title: Advancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping.
abstract: Since the initial publication of the trypanosomatid genomes, curation has been ongoing. Here we make use of existing Trypanosoma brucei ribosome profiling data to provide evidence of ribosome occupancy (and likely translation) of mRNAs from 225 currently unannotated coding sequences (CDSs). A small number of these putative genes correspond to extra copies of previously annotated genes, but 85% are novel. The median size of these novels CDSs is small (81 aa), indicating that past annotation work has excelled at detecting large CDSs. Of the unique CDSs confirmed here, over half have candidate orthologues in other trypanosomatid genomes, most of which were not yet annotated as protein-coding genes. Nonetheless, approximately one-third of the new CDSs were found only in T. brucei subspecies. Using ribosome footprints, RNA-Seq and spliced leader mapping data, we updated previous work to definitively revise the start sites for 414 CDSs as compared to the current gene models. The data pointed to several regions of the genome that had sequence errors that altered coding region boundaries. Finally, we consolidated this data with our previous work to propose elimination of 683 putative genes as protein-coding and arrive at a view of the translatome of slender bloodstream and procyclic culture form T. brucei.
authors.affiliation: The Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave. N., Seattle, WA 98109, USA; Dept of Global Health, University of Washington, Seattle, WA 98195, USA. Electronic address: marilyn.parsons@cidresearch.org.
authors.forename: Marilyn
authors.initials: M
authors.lastname: Parsons
authors.affiliation: The Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave. N., Seattle, WA 98109, USA.
authors.forename: Gowthaman
authors.initials: G
authors.lastname: Ramasamy
authors.affiliation: The Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave. N., Seattle, WA 98109, USA.
authors.forename: Elton J R
authors.initials: EJ
authors.lastname: Vasconcelos
authors.affiliation: The Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave. N., Seattle, WA 98109, USA.
authors.forename: Bryan C
authors.initials: BC
authors.lastname: Jensen
authors.affiliation: The Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave. N., Seattle, WA 98109, USA; Dept of Global Health, University of Washington, Seattle, WA 98195, USA; Dept of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Myler
mesh_terms: D018387:Codon, Initiator / Q000235:genetics*; D019143:Evolution, Molecular; D017125:Genes, Protozoan; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D020038:RNA, Spliced Leader / Q000235:genetics*; D012270:Ribosomes / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D014346:Trypanosoma brucei brucei / Q000235:genetics*
chemical_list: D018387:Codon, Initiator; D020038:RNA, Spliced Leader
keywords: De novo gene evolution; Genome annotation; Ribosome profiling; Translation; Trypanosomes