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Tree Genetics & Genomes

, Volume 10, Issue 3, pp 721–737 | Cite as

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

  • Inês Chaves
  • Yao-Cheng Lin
  • C. Pinto-Ricardo
  • Yves Van de Peer
  • Célia Miguel
Original Paper

Abstract

The differentiation of cork (phellem) cells from the phellogen (cork cambium) is a secondary growth process observed in the cork oak tree conferring a unique ability to produce a thick layer of cork. At present, the molecular regulators of phellem differentiation are unknown. The previously documented involvement of microRNAs (miRNAs) in the regulation of developmental processes, including secondary growth, motivated the search for these regulators in cork oak tissues. We performed deep sequencing of the small RNA fraction obtained from cork oak leaves and differentiating phellem. RNA sequences with lengths of 19–25 nt derived from the two libraries were analysed, leading to the identification of 41 families of conserved miRNAs, of which the most abundant were miR167, miR165/166, miR396 and miR159. Thirty novel miRNA candidates were also unveiled, 11 of which were unique to leaves and 13 to phellem. Northern blot detection of a set of conserved and novel miRNAs confirmed their differential expression profile. Prediction and analysis of putative miRNA target genes provided clues regarding processes taking place in leaf and phellem tissues, but further experimental work will be needed for functional characterization. In conclusion, we here provide a first characterization of the miRNA population in a Fagacea species, and the comparative analysis of miRNA expression in leaf and phellem libraries represents an important step to uncovering specific regulatory networks controlling phellem differentiation.

Keywords

Small RNA miRNA Quercus suber Phellem Tree Secondary growth 

Notes

Acknowledgments

The authors thank Sónia Gonçalves from CEBAL (Beja, Portugal) for providing the tissue samples. This research was supported by Fundação para a Ciência e Tecnologia (FCT), through projects PEst-OE/EQB/LA0004/2011 and PTDC/AGR-GPL/098369/2008, and grant SFRH/BPD/20833/2004 (to I. Chaves).

Data Archiving Statement

The small RNA sequences obtained for leaf and cork are deposited in the NCBI GenBank database under the accession numbers SRR988108 and SRR988109, respectively.

Supplementary material

11295_2014_717_MOESM1_ESM.pdf (105 kb)
SM1 Electropherogram of HMW RNA and LMW RNA enriched fractions from Q. suber cork tissues (PDF 104 kb)
11295_2014_717_MOESM2_ESM.xlsx (83 kb)
SM2 miRCat results for cork oak leaf tissues (XLSX 83 kb)
11295_2014_717_MOESM3_ESM.xlsx (78 kb)
SM3 miRCat results for cork oak phellem tissues (XLSX 77 kb)
11295_2014_717_MOESM4_ESM.pdf (106 kb)
SM4 Northern blot DNA probes (PDF 105 kb)
11295_2014_717_MOESM5_ESM.pdf (398 kb)
SM5 Target genes for non-conserved miRNAs (PDF 398 kb)
11295_2014_717_MOESM6_ESM.xlsx (246 kb)
SM6 Target gene contigs in leaf tissues (XLSX 246 kb)
11295_2014_717_MOESM7_ESM.xlsx (191 kb)
SM7 Target gene contigs in cork tissues (XLSX 190 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Inês Chaves
    • 1
    • 2
  • Yao-Cheng Lin
    • 3
    • 4
  • C. Pinto-Ricardo
    • 2
  • Yves Van de Peer
    • 3
    • 4
    • 5
  • Célia Miguel
    • 1
    • 2
  1. 1.Instituto de Biologia Experimental e Tecnológica (iBET)OeirasPortugal
  2. 2.Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
  3. 3.Department of Plant Systems BiologyVIBGhentBelgium
  4. 4.Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
  5. 5.Genomics Research Institute (GRI)University of PretoriaPretoriaSouth Africa

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