Parsons et al. 2015 (PRJNA294100)

General Details

Title Advancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping
Organism
Number of Samples 9
Release Date 2015/08/27 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP062914
ENA SRP062914
GEO GSE72463
BioProject PRJNA294100

Publication

Title
Authors Parsons M, Ramasamy G, Vasconcelos EJ, Jensen BC, Myler PJ
Journal Molecular and biochemical parasitology
Publication Date 2015 Aug
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. Copyright © 2015 Elsevier B.V. All rights reserved.
PMC PMC4644489
PMID 26393539
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR2188086 PRJNA294100 Trypanosoma brucei 0.0 Ribo-Seq 0.0
SRR2188087 PRJNA294100 Trypanosoma brucei 0.0 Ribo-Seq 0.0
SRR2188088 PRJNA294100 Trypanosoma brucei 0.0 Ribo-Seq 0.0
SRR2188089 PRJNA294100 Trypanosoma brucei 0.0 Ribo-Seq 0.0
SRR2188090 PRJNA294100 Trypanosoma brucei 0.0 Ribo-Seq 0.0
SRR2188091 PRJNA294100 Trypanosoma brucei 0.0 Ribo-Seq 0.0
SRR2188092 PRJNA294100 Trypanosoma brucei 0.0 Ribo-Seq 0.0
SRR2188093 PRJNA294100 Trypanosoma brucei 0.0 Ribo-Seq 0.0
SRR2188094 PRJNA294100 Trypanosoma brucei 0.0 Ribo-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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