BACKGROUND: Protists of the family Trypanosomatidae (phylum Euglenozoa) have gained notoriety as parasites affecting humans, domestic animals, and agricultural plants. However, the true extent of the group's diversity spreads far beyond the medically and veterinary relevant species. We address several knowledge gaps in trypanosomatid research by undertaking sequencing, assembly, and analysis of genomes from previously overlooked representatives of this protistan group. RESULTS: We assembled genomes for twenty-one trypanosomatid species, with a primary focus on insect parasites and Trypanosoma spp. parasitizing non-human hosts. The assemblies exhibit sizes consistent with previously sequenced trypanosomatid genomes, ranging from approximately 18 Mb for Obscuromonas modryi to 35 Mb for Crithidia brevicula and Zelonia costaricensis. Despite being the smallest, the genome of O. modryi has the highest content of repetitive elements, contributing nearly half of its total size. Conversely, the highest proportion of unique DNA is found in the genomes of Wallacemonas spp., with repeats accounting for less than 8% of the assembly length. The majority of examined species exhibit varying degrees of aneuploidy, with trisomy being the most frequently observed condition after disomy. CONCLUSIONS: The genome of Obscuromonas modryi represents a very unusual, if not unique, example of evolution driven by two antidromous forces: i) increasing dependence on the host leading to genomic shrinkage and ii) expansion of repeats causing genome enlargement. The observed variation in somy within and between trypanosomatid genera suggests that these flagellates are largely predisposed to aneuploidy and, apparently, exploit it to gain a fitness advantage. High heterogeneity in the genome size, repeat content, and variation in chromosome copy numbers in the newly-sequenced species highlight the remarkable genome plasticity exhibited by trypanosomatid flagellates. These new genome assemblies are a robust foundation for future research on the genetic basis of life cycle changes and adaptation to different hosts in the family Trypanosomatidae.

Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1QW UK

Department of Parasitology Faculty of Science Charles University 128 44 Prague Czech Republic

Department of Parasitology Faculty of Science Charles University BIOCEV 252 50 Vestec Czech Republic

Division of Infectious Diseases Department of Medicine University of Alberta Edmonton T6G 2G3 Canada

Duluth Campus University of Minnesota Medical School Duluth MN 55812 USA

Faculty of Biology M 5 Lomonosov Moscow State University 119991 Moscow Russia

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

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

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

Martsinovsky Institute of Medical Parasitology Sechenov University 119435 Moscow Russia

Zoological Institute of the Russian Academy of Sciences 199034 St Petersburg Russia

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Somy evolution in the honey bee infecting trypanosomatid parasite Lotmaria passim

Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote

A novel strain of Leishmania braziliensis harbors not a toti- but a bunyavirus

Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae)

Multiple and frequent trypanosomatid co-infections of insects: the Cuban case study

Distribution and Functional Analysis of Isocitrate Dehydrogenases across Kinetoplastids

In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code