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Fig. S1. PhyML Maximum likelihood phylogeny (GTR model) of 18S rRNA gene sequences references (from Jones et al., 2011b, 1536 nucleotide alignment). Bootstrap values (500 replicates) are shown on all branches. The out-group and other fungal references sequences are the same as those used in Jones and colleagues (2011b).

Fig. S2. PhyML Maximum likelihood phylogeny (GTR model) of 18S rRNA gene OTUs from targeted pyrosequencing with Cryptomycota reference sequences (Jones et al., 2011b, 313 nucleotide alignment). Aquifer sequences are highlighted with circles on branches with bootstrap values (500 replicates) greater 50% and larger circles denoting higher bootstrap value.

Fig. S3. Linear regressions based on Tamura Nei 1993 distances computed using two different hypervariable regions to compare a sequence pair of Cryptomycota sequences. Top left comparison of V4 and V3 distances per sequence, Top right: comparison of V9 and V3 distances, Bottom: comparison of V9 and V4 distance.

Fig. S4. High resolution, zoomable version of Fig. 3. FastTree summary phylogeny of reference Cryptomycota sequences from a previous study and candidate sequences from 13 pyrosequencing sets. Pink names indicate marine sequences, blue names indicate freshwaters sequences, and yellow names indicate locations of sequences from the Iowa Aquifer. Dots on a branch indicate SH (Shimodaira–Hasegawa) test > 0.7, Brown circles on perimeter indicate reference sequences.

Table S1. Accession numbers for clone sequence identifiers in Figs 1, 3, S1 and S2.

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