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Subgenomic analysis of microRNAs in polyploid wheat

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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.

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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

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Acknowledgments

Financial support by the Sabanci University Internal Grant, Spanish Ministry of Science and Innovation (MICINN grants BIO2009-07443, AGL2010-17316, and BIO2011-15237) and the Ministry of Education, Youth and Sports of the Czech Republic and the European Regional Development Fund (Operational Program Research and Development for Innovations No. ED0007/01/01) is gratefully acknowledged. The authors also acknowledge the help of D. Adali, E. Toklu, R. Fayotorbay, and The International Wheat Genome Sequencing Consortium for access to the 4A survey sequence developed under the IWGSC Survey Sequencing Initiative.

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Authors and Affiliations

  1. Biological Sciences and Bioengineering Program, Sabanci University, Tuzla, 34956, Istanbul, Turkey

    Melda Kantar, Bala Anı Akpınar, Stuart J. Lucas & Hikmet Budak

  2. Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, CZ-77200, Olomouc, Czech Republic

    Miroslav Valárik & Jaroslav Doležel

  3. Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo s/n, Apdo. 4084, 14080, Cordoba, Spain

    Pilar Hernández

Authors
  1. Melda Kantar
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  2. Bala Anı Akpınar
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  3. Miroslav Valárik
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  4. Stuart J. Lucas
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  5. Jaroslav Doležel
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  6. Pilar Hernández
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  7. Hikmet Budak
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Consortia

International Wheat Genome Sequencing Consortium, executive director Kellye Eversole (IWGSC) (eversole@eversoleassociates.com and www.wheatgenome.org)

Corresponding author

Correspondence to Hikmet Budak.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Table 1

A) 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)

Supplementary Table 2

List 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)

Supplementary Table 3

Number of sequence reads of 4AL from which potential miRNA stem-loop structures were retrieved. (DOC 3363 kb)

Supplementary Table 4

Number of sequence reads of 4AS from which potential miRNA stem-loop structures were retrieved. (DOC 1908 kb)

Supplementary Table 5

Homology 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)

Supplementary Table 6

Predicted targets of newly identified T. aestivum miRNAs. Targets were retrieved using psRNATarget software. (DOC 256 kb)

Supplementary Table 7

Number of Blast hits for each miRNA (DOC 56 kb)

Supplementary Table 8

Distribution of conserved miRNAs on B. distachyon chromosomes. (DOC 82 kb)

Supplementary Table 9

Distribution of conserved miRNAs on O. sativa chromosomes. (DOC 249 kb)

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Kantar, M., Akpınar, B.A., Valárik, M. et al. Subgenomic analysis of microRNAs in polyploid wheat. Funct Integr Genomics 12, 465–479 (2012). https://doi.org/10.1007/s10142-012-0285-0

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