Kantar, M., Akpınar, B.A., Valárik, M., Lucas, S.J., Doležel, J., Hernández, P., Budak, H.
FUNCTIONAL & INTEGRATIVE GENOMICS 12: 465-479, 2012

Keywords: Triticum aestivum, microRNA, miRNA prediction, Sub-genomic analysis, Next-generation sequencing
Abstract: In this study, a survey of miRNAs using the nextgeneration sequencing data was performed at subgenomic level. After analyzing shotgun sequences from chromosome 4A of bread wheat (Triticum aestivum L.), a total of 68 different miRNAs were predicted in silico, of which 37 were identified in wheat for the first time. The long arm of the chromosome was found to harbor a higher variety (51) and representation (3,928) of miRNAs compared with the short arm (49; 2,226). Out of the 68 miRNAs, 32 were detected to be common to both arms, revealing the presence of separate miRNA clusters in the two chromosome arms. The differences in degree of representation of the different miRNAs were found to be highly variable, ranging 592-fold, which may have an effect on target regulation. Targets were retrieved for 62 (out of 68) of wheat-specific, newly identified miRNAs indicated that fundamental aspects of plant morphology such as height and flowering were predicted to be affected. In silico expression blast analysis indicated 24 (out of 68) were found to give hits to expressed sequences. This is the first report of species- and chromosome-specific miRNAs.
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IEB authors: Jaroslav Doležel, Miroslav Valárik