Lotmaria passim is a ubiquitous trypanosomatid parasite of honey bees nestled within the medically important subfamily Leishmaniinae. Although this parasite is associated with honey bee colony losses, the original draft genome-which was completed before its differentiation from the closely related Crithidia mellificae-has remained the reference for this species despite lacking improvements from newer methodologies. Here, we report the updated sequencing, assembly, and annotation of the BRL-type (Bee Research Laboratory) strain (ATCC PRA-422) of Lotmaria passim. The nuclear genome assembly has been resolved into 31 complete chromosomes and is paired with an assembled kinetoplast genome consisting of a maxicircle and 30 minicircle sequences. The assembly spans 33.7 Mb and contains very little repetitive content, from which our annotation of both the nuclear assembly and kinetoplast predicted 10,288 protein-coding genes. Analyses of the assembly revealed evidence of a recent chromosomal duplication event within chromosomes 5 and 6 and provided evidence for a high level of aneuploidy in this species, mirroring the genomic flexibility employed by other trypanosomatids as a means of adaptation to different environments. This high-quality reference can therefore provide insights into adaptations of trypanosomatids to the thermally regulated, acidic, and phytochemically rich honey bee hindgut niche, which offers parallels to the challenges faced by other Leishmaniinae during the challenges they undergo within insect vectors, during infection of mammals, and exposure to antiparasitic drugs throughout their multi-host life cycles. This reference will also facilitate investigations of strain-specific genomic polymorphisms, their role in pathogenicity, and the development of treatments for pollinator infection.

Czech Academy of Sciences Institute of Parasitology České Budějovice 370 05 Czech Republic

Department of Biology Fort Lewis College 1000 Rim Drive Durango CO 81301 USA

Department of Biology University of Maryland Biology Psychology Building 4094 Campus Drive College Park MD 20742 USA

Department of Microbiology University of Massachusetts Fernald Hall Amherst MA 01003 USA

Department of Parasitology Biochemical and Molecular Parasitology Group CTS 183 University of Granada Granada 18071 Spain

Faculty of Science University of South Bohemia České Budějovice 370 05 Czech Republic

Institute of Biotechnology University of Granada Granada 18071 Spain

Life Science Research Centre Faculty of Science University of Ostrava Ostrava 710 00 Czech Republic

Omics Bioinformatics S L Calle Senderos 2 Bajo Granada 18005 Spain

USDA ARS Bee Research Laboratory 10300 Baltimore Ave BARC East Bldg 306 Rm 313 Beltsville MD 20705 USA

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