New genomic and transposable element annotation of the microsporidian parasite Anncaliia algerae.

Anncaliia algerae Undeen is an obligate intracellular microsporidian parasite with an unusually broad host range and a genome enriched in transposable elements (TEs). Using PacBio HiFi sequencing and transcriptomic support, we generated a near chromosome-level assembly of the A. algerae Undeen strain. The haploid genome spans 11.78 Mb in 17 contigs and contains 2705 protein-coding genes. This high-quality assembly provides a detailed view of genome architecture and ploidy. Remarkably, TEs occupy about 24% of the genome and are represented by 4972 copies distributed across 260 families, highlighting exceptional diversity. Among these, Merlin DNA transposons and Ty3 LTR retrotransposons are the most abundant, while other TE classes occur at lower frequencies. This improved genome assembly and annotation provide a robust framework for future studies of genome evolution, TE dynamics, and host adaptation in A. algerae.