Genome Structure, Evolution, and Host Shift of .

is a diverse fungal genus of unicellular, obligate symbionts infecting various arthropods. We performed comparative genomic analyses of seven species that infect bees, wasps, moths, butterflies, and amphipods. As intracellular parasites, these species exhibit significant genome reduction, retaining only about half of the genes found in free-living yeast genomes. Notably, genes related to oxidative phosphorylation are entirely absent ( < 0.001), and those associated with endocytosis are significantly diminished compared to other pathways ( < 0.05). All seven genomes display significantly lower G-C content compared to their microsporidian outgroup. Species-specific 5~12 bp motifs were identified immediately upstream of start codons for coding genes in all species ( ≤ 1.6 × 10). Our RNA-seq data from showed that this motif is enriched in highly expressed genes but depleted in lowly expressed ones ( < 0.05), suggesting it functions as a -regulatory element in gene expression. We also discovered diverse telomeric repeats within the genus. Phylogenomic analyses revealed two major clades and incongruency between the species tree and their hosts' phylogeny, indicating potential host switch events (100% bootstrap values). This study advances the understanding of genomic architecture, gene regulation, and evolution of , offering valuable insights for developing strategies to control these microbial pathogens.