Abstract
MicroRNAs are a class of post-transcriptional regulators of plant developmental and physiological processes and responses to environmental stresses. Here, we present the study regarding the annotation and characterization of MIR genes conducted in durum wheat. We characterized the miRNAome of leaf and root tissues at tillering stage under two environmental conditions: irrigated with 100% (control) and 55% of evapotranspiration (early water stress). In total, 90 microRNAs were identified, of which 32 were classified as putative novel and species-specific miRNAs. In addition, seven microRNA homeologous groups were identified in each of the two genomes of the tetraploid durum wheat. Differential expression analysis highlighted a total of 45 microRNAs significantly differentially regulated in the pairwise comparisons leaf versus root. The miRNA families, miR530, miR395, miR393, miR5168, miR396 and miR166, miR171, miR319, and miR167, were the most expressed in leaves in comparison to roots. Putative microRNA targets were predicted for both five and three prime sequences derived from the stem-loop of the MIR gene. Gene ontology analysis showed significant overrepresented gene categories in microRNA targets belonging to transcription factors, phenylpropanoids, oxydases, and lipid binding-protein. This work represents one of the first genome wide characterization of MIR genes in durum wheat, identifying leaf and root tissue-specific microRNAs. This genomic identification of microRNAs together with the analysis of their expression profiles is a well-accepted starting point leading to a better comprehension of the role of MIR genes in the genus Triticum.
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Acknowledgments
The present research was supported by the MIUR (Italian Minister of University & Research) project “Sviluppo tecnologico e innovazione per la sostenibilità e competitività della cerealicoltura meridionale” - PON01_01145/5-ISCOCEM.
Author’s contributions
FM conceived and designed the experiments. Experimental work was mostly performed by VF. EB designed and carried out all the computational analyses. Plant and soil measurements and analyses were performed by PR and DG. CC contributed to the discussion of experimental data. All authors contributed to write the manuscript.
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Veronica Fileccia and Edoardo Bertolini contributed equally to this work.
Electronic supplementary material
ESM 1
BlastN tabular output of known miRNA identified in this work. (TXT 3 kb)
ESM 2
List of all potential miRNA targets generated using the 5P sequences identified in this work. (TXT 350 kb)
ESM 3
List of all potential miRNA targets generated using the 3P sequences identified in this work. (TXT 292 kb)
ESM 4
Gene ontology of potential targets of differentially regulated microRNA (score between 0 and 3). Biological processes, cellular locations and molecular functions of potential targets mRNAs are indicated. (PDF 57 kb)
ESM 5
GO terms associated to the miRNA targets. Transcript ID, gene ontologies and description are indicated. (TXT 234 kb)
ESM 6
Interpro description associated to the miRNA targets (transcript ID) are shown. (TXT 28 kb)
ESM 7
Gene family ID associated to the miRNA targets (transcript ID) are shown. (TXT 7 kb)
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Fileccia, V., Bertolini, E., Ruisi, P. et al. Identification and characterization of durum wheat microRNAs in leaf and root tissues. Funct Integr Genomics 17, 583–598 (2017). https://doi.org/10.1007/s10142-017-0551-2
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DOI: https://doi.org/10.1007/s10142-017-0551-2