Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing

Liu, Minmin; Yu, Huiyang; Zhao, Gangjun; Huang, Qiufeng; Lu, Yongen; Ouyang, Bo

doi:10.1186/s12864-017-3869-1

Cited by 98 publications

(81 citation statements)

References 100 publications

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“…The tomato miRNA sequences were extracted from Kaur et al and Liu et al (90, 91). Next, we used psRNATarget (51) against ITAG3.2 mRNA sequences to identify potential miRNA targets.…”

Section: Methodsmentioning

confidence: 99%

Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling

Song

Walley

et al. 2019

Preprint

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25mRNA translation is a critical step in gene expression, but our understanding of the 26 landscape and control of translation in diverse crops remains lacking. Here, we combined de 27 novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato 28 roots. Taking advantage of the 3-nucleotide periodicity displayed by translating ribosomes, we 29 identified 354 novel small ORFs (sORFs) translated from previously unannotated transcripts, as 30 well as 1329 upstream ORFs (uORFs) translated within the 5' UTRs of annotated protein-coding 31 genes. Proteomic analysis confirmed that some of these novel uORFs and sORFs generate 32 stable proteins in planta. Compared with the annotated ORFs, the uORFs use more flexible 33 Kozak sequences around translation start sites. Interestingly, uORF-containing genes are 34 enriched for protein phosphorylation/dephosphorylation and signaling transduction pathways, 35 suggesting a regulatory role for uORFs in these processes. We also demonstrated that 36 ribosome profiling is useful to facilitate the annotation of translated ORFs and noncanonical 37 translation initiation sites. In addition to defining the translatome, our results revealed the global 38 control of mRNA translation by uORFs and microRNAs in tomato. In summary, our approach 39 provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily 40 conserved translational features, and identifies new regulatory mechanisms hidden in a crop 41 genome. 42 43 48 transcriptome assembly and ribosome profiling, we mapped and quantified translating 49 ribosomes across the entire transcriptome in tomato roots. This is the first experiment-based 50 survey to systematically identify actively translated ORFs in a crop. Our results reveal numerous 51 unannotated translation events and uncover new regulatory mechanisms of gene expression in 52 tomato. Our approach not only facilitates our understanding of the tomato translational 53 landscape but also provides a practical strategy to study the translatomes of other species. 54 55 56 Introduction 57Besides being an essential step in gene expression, mRNA translation directly shapes 58 the proteome, which contributes to cellular structure, function, and activity in all organisms. The 59 characterization of translational regulation has enabled crop improvement, including increasing 60 tomato sweetness, rice immunity and lettuce resistance to oxidative stress (1-3). However, due 61 to limited genomic resources and methods, most crop translatomes remain understudied. 62Ribosome profiling, or Ribo-seq, has emerged as a high-throughput technique to study 63 global translation (4-6). In a Ribo-seq experiment, ribosomes in the sample of interest are 64 immobilized, and the lysate is treated with nucleases to obtain ribosome-protected mRNA 65 fragments (i.e. ribosome footprints). Finally, sequencing of the ribosome footprints reveals the 66 quantity and positions of ribosomes on a given transcript. Features corresponding to active 67 translat...

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“…The tomato miRNA sequences were extracted from Kaur et al and Liu et al (90, 91). Next, we used psRNATarget (51) against ITAG3.2 mRNA sequences to identify potential miRNA targets.…”

Section: Methodsmentioning

confidence: 99%

Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling

Song

Walley

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…The tomato microRNA sequences were extracted from Kaur et al (2017) and Liu et al (2017). Next, we used psRNATarget (Dai et al, 2018) against ITAG3.2 mRNA sequences to identify potential microRNA targets.…”

Section: Microrna Target Identificationmentioning

confidence: 99%

The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling

Song

Walley

et al. 2019

Plant Physiol.

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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 59 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.

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“…QTL‐by‐watering regime interactions were recently reported for tomato fruit quality traits, emphasizing their importance for its improvement (Gur et al ., ; Albert et al ., ,b). However, genetic variation in gene expression levels under water deficit has only been considered so far on a limited number of contrasted tomato accessions (Albert et al ., 2016a; Liu et al ., ) and the underlying genetic architecture remains to be explored.…”

Section: Introductionmentioning

confidence: 99%

Allele‐specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

et al. 2018

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Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype-by-environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome-wide scale. We sequenced the transcriptome of growing leaves and fruit pericarps at cell expansion stage in a cherry and a large fruited accession and their F hybrid grown under two watering regimes. Gene expression levels were steadily affected by the genotype and the watering regime. Whereas phenotypes showed mostly additive inheritance, ~80% of the genes displayed non-additive inheritance. By comparing allele-specific expression (ASE) in the F hybrid to the allelic expression in both parental lines, respectively, 3005 genes in leaf and 2857 genes in fruit deviated from 1:1 ratio independently of the watering regime. Among these genes, ~55% were controlled by cis factors, ~25% by trans factors and ~20% by a combination of both types of factors. A total of 328 genes in leaf and 113 in fruit exhibited significant ASE-by-watering regime interaction, among which ~80% presented trans-by-watering regime interaction, suggesting a response to water deficit mediated through a majority of trans-acting loci in tomato. We cross-validated the expression levels of 274 transcripts in fruit and leaves of 124 recombinant inbred lines (RILs) and identified 163 expression quantitative trait loci (eQTLs) mostly confirming the divergences identified by ASE. Combining phenotypic and expression data, we observed a complex network of variation between genes encoding enzymes involved in the sugar metabolism.

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Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing

Cited by 98 publications

References 100 publications

Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling

Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling

The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling

Allele‐specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

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