Comparative Genomic Analysis Reveals Evolutionary Features of Glugea plecoglossi, a Fish-Infecting Microsporidian Parasite of Ayu (Plecoglossus altivelis)

Microsporidia are obligate intracellular parasites with extensively reduced genomes, yet substantial genomic variation occurs among lineages. Glugea plecoglossi infects ayu (Plecoglossus altivelis) and forms conspicuous xenomas, but its genome characteristics and evolutionary position remain poorly resolved. We generated a genome assembly of G. plecoglossi and compared it with 42 additional microsporidian taxa using phylogenomics, functional profiling, repeat analysis, and multi-copy orthogroup analysis. The 16.71 Mb assembly comprised 59 scaffolds, with a scaffold N50 of 557.5 kb and 78.5% complete BUSCOs, and contained 4331 predicted protein-coding gene loci. Phylogenomic analysis recovered G. plecoglossi as the sister taxon to Pseudoloma neurophilia. Compared with closely related taxa, G. plecoglossi had a substantially larger genome and more predicted protein-coding genes. Major Gene Ontology profiles were broadly similar across taxa, whereas metabolism-related profiles varied considerably. Among 11 genomes, repetitive-sequence composition differed markedly, with G. plecoglossi showing particularly high long terminal repeat coverage and substantial DNA-transposon coverage. The retained multi-copy orthogroups showed highly heterogeneous member distributions across taxa, with relatively high member numbers in G. plecoglossi restricted to a limited subset. These findings highlight genomic and functional variation among microsporidian lineages and provide a comparative genomic resource for future studies of fish-infecting microsporidia.