600 Gene Phylogeny of Microsporidia.

(A) ASTRAL [75] phylogeny summarizing individual phylogenies of 600 BUSCO genes (microsporidia_odb10) [76] across all publicly available microsporidian genome assemblies (including multiple strains where they are available), and the genome assemblies generated in this study (n = 40, marked in purple). Branch lengths were estimated with IQ-TREE using a concatenated alignment of the individual BUSCOs [77]. Nodes with less than 95% support are marked with pink circles. Ploidy is marked in circles at the tips of the tree for genomes where it was characterizable. (B) Genome assembly span (Mb) as calculated by assembly-stats (Github: https://github.com/sanger-pathogens/assembly-stats), with black circles marking chromosome-level genome assemblies. (C) N50 values (Mb) as calculated by assembly-stats (Github: https://github.com/sanger-pathogens/assembly-stats), with asterisks marking purged genome assemblies. (D) BUSCO gene (microsporidia_odb10) completeness percentage, marked in green for single-copy genes, and beige for duplicated genes. (E) Transposable element percentage as predicted by RepeatModeler and RepeatMasker [78,79], marked in burgundy for retroelements, peach for DNA transposons, and blue for rolling circles. Neop.: Neopereziida; Or. Lin.: Orphan Lineage. The data underlying A can be found in S1 Text. The data underlying B, C, D, and E can be found in S1 Table. The figure was generated using ToyTree [73], and manually annotated using InkScape (version 1.2.2). (ZIP)