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Functional & Integrative Genomics

, Volume 14, Issue 2, pp 363–379 | Cite as

New wheat microRNA using whole-genome sequence

  • Kuaybe Yucebilgili Kurtoglu
  • Melda Kantar
  • Hikmet Budak
Original Paper

Abstract

MicroRNAs are post-transcriptional regulators of gene expression, taking roles in a variety of fundamental biological processes. Hence, their identification, annotation and characterization are of great significance, especially in bread wheat, one of the main food sources for humans. The recent availability of 5× coverage Triticum aestivum L. whole-genome sequence provided us with the opportunity to perform a systematic prediction of a complete catalogue of wheat microRNAs. Using an in silico homology-based approach, stem-loop coding regions were derived from two assemblies, constructed from wheat 454 reads. To avoid the presence of pseudo-microRNAs in the final data set, transposable element related stem-loops were eliminated by repeat analysis. Overall, 52 putative wheat microRNAs were predicted, including seven, which have not been previously published. Moreover, with distinct analysis of the two different assemblies, both variety and representation of putative microRNA-coding stem-loops were found to be predominant in the intergenic regions. By searching available expressed sequences and small RNA library databases, expression evidence for 39 (out of 52) putative wheat microRNAs was provided. Expression of three of the predicted microRNAs (miR166, miR396 and miR528) was also comparatively quantified with real-time quantitative reverse transcription PCR. This is the first report on in silico prediction of a whole repertoire of bread wheat microRNAs, supported by the wet-lab validation.

Keywords

Triticum aestivum MicroRNA MicroRNA prediction Next-generation sequencing Real-time quantitative reverse transcription PCR 

Abbreviations

miRNA

MicroRNA

pri-miRNA

Primary miRNA

pre-miRNA

Precursor miRNA

RISC

RNA-induced silencing complex

SVM

Support vector machine

EST

Expressed sequence tag

LCG

Low copy number assembly

TREP

Triticeae repeat database

OG

Orthologous group assembly

OGR

Orthologous group representatives

cDNA

Complementary DNA

MFE

Minimal folding free energy

MITE

Miniature inverted terminal repeat element

TE-MIR

Transposable element-related miRNA group

GEO

Gene expression omnibus

TIR

Terminal inverted repeat

LTR

Long terminal repeat

siRNA

Small interfering RNA

Notes

Acknowledgments

The authors are grateful to Dr. Rachel Brenchley and her collegues (Centre for Genome Research, University of Liverpool, UK) for use of the 5× coverage wheat genome assemblies and the transcriptome assembly.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

Experiments comply with the current laws of the country in which they were performed.

Supplementary material

10142_2013_357_MOESM1_ESM.pdf (88 kb)
Table S1 (.xls) Primer Sequences Used in This Study List of all primers used in this study (PDF 87.6 kb)
10142_2013_357_MOESM2_ESM.pdf (129 kb)
Table S2 (.xls) Repeat Elements Found in Putative miRNA-Coding Regions List of repeat elements found to be present in stem-loop coding regions (RepeatMasker data) (PDF 129 kb)
10142_2013_357_MOESM3_ESM.pdf (25 kb)
Table S3 (.xls) miRNAs and miRNA*s Expressed by Evidence of Small RNA Library Blast Search Results of in silico small RNA library search of predicted miRNA-coding stem-loops (PDF 24.7 KB)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Kuaybe Yucebilgili Kurtoglu
    • 1
  • Melda Kantar
    • 1
  • Hikmet Budak
    • 1
  1. 1.Biological Sciences and Bioengineering ProgramSabanci UniversityOrhanliTurkey

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