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Table S2:SRA accession numbers, species name, linear GenomeScope2 plots, transformed GenomeScope2 plots, and Smudgeplot plots of the 66 samples for which we were able to estimate ploidy in this study. Index SRA Accession Species Estimated Ploidy Genomscope2 Linear Plot Genomscope2 Transformed Linear Plot Smudgeplot Comments 1 SRR17317295 Vairimorpha ceranae 4 2 SRR17317294 Vairimorpha ceranae 4 3 SRR17317293 Vairimorpha ceranae 4 4 SRR17317292 Vairimorpha ceranae 4 5 SRR17317291 Vairimorpha ceranae 4 6 SRR17317296 Vairimorpha ceranae 4 7 SRR18590839 Vairimorpha ceranae 4 8 SRR18590838 Vairimorpha ceranae 4 9 SRR18590835 Vairimorpha ceranae 4Low coverage contaminant
Index SRA Accession Species Estimated Ploidy Genomscope2 Linear Plot Genomscope2 Transformed Linear Plot Smudgeplot Comments 10 SRR23560257 Encephalitozoon hellem 2 Genome is highly homozygous. The 4n smudge appears because imperfect duplications dominate over nearly negligible heterozygosity 11 SRR23560258 Encephalitozoon hellem 2 Genome is highly homozygous. The 4n smudge appears because imperfect duplications dominate over nearly negligible heterozygosity 12 SRR23560420 Encephalitozoon hellem 2 Genome is highly homozygous. Signal at the edges of the smudgeplot is noise 13 SRR24007516 Encephalitozoon intestinalis 2 Genome is highly homozygous. The 4n smudge appears because imperfect duplications dominate over nearly negligible heterozygosity 14 SRR24007515 Encephalitozoon intestinalis 2Genome is highly homozygous. The 4n smudge appears because
Index SRA Accession Species Estimated Ploidy Genomscope2 Linear Plot Genomscope2 Transformed Linear Plot Smudgeplot Comments imperfect duplications dominate over nearly negligible heterozygosity 15 SRR24007514 Encephalitozoon intestinalis 2 Genome is highly homozygous. The 4n smudge appears because imperfect duplications dominate over nearly negligible heterozygosity 16 SRR16954902 Hamiltosporidium magnivora 2Low coverage contaminant 17 SRR16954901 Hamiltosporidium tvaerminnensis 2Low coverage contaminant 18 SRR16954899 Hamiltosporidium tvaerminnensis 2Low coverage contaminant 19 SRR16954898 Hamiltosporidium tvaerminnensis 2 20 SRR16954897 Hamiltosporidium tvaerminnensis 2Low coverage contaminant 21 SRR16954895 Hamiltosporidium tvaerminnensis 2Low coverage contaminant
Index SRA Accession Species Estimated Ploidy Genomscope2 Linear Plot Genomscope2 Transformed Linear Plot Smudgeplot Comments 22 SRR16954906 Hamiltosporidium tvaerminnensis 2Low coverage contaminant 23 SRR16954905 Hamiltosporidium tvaerminnensis 2Low coverage contaminant 24 SRR16954904 Hamiltosporidium tvaerminnensis 2Low coverage contaminant 25 SRR23214363 Nematocida ausubeli 2Low coverage contaminant 26 SRR23214355 Nematocida ausubeli 2 Sample has a low coverage contaminant 27 SRR23214353 Nematocida ausubeli 2Low coverage contaminant 28 SRR23214358 Nematocida ausubeli 2Low coverage contaminant 29 SRR17622377 Nematocida major 2Low coverage contaminant 30 SRR23214350 Pancytospora philotis 2 31 ERR3154977 Tubulinosema ratisbonensis 4
Index SRA Accession Species Estimated Ploidy Genomscope2 Linear Plot Genomscope2 Transformed Linear Plot Smudgeplot Comments 32 SRR2105612 Encephalitozoon cuniculi EcunIII-L 2 33 SRR8476225 Astathelohania contejeani 4 34 SRR8476226 Astathelohania contejeani 4 35 SRR8495097 Cucumispora dikerogammari 4 36 SRR8495098 Cucumispora dikerogammari 4 37 SRR9597065 Hamiltosporidium tvaerminnensis 2 38 SRR14017862 Encephalitozoon hellem 2 39 SRR14062087 Encephalitozoon hellem 2 40 SRR16954910 Hamiltosporidium tvaerminnensis 2Low coverage contaminant 41 SRR16954909 Hamiltosporidium tvaerminnensis 2Low coverage contaminant
Index SRA Accession Species Estimated Ploidy Genomscope2 Linear Plot Genomscope2 Transformed Linear Plot Smudgeplot Comments 42 SRR16954908 Hamiltosporidium tvaerminnensis 2Low coverage contaminant 43 SRR543737 Anncaliia algerae 4 44 SRR630040 Anncaliia algerae 4 45 SRR489790 Anncaliia algerae 4 46 SRR489792 Anncaliia algerae 4 47 SRR653671 Anncaliia algerae PRA109 4 48 SRR122310 Encephalitozoon cuniculi 2 49 SRR122316 Encephalitozoon cuniculi 2 50 SRR122317 Encephalitozoon cuniculi 2 51 SRR065293 Vittaforma corneae 2
Index SRA Accession Species Estimated Ploidy Genomscope2 Linear Plot Genomscope2 Transformed Linear Plot Smudgeplot Comments 52 SRR926312 Pseudoloma neurophilia 2 53 SRR926320 Vairimorpha ceranae 4 54 SRR1596197 Vairimorpha ceranae 4 55 SRR926341 Agmasoma penaei 2012 - Plaquemines Parish LA 4 56 SRR926400 Agmasoma penaei 2012 - Plaquemines Parish LA 4 57 SRR058692 Nematocida ausubeli 2 58 SRR350188 Nematocida ausubeli 2 59 SRR17853474 Encephalitozoon hellem 2 Smudgeplot is noisy, but genome appears to be highly homozygous 60 SRR17853475 Encephalitozoon hellem 2 Smudgeplot is noisy, but genome appears to be highly homozygous
Index SRA Accession Species Estimated Ploidy Genomscope2 Linear Plot Genomscope2 Transformed Linear Plot Smudgeplot Comments 61 SRR17865589 Encephalitozoon intestinalis 2 Smudgeplot is noisy, but genome appears to be highly homozygous 62 SRR17865590 Encephalitozoon intestinalis 2 Smudgeplot is noisy, but genome appears to be highly homozygous 63 SRR17865591 Encephalitozoon intestinalis 2 Smudgeplot is noisy, but genome appears to be highly homozygous. The reason for a smudge at 4n is that due to the high homozygosity, imperfect duplications appear overrepresented. 64 SRR17858634 Encephalitozoon cuniculi 2 Smudgeplot is really noisy, but genome appears to be highly homozygous 65 SRR17858635 Encephalitozoon cuniculi 2 Smudgeplot is noisy, but genome appears to be highly homozygous. The reason for a smudge at 4n is that due to the high homozygosity, imperfect duplications appear overrepresented.
Index SRA Accession Species Estimated Ploidy Genomscope2 Linear Plot Genomscope2 Transformed Linear Plot Smudgeplot Comments 66 SRR17858636 Encephalitozoon cuniculi 2 Smudgeplot is noisy, but genome appears to be highly homozygous. The reason for a smudge at 4n is that due to the high homozygosity, imperfect duplications appear overrepresented.
