Plant Molecular Biology Reporter

, Volume 32, Issue 2, pp 487–500 | Cite as

Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes

  • Pingchuan Deng
  • Xiaojun Nie
  • Le Wang
  • Licao Cui
  • Peixun Liu
  • Wei Tong
  • Siddanagouda S. Biradar
  • David Edwards
  • Paul Berkman
  • Hana Šimková
  • Jaroslav Doležel
  • Mincheng Luo
  • Frank You
  • Jacqueline Batley
  • Delphine Fleury
  • Rudi Appels
  • Song Weining
Original Paper

Abstract

MicroRNAs (miRNAs) are a class of important biological elements that regulates gene expression by translational repression or transcript degradation both in plants and animals. The origin, distribution and evolution of the miRNA genes have been systematically studied in many model plants, but they are not well understood in wheat. In this study, we have systematically identified the miRNA precursors and mature miRNAs in wheat group 7 chromosomes by computational analysis in the isolated chromosome sequences. A total of 716 precursors belonging to 43 miRNA families were identified, of which 12 miRNAs families (27.91 %) were not reported in wheat. Further analysis found that there were less mature miRNAs but more miRNA precursors distributing on 7D compared to 7A and 7B, suggesting that wheat group 7 homoeologous chromosome eliminated some miRNA precursors with the potential to yield the same miRNA and formed a more precise regulatory network via the two hybridization events. The target genes of all the newly identified miRNAs were also predicted. The results of this study are beneficial to improve our understanding of the distribution of wheat miRNAs and its evolutionary role in polyploidisation.

Keywords

Wheat miRNA Group 7 chromosomes Next-generation sequencing Comparative genomics 

Supplementary material

11105_2013_669_MOESM1_ESM.doc (44 kb)
Table S1Primers used for qRT-PCR analysis (DOC 44 kb)
11105_2013_669_MOESM2_ESM.doc (1.1 mb)
Table S2List of computational identified miRNAs of group 7 chromosomes in T. aestivum and their characteristics (DOC 1141 kb)
11105_2013_669_MOESM3_ESM.doc (62 kb)
Table S3The detail lists of miRNA families shared by wheat group 7 chromosomes (DOC 62 kb)
11105_2013_669_MOESM4_ESM.doc (694 kb)
Table S4List of predicted targets of total miRNAs distribution on wheat group 7 chromosomes (DOC 694 kb)
11105_2013_669_MOESM5_ESM.doc (245 kb)
Table S5List of predicted targets of newly identified miRNAs distribution on wheat group 7 chromosomes (DOC 245 kb)
11105_2013_669_MOESM6_ESM.doc (96 kb)
Table S6The detail list of functional enrichment for the miRNA targets identified (DOC 96 kb)

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Pingchuan Deng
    • 1
  • Xiaojun Nie
    • 1
  • Le Wang
    • 1
  • Licao Cui
    • 1
  • Peixun Liu
    • 1
  • Wei Tong
    • 1
  • Siddanagouda S. Biradar
    • 1
  • David Edwards
    • 2
  • Paul Berkman
    • 2
  • Hana Šimková
    • 3
  • Jaroslav Doležel
    • 3
  • Mincheng Luo
    • 4
  • Frank You
    • 5
  • Jacqueline Batley
    • 6
  • Delphine Fleury
    • 7
  • Rudi Appels
    • 8
  • Song Weining
    • 1
  1. 1.State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingChina
  2. 2.School of Agriculture and Food Sciences and Australian Centre for Plant Functional GenomicsUniversity of QueenslandBrisbaneAustralia
  3. 3.Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
  4. 4.Department of Plant SciencesUniversity of CaliforniaDavisUSA
  5. 5.Agriculture and Agri-Food CanadaCereal Research CentreWinnipegCanada
  6. 6.ARC Centre of Excellence for Integrative Legume Research and School of Land, Crop and Food SciencesUniversity of QueenslandBrisbaneAustralia
  7. 7.Australian Centre of Plant Functional GenomicsUniversity of AdelaideGlen OsmondAustralia
  8. 8.Murdoch UniversityPerthAustralia

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