TableS3

Mutation 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->A) marks substitution, (231-232:-->G) marks insertion, (61:G->-) 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.