title: Transcriptome analysis of the bloodstream stage from the parasite Trypanosoma vivax.
abstract: BACKGROUND
  Trypanosoma vivax is the earliest branching African trypanosome. This crucial phylogenetic position makes T. vivax a fascinating model to tackle fundamental questions concerning the origin and evolution of several features that characterize African trypanosomes, such as the Variant Surface Glycoproteins (VSGs) upon which antibody clearing and antigenic variation are based. Other features like gene content and trans-splicing patterns are worth analyzing in this species for comparative purposes.
  
  
  RESULTS
  We present a RNA-seq analysis of the bloodstream stage of T. vivax from data obtained using two complementary sequencing technologies (454 Titanium and Illumina). Assembly of 454 reads yielded 13385 contigs corresponding to proteins coding genes (7800 of which were identified). These sequences, their annotation and other features are available through an online database presented herein. Among these sequences, about 1000 were found to be species specific and 50 exclusive of the T. vivax strain analyzed here. Expression patterns and levels were determined for VSGs and the remaining genes. Interestingly, VSG expression level, although being high, is considerably lower than in Trypanosoma brucei. Indeed, the comparison of surface protein composition between both African trypanosomes (as inferred from RNA-seq data), shows that they are substantially different, being VSG absolutely predominant in T. brucei, while in T. vivax it represents only about 55%. This raises the question concerning the protective role of VSGs in T. vivax, hence their ancestral role in immune evasion.It was also found that around 600 genes have their unique (or main) trans-splice site very close (sometimes immediately before) the start codon. Gene Ontology analysis shows that this group is enriched in proteins related to the translation machinery (e.g. ribosomal proteins, elongation factors).
  
  
  CONCLUSIONS
  This is the first RNA-seq data study in trypanosomes outside the model species T. brucei, hence it provides the possibility to conduct comparisons that allow drawing evolutionary and functional inferences. This analysis also provides several insights on the expression patterns and levels of protein coding sequences (such as VSG gene expression), trans-splicing, codon patterns and regulatory mechanisms. An online T. vivax RNA-seq database described herein could be a useful tool for parasitologists working with trypanosomes.
authors.affiliation: Sección Biomatemática, Facultad de Ciencias, Universidad de la Republica Uruguay, Montevideo, Uruguay. falvarez@fcien.edu.uy.
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Greif
authors.forename: Miguel
authors.initials: M
authors.lastname: Ponce de Leon
authors.forename: Guillermo
authors.initials: G
authors.lastname: Lamolle
authors.forename: Matías
authors.initials: M
authors.lastname: Rodriguez
authors.forename: Dolores
authors.initials: D
authors.lastname: Piñeyro
authors.forename: Lucinda M
authors.initials: LM
authors.lastname: Tavares-Marques
authors.forename: Armando
authors.initials: A
authors.lastname: Reyna-Bello
authors.forename: Carlos
authors.initials: C
authors.lastname: Robello
authors.forename: Fernando
authors.initials: F
authors.lastname: Alvarez-Valin
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D001483:Base Sequence; D020451:Contig Mapping; D020869:Gene Expression Profiling; D017125:Genes, Protozoan; D008018:Life Cycle Stages; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D015800:Protozoan Proteins / Q000235:genetics / Q000378:metabolism*; D022821:RNA Splice Sites; D017422:Sequence Analysis, DNA; D012756:Sheep; D059467:Transcriptome; D016689:Trypanosoma vivax / Q000235:genetics / Q000378:metabolism*; D014643:Variant Surface Glycoproteins, Trypanosoma / Q000235:genetics / Q000378:metabolism
chemical_list: D020121:5' Untranslated Regions; D015800:Protozoan Proteins; D022821:RNA Splice Sites; D014643:Variant Surface Glycoproteins, Trypanosoma