Unknown,Transcriptomics,Genomics,Proteomics

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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 apply the technique of ribosome profiling to Trypanosoma brucei, identifying 223 new coding regions by virtue of ribosome occupancy in the corresponding transcripts. 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 (74 aa) indicating that past annotation work has excelled at detecting large CDSs. Of the unique CDSs discovered here, over half have candidate orthologues in other trypanosomatid genomes, most of which were not yet annotated as genes. Still, approximately one-third of the new CDSs were found only in T. brucei subspecies. When combined with RNA-seq and spliced leader mapping, we were able to definitively revise the start sites for 430 CDSs as compared to the current gene models. Such data also allowed us to use a structured approach to eliminate 701 putative genes as protein-coding. Finally, the data pointed to several regions of the genome that had sequence errors that altered coding region boundaries. Ribosome profiling and mRNA libraries were constructed in triplicate from in vitro PCF and in vivo BF lifestages of theT. brucei Treu927 and in vitro T. brucei Lister427, to evaluate role of translational gene regulation

ORGANISM(S): Trypanosoma brucei

SUBMITTER: Gowthaman Ramasamy 

PROVIDER: E-GEOD-72463 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Advancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping.

Parsons Marilyn M   Ramasamy Gowthaman G   Vasconcelos Elton J R EJ   Jensen Bryan C BC   Myler Peter J PJ  

Molecular and biochemical parasitology 20150801 2


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  ...[more]

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