Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

Biology Centre Institute of Parasitology Czech Academy of Sciences České Budějovice Czech Republic

Biology Centre Institute of Parasitology Czech Academy of Sciences České Budějovice Czech Republic; Canadian Institute for Advanced Research Toronto Canada

Biology Centre Institute of Parasitology Czech Academy of Sciences České Budějovice Czech Republic; Center for Parasitic Organisms State Key Laboratory of Biocontrol School of Life Sciences and Key Laboratory of Tropical Disease Control of Ministry of Education Zhongshan School of Medicine Sun Yat Sen University Guangzhou People's Republic of China

Center for Parasitic Organisms State Key Laboratory of Biocontrol School of Life Sciences and Key Laboratory of Tropical Disease Control of Ministry of Education Zhongshan School of Medicine Sun Yat Sen University Guangzhou People's Republic of China

Centre for Genomic Research Institute of Integrative Biology University of Liverpool Liverpool United Kingdom

Centre of Immunity Infection and Evolution University of Edinburgh Edinburgh United Kingdom

Centre of Immunity Infection and Evolution University of Edinburgh Edinburgh United Kingdom; Institute of Immunology and Infection Research University of Edinburgh Edinburgh United Kingdom

CIRAD UMR InterTryp Montpellier France; Faculty of Veterinary Medicine Kasetsart University Bangkok Thailand

Department of Infection Biology Institute of Infection and Global Health University of Liverpool Liverpool United Kingdom

Department of Pathogen Molecular Biology Faculty of Infectious and Tropical Diseases London School of Hygiene and Tropical Medicine London United Kingdom

Seattle Biomedical Research Institute Seattle United States of America

Seattle Biomedical Research Institute Seattle United States of America; Department of Global Health University of Washington Seattle United States of America

Swiss Tropical and Public Health Institute Basel Switzerland

Unit of Molecular Parasitology Department of Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium

Wellcome Trust Centre for Molecular Parasitology Institute of Biodiversity Animal Health and Comparative Medicine College of Medical Veterinary and Life Sciences University of Glasgow Glasgow United Kingdom

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