Functional & Integrative Genomics

, Volume 12, Issue 3, pp 465–479

Subgenomic analysis of microRNAs in polyploid wheat

  • Melda Kantar
  • Bala Anı Akpınar
  • Miroslav Valárik
  • Stuart J. Lucas
  • Jaroslav Doležel
  • Pilar Hernández
  • Hikmet Budak
  • International Wheat Genome Sequencing Consortium, executive director Kellye Eversole (IWGSC) (eversole@eversoleassociates.com and www.wheatgenome.org)
Original Paper

DOI: 10.1007/s10142-012-0285-0

Cite this article as:
Kantar, M., Akpınar, B.A., Valárik, M. et al. Funct Integr Genomics (2012) 12: 465. doi:10.1007/s10142-012-0285-0

Abstract

In this study, a survey of miRNAs using the next-generation 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.

Keywords

Triticum aestivummicroRNAmiRNA predictionSub-genomic analysisNext-generation sequencing

Abbreviations

miRNA

MicroRNA

4AS

Short arm of chromosome 4A

4AL

Long arm of chromosome 4A

e value

Expectation value

ΔG

Folding-free energies

EST

Expressed sequence tag

MFE

Minimal folding-free energy

MFEI

Minimal folding-free energy index

miRNA*

miRNA star strand

NCBI

National center for biotechnology information

nt

Nucleotide(s)

premiRNA

MicroRNA precursor

siRNA

Small interfering RNA

TE

Transposable element

mRNA

Messenger RNA

Supplementary material

10142_2012_285_MOESM1_ESM.doc (67 kb)
Supplementary Table 1A) Perl Program SUmirFind.pl This script uses NCBI BLAST to search for potential homologs of known miRNAs. B) Perl Program SumiRFold. This script uses a BLAST results table to retrieve sequences from the BLAST database and to obtain their predicted secondary structure using UNAfold, after which viable hairpins are detected and retrieved. (DOC 67 kb)
10142_2012_285_MOESM2_ESM.doc (406 kb)
Supplementary Table 2List of computer based, newly identified miRNAs of chromosome 4A in T. aestivum and their characteristics. This table lists characteristics of only one identified wheat miRNA, derived from one sequence read, corresponding to each query sequence (DOC 405 kb)
10142_2012_285_MOESM3_ESM.doc (3.3 mb)
Supplementary Table 3Number of sequence reads of 4AL from which potential miRNA stem-loop structures were retrieved. (DOC 3363 kb)
10142_2012_285_MOESM4_ESM.doc (1.9 mb)
Supplementary Table 4Number of sequence reads of 4AS from which potential miRNA stem-loop structures were retrieved. (DOC 1908 kb)
10142_2012_285_MOESM5_ESM.doc (563 kb)
Supplementary Table 5Homology of newly identified T. aestivum miRNAs to miRNAs in other plant species. A) Only 4AS; B) only 4AL; C) both chromosome arms (DOC 563 kb)
10142_2012_285_MOESM6_ESM.doc (256 kb)
Supplementary Table 6Predicted targets of newly identified T. aestivum miRNAs. Targets were retrieved using psRNATarget software. (DOC 256 kb)
10142_2012_285_MOESM7_ESM.doc (56 kb)
Supplementary Table 7Number of Blast hits for each miRNA (DOC 56 kb)
10142_2012_285_MOESM8_ESM.doc (82 kb)
Supplementary Table 8Distribution of conserved miRNAs on B. distachyon chromosomes. (DOC 82 kb)
10142_2012_285_MOESM9_ESM.doc (250 kb)
Supplementary Table 9Distribution of conserved miRNAs on O. sativa chromosomes. (DOC 249 kb)

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Melda Kantar
    • 1
  • Bala Anı Akpınar
    • 1
  • Miroslav Valárik
    • 2
  • Stuart J. Lucas
    • 1
  • Jaroslav Doležel
    • 2
  • Pilar Hernández
    • 3
  • Hikmet Budak
    • 1
  • International Wheat Genome Sequencing Consortium, executive director Kellye Eversole (IWGSC) (eversole@eversoleassociates.com and www.wheatgenome.org)
  1. 1.Biological Sciences and Bioengineering ProgramSabanci UniversityIstanbulTurkey
  2. 2.Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
  3. 3.Instituto de Agricultura Sostenible (IAS-CSIC)CordobaSpain