Supporting data for: Global Environmental Genomics Reveals Vast Uncultivated Protist Diversity and Taxonomic Blind Spots

File description: 18S_cluster.tsv (173.60 MB) - Table with annotations and metrics at the 18S rRNA OTU level at 85% identity. 18S_sequence.tsv (787.57 MB) - Table with annotations and metrics at the 18S rRNA sequence level. eukcensus_2025_18S.fna (616.19 MB) - Fasta file of 18S rRNA sequences. rarefied-diversity.tsv (12.41 MB ) - Sample by 18S rRNA OTU count table rarefied using rrarefy with the R vegan package. eukcensus_2025_img_metadata.tsv (18.08 MB) - Metadata table for IMG/M derived environmental sequencing samples. eukcensus_2025_sag_assemblies.tar.gz (146.03 MB) - Assemblies for the Single cell Amplified Genomes. F1_tree.nwk.txt (56.29 KB) - Tree with environmental representative clusters shown in Figure 1 in newick format. F3A_tree.nwk.txt (190.81 KB) - Tree with environmental representative clusters and orphan representative sequences shown in Figure 3A in newick format. F3D_tree.nwk.txt (7.42 KB) - Phylogenomic tree including SAGs in the eukaryotic tree shown in Figure 3D in newick format. marine-correlations-coeff.tsv (868.62 KB) - Correlation coefficients for 18S rRNA and 16S rRNA OTU pairs in marine environments. marine-correlations-pvalues.tsv (930.37 KB) - Adjusted p-values for 18S rRNA and 16S rRNA OTU pairs in marine environments. marine-eukcorrelations-coeff.tsv (582.72 KB) - Correlation coefficients for 18S rRNA OTU pairs in marine environments. marine-eukcorrelations-pvalues.tsv (620.31 KB) - Adjusted p-values for 18S rRNA OTU pairs in marine environments. freshw-correlations-coeff.tsv (3.00 MB) - Correlation coefficients for 18S rRNA and 16S rRNA OTU pairs in freshwater environments. freshw-correlations-pvalues.tsv (3.23 MB) - Adjusted p-values for 18S rRNA and 16S rRNA OTU pairs in freshwater environments. freshw-eukcorrelations-coeff.tsv (9.15 MB) - Correlation coefficients for 18S rRNA OTU pairs in freshwater environments. freshw-eukcorrelations-pvalues.tsv (9.56 MB) - Adjusted p-values for 18S rRNA OTU pairs in freshwater environments. soil-correlations-coeff.tsv (547.88 KB) - Correlation coefficients for 18S rRNA and 16S rRNA OTU pairs in soil environments. soil-correlations-pvalues.tsv (586.42 KB) - Adjusted p-values for 18S rRNA and 16S rRNA OTU pairs in soil environments. soil-eukcorrelations-coeff.tsv (146.94 KB) - Correlation coefficients for 18S rRNA OTU pairs in soil environments. soil-eukcorrelations-pvalues.tsv (157.01 KB) - Adjusted p-values for 18S rRNA OTU pairs in soil environments. 16S_cluster.tsv (38.39 MB) - Table with annotations and metrics at the 16S rRNA OTU level at 85% identity. 16S_sequence.tsv (689.23 MB) - Table with annotations and metrics at the 16S rRNA sequence level. eukcensus_2025_16S.fna (1.78 GB) - Fasta file of 18S rRNA sequences. eukcensus_ssuextract.tar.gz (30.54 MB) - Code for the ssuextract software.