Abstract
MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and exploiting their roles on a functional context, providing valuable clues into the regulation of important biological processes, such as stress tolerance or environmental adaptation. Wheat is a hardy crop, extensively harvested in temperate regions, and is a major component of the human diet. With the advent of the next generation sequencing technologies considerably decreasing sequencing costs per base-pair, genomic, and transcriptomic data from several wheat species, including the progenitors and wild relatives have become available. In this study, we performed in silico identification and comparative analysis of microRNA repertoires of bread wheat (Triticum aestivum L.) and its diploid progenitors and relatives, Aegilops sharonensis, Aegilops speltoides, Aegilops tauschii, Triticum monococcum, and Triticum urartu through the utilization of publicly available transcriptomic data. Over 200 miRNA families were identified, majority of which have not previously been reported. Ancestral relationships expanded our understanding of wheat miRNA evolution, while T. monococcum miRNAs delivered important clues on the effects of domestication on miRNA expression. Comparative analyses on wild Ae. sharonensis accessions highlighted candidate miRNAs that can be linked to stress tolerance. The miRNA repertoires of bread wheat and its diploid progenitors and relatives provide important insight into the diversification and distribution of miRNA genes, which should contribute to the elucidation of miRNA evolution of Poaceae family. A thorough understanding of the convergent and divergent expression profiles of miRNAs in different genetic backgrounds can provide unique opportunities to modulation of gene regulation for better crop performance.
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This research was funded by Sabanci University and Montana Plant Science Endowment.
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This article forms part of a special issue of Functional & Integrative Genomics entitled “miRNA in model and complex organisms” (Issue Editors: Hikmet Budak and Baohong Zhang
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Supplementary Figure S1
Correlation analysis between assembly length (Mb), number of identified miRNA families and corresponding stem-loop counts. Correlation coefficients were calculated respect to “Pearson”-type correlation. (GIF 130 kb)
Supplementary Figure S2
Comparative analysis of retained/lost miRNA percentage between different relatives & progenitors and bread wheat. Whole miRNA families, identified through 16 different genotypes, were counted in case of Ae. sharonensis. (GIF 53 kb)
Supplementary Figure S3
GO annotations for (A) Biological Process, (B) Cellular Component and (C) for Molecular Function, for all 16 Ae. sharonensis genotypes. All target annotations as given in Supplementary File 3 can be provided upon request. (GIF 261 kb)
Supplementary File S1
(xlsx) Assembly metrics for all genotypes included in this study. (XLSX 11 kb)
Supplementary File S2
(xlsx) The list of all putative miRNAs and pre-miRNAs identified from all genotypes. Ash: Ae. sharonensis, Asp: Ae. speltoides, Ata: Ae. tauschii, Tae: T. aestivum, Tm_a: T. monococcum ssp. aegilopoides, Tm_m: T. monococcum ssp. monococcum, Tur: T. urartu.(XLSX 882 kb)
Supplementary File S3
(xlsx) Putative miRNA targets and target annotations for, Asp: Ae. speltoides, Ata: Ae. tauschii, Tae: T. aestivum, Tm_a: T. monococcum ssp. aegilopoides, Tm_m: T. monococcum ssp. monococcum, Tur: T. urartu (XLSX 14497 kb)
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Alptekin, B., Budak, H. Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors. Funct Integr Genomics 17, 171–187 (2017). https://doi.org/10.1007/s10142-016-0487-y
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DOI: https://doi.org/10.1007/s10142-016-0487-y