Abstract
Tritrichomonas musculus is a commensal protist colonizing the large intestine of laboratory mice. Parasite colonization reshapes the gut microbiome and modulates mucosal immunity. This parasite is refractory to axenic culture. In order to facilitate functional genomic investigations we assembled a 193.49 Mbp high quality reference genome from FACS-purified parasites recovered from monocolonized mice using an integrated approach that combined long-read (PacBio and Oxford Nanopore) sequencing technologies for the draft genome assembly. The genome assembled into 756 contigs and RNA-Seq data was used to support the gene models for 46,131 annotated genes. Of these, 24,215 genes had an InterPro, Enzyme Commission and/or a Gene Ontology annotation. BUSCO analyses established that 53% of the genome annotations matched with available BUSCO genes in the eukaryote_odb10 database. This high quality reference genome will serve as a valuable resource to develop a metabolic and genetic model to grow T. musculus axenically and study genes relevant to its biology, life cycle transmission, and pathogenesis.