Text S1. Distribution of rRNA gene variants in nuclei: experimental details.

Table S1. Nucleotide substitution parameters estimated from gene sequence alignments in Glomeromycota.

Table S2. Outgroup sequences used in the phylogenetic analysis of the 28S rRNA genes in Figure 2A.

Table S3. Stabilities of representative predicted ITS2 secondary structures in Claroideoglomus.

Table S4. Secondary structure stability and mutation accumulation patterns in the 5.8S and 5′ ∼350 bp of the 28S rRNAs of the Claroideoglomus lineage relative to their most recent common ancestor.

Table S5. Estimates of nucleotide substitution rates at protein-coding loci of Glomeromycota at synonymous and nonsynonymous nucleotide positions.

Figure S1. Predicted ITS2 secondary structures of select rRNA genes recovered from individual spores of the Claroideoglomus lineage.

Figure S2. Representative secondary structure predictions for portions of the 5.8S rRNA and 5′-end of the 28S rRNA recovered from spores of the Claroideoglomus lineage.

Figure S3. S variant rRNA genes are transcribed in symbiotic mycelia and spores in Claroideoglomus etunicatum CA-OT135–4-2.

Movie S1. S and L rRNA variant probes target distinct domains of the nucleus. Green, L variant probe; red, S variant probe; blue, DAPI.

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