title: Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty.
abstract: 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.
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Jason
authors.initials: J
authors.lastname: Carnes
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Atashi
authors.initials: A
authors.lastname: Anupama
authors.affiliation: Swiss Tropical and Public Health Institute, Basel, Switzerland.
authors.forename: Oliver
authors.initials: O
authors.lastname: Balmer
authors.affiliation: Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Jackson
authors.affiliation: Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
authors.forename: Michael
authors.initials: M
authors.lastname: Lewis
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Rob
authors.initials: R
authors.lastname: Brown
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Igor
authors.initials: I
authors.lastname: Cestari
authors.affiliation: CIRAD, UMR-InterTryp, Montpellier, France; Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand.
authors.forename: Marc
authors.initials: M
authors.lastname: Desquesnes
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Claire
authors.initials: C
authors.lastname: Gendrin
authors.affiliation: Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
authors.forename: Christiane
authors.initials: C
authors.lastname: Hertz-Fowler
authors.affiliation: Unit of Molecular Parasitology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
authors.forename: Hideo
authors.initials: H
authors.lastname: Imamura
authors.affiliation: Centre of Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Alasdair
authors.initials: A
authors.lastname: Ivens
authors.affiliation: Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, Centre, České Budějovice (Budweis), Czech Republic.
authors.forename: Luděk
authors.initials: L
authors.lastname: Kořený
authors.affiliation: Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, Centre, České Budějovice (Budweis), 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.
authors.forename: De-Hua
authors.initials: DH
authors.lastname: Lai
authors.affiliation: 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.
authors.forename: Annette
authors.initials: A
authors.lastname: MacLeod
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: McDermott
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Chris
authors.initials: C
authors.lastname: Merritt
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Severine
authors.initials: S
authors.lastname: Monnerat
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Wonjong
authors.initials: W
authors.lastname: Moon
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Peter
authors.initials: P
authors.lastname: Myler
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Phan
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Gowthaman
authors.initials: G
authors.lastname: Ramasamy
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.
authors.forename: Dhileep
authors.initials: D
authors.lastname: Sivam
authors.affiliation: 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.
authors.forename: Zhao-Rong
authors.initials: ZR
authors.lastname: Lun
authors.affiliation: Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, Centre, České Budějovice (Budweis), Czech Republic; Canadian Institute for Advanced Research, Toronto, Canada.
authors.forename: Julius
authors.initials: J
authors.lastname: Lukeš
authors.affiliation: Seattle Biomedical Research Institute, Seattle, United States of America; Department of Global Health, University of Washington, Seattle, United States of America.
authors.forename: Ken
authors.initials: K
authors.lastname: Stuart
authors.affiliation: Centre of Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom; Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Achim
authors.initials: A
authors.lastname: Schnaufer
mesh_terms: D005786:Gene Expression Regulation; D018503:Genome, Protozoan; D018895:Microsatellite Repeats; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D015800:Protozoan Proteins / Q000235:genetics / Q000378:metabolism*; D014345:Trypanosoma / Q000145:classification* / Q000235:genetics*; D014643:Variant Surface Glycoproteins, Trypanosoma / Q000235:genetics / Q000378:metabolism
chemical_list: D015800:Protozoan Proteins; D014643:Variant Surface Glycoproteins, Trypanosoma