Wu et al. 2019 (PRJNA514710)

General Details

Title The landscape of mRNA translation in tomato roots
Organism
Number of Samples 3
Release Date 2019/01/11 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP178496
ENA SRP178496
GEO GSE124962
BioProject PRJNA514710

Publication

Title
Authors Wu HL, Song G, Walley JW, Hsu PY
Journal Plant physiology
Publication Date 2019 Sep
Abstract Recent applications of translational control in Arabidopsis ( Arabidopsis thaliana ) highlight the potential power of manipulating mRNA translation for crop improvement. However, to what extent translational regulation is conserved between Arabidopsis and other species is largely unknown, and the translatome of most crops remains poorly studied. Here, we combined de novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato ( Solanum lycopersicum ) roots. Exploiting features corresponding to active translation, we discovered widespread unannotated translation events, including 1,329 upstream open reading frames (uORFs) within the 5' untranslated regions of annotated coding genes and 354 small ORFs (sORFs) among unannotated transcripts. uORFs may repress translation of their downstream main ORFs, whereas sORFs may encode signaling peptides. Besides evolutionarily conserved sORFs, we uncovered 96 Solanaceae-specific sORFs, revealing the importance of studying translatomes directly in crops. Proteomic analysis confirmed that some of the unannotated ORFs generate stable proteins in planta. In addition to defining the translatome, our results reveal the global regulation by uORFs and microRNAs. Despite diverging over 100 million years ago, many translational features are well conserved between Arabidopsis and tomato. Thus, our approach provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily conserved and unique translational features, and identifies regulatory mechanisms hidden in a crop genome. © 2019 American Society of Plant Biologists. All Rights Reserved.
PMC PMC6716236
PMID 31248964
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR8434774 PRJNA514710 Solanum lycopersicum 0.0 Ribo-Seq 0.0
SRR8434775 PRJNA514710 Solanum lycopersicum 0.0 Ribo-Seq 0.0
SRR8434776 PRJNA514710 Solanum lycopersicum 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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