Polyploidy in Microsporidia

Supplementary material for "Polyploidy is widespread in Microsporidia" (https://doi.org/10.1128/spectrum.03669-23), with an additional ploidy estimation plot from "Microsporidia and invertebrate hosts: genome-informed taxonomy surrounding a new lineage of crayfish-infecting Nosema spp. (Nosematida)" (https://doi.org/10.1007/s13225-024-00543-w). File_1 contains: Table S1: SRA accession numbers, species name, and reason for exclusion of the SRA samples for which we were not able to reliably estimate ploidy in this study ("Polyploidy is widespread in Microsporidia"). Table S3: Ribosomal small subunit (SSU) sequences reconstructed from unassembled reads using PhyloFlash (with –emirge enabled). Table S4: NCBI NT accession numbers of additional contextual species included in phylogenetic tree. Text S1: Newick file format of generated phylogenetic tree. Figure S1: Box plot of spore volume in diploid (n = 10) and tetraploid species (n = 6), calculated using data from Bojko et al. (2022). Figure S2: Bar plot of habitats the diploid (n = 10) and tetraploid species (n = 6) identified in this study are found in according to Bojko et al. (2022). Figure S3: Bar plot of different host groups the diploid (n = 10) and tetraploid species (n = 6) identified in this study occur in, according to Bojko et al. (2022). Figure S4: Bar plot of different transmission modes the diploid (n = 10) and tetraploid species (n = 6) identified in this study possess, according to Bojko et al. (2022). Figure S5: Box plot of average haploid genome size estimated for the diploid (n = 10) and tetraploid (n = 6) species identified in this study, using GenomeScope2. Figure S6: Bar plot of number of nuclei in the spores of the diploid (n = 10) and tetraploid species (n = 6) identified in this study, according to Bojko et al. (2022). File_2 contains: 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 ("Polyploidy is widespread in Microsporidia"). Figure S7: (a) GenomeScope2 plot estimated a haploid genome size of ~6.6 Mbp for N. rusticus n. sp., with a tetraploidy model fit. (b) Smudgeplot indicates tetraploidy for N. rusticus. From "Microsporidia and invertebrate hosts: genome-informed taxonomy surrounding a new lineage of crayfish-infecting Nosema spp. (Nosematida)".