.
description: TableS3Mutation analysis of rDNA and its transcripts in 33A and 33B individuals. The NGS reads are clustered based on similarity. () - reads with 100% identity to the reference, (G-&gt;A) marks substitution, (231-232:--&gt;G) marks insertion, (61:G-&gt;-) marks deletion. The order of data sets in Microsoft Excel sheets is as follows: • Sheet “33A_gDNA-duRef”: Mutation analysis of genomic rDNA of 33A plant. Reads mapped to the T. dubius ITS1 reference. • Sheet “33B_gDNA-duRef”: Mutation analysis of genomic rDNA of 33B plant. Reads mapped to the T. dubius ITS1 reference. • Sheet “33A_RNA_leaf”: Mutation analysis of rRNA pools in 33A leaf. Reads mapped to the T. dubius ITS1 reference. • Sheet “33A_RNA_root”: Mutation analysis of rRNA pools in 33A root. Reads mapped to the T. dubius ITS1 reference. • Sheet “33B_RNA_leaf”: Mutation analysis of rRNA pools in 33B leaf. Reads mapped to the T. dubius ITS1 reference. • Sheet “33B_RNA_root”: Mutation analysis of rRNA pools in 33B root. Reads mapped to the T. dubius ITS1 reference. • Sheet “33A_gDNA-poRef”: Mutation analysis of genomic rDNA of 33A plant. Reads mapped to the T. porrifolius ITS1 reference. • Sheet “33B_gDNA-poRef”: Mutation analysis of genomic rDNA of 33B plant. Reads mapped to the T. porrifolius ITS1 reference. • Sheet “statistics”: A chi square test for differential distribution of P1 and P2 variants in parental T. porrifolius and T. mirus allotetraploid.