title: De Novo Genome Assembly Shows Genome Wide Similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense.
abstract: BACKGROUND
  Trypanosoma brucei is a eukaryotic pathogen which causes African trypanosomiasis. It is notable for its variant surface glycoprotein (VSG) coat, which undergoes antigenic variation enabled by a large suite of VSG pseudogenes, allowing for persistent evasion of host adaptive immunity. While Trypanosoma brucei rhodesiense (Tbr) and T. b gambiense (Tbg) are human infective, related T. b. brucei (Tbb) is cleared by human sera. A single gene, the Serum Resistance Associated (SRA) gene, confers Tbr its human infectivity phenotype. Potential genetic recombination of this gene between Tbr and non-human infective Tbb strains has significant epidemiological consequences for Human African Trypanosomiasis outbreaks.
  
  
  RESULTS
  Using long and short read whole genome sequencing, we generated a hybrid de novo assembly of a Tbr strain, producing 4,210 scaffolds totaling approximately 38.8 megabases, which comprise a significant proportion of the Tbr genome, and thus represents a valuable tool for a comparative genomics analyses among human and non-human infective T. brucei and future complete genome assembly. We detected 5,970 putative genes, of which two, an alcohol oxidoreductase and a pentatricopeptide repeat-containing protein, were members of gene families common to all T. brucei subspecies, but variants specific to the Tbr strain sequenced in this study. Our findings confirmed the extremely high level of genomic similarity between the two parasite subspecies found in other studies.
  
  
  CONCLUSIONS
  We confirm at the whole genome level high similarity between the two Tbb and Tbr strains studied. The discovery of extremely minor genomic differentiation between Tbb and Tbr suggests that the transference of the SRA gene via genetic recombination could potentially result in novel human infective strains, thus all genetic backgrounds of T. brucei should be considered potentially human infective in regions where Tbr is prevalent.
authors.affiliation: School of Natural Sciences, University of California, Merced, 5200 N. Lake Rd, Merced, CA, 95343, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Sistrom
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street New Haven, CT 06520, United States of America.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Evans
authors.affiliation: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, United States of America.
authors.forename: Joshua
authors.initials: J
authors.lastname: Benoit
authors.affiliation: Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland.
authors.forename: Oliver
authors.initials: O
authors.lastname: Balmer
authors.affiliation: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, United States of America.
authors.forename: Serap
authors.initials: S
authors.lastname: Aksoy
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street New Haven, CT 06520, United States of America.
authors.forename: Adalgisa
authors.initials: A
authors.lastname: Caccone
mesh_terms: D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D023281:Genomics; D006801:Humans; D008562:Membrane Glycoproteins / Q000235:genetics; D015800:Protozoan Proteins / Q000235:genetics; D017421:Sequence Analysis; D014346:Trypanosoma brucei brucei / Q000235:genetics* / Q000502:physiology; D016833:Trypanosoma brucei rhodesiense / Q000235:genetics* / Q000502:physiology; D014353:Trypanosomiasis, African / Q000453:epidemiology
chemical_list: D008562:Membrane Glycoproteins; D015800:Protozoan Proteins; C403774:serum resistance associated protein, Trypanosoma brucei