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Conserved microRNAs and their targets in rubber tree and the related Euphorbiaceous species

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Abstract

Plant microRNAs (miRNAs) have been demonstrated to play an important regulatory role in a variety of biological processes ranging from plant growth and development, defensive pathways, as well as biotic and abiotic stress responses. MiRNAs have been extensively studied in plant models with available genome sequence data. The Euphorbiaceae family is a large flowering plant family, which is of considerable economic importance, but relatively limited genome sequence data. The four Euphorbiaceous species; rubber tree, cassava, castor bean and leafy spurge; were selected for this study. Using conserved plant miRNAs sequences aligned to the GenBank expressed sequenced tag database of each target plants, and further potential precursor miRNA-secondary structure analysis, the 526 potential miRNAs belonging to 17 miRNA families and their targets were identified. The majority of miRNA families was able to be identified in cassava. The minimal folding free energy index of precursor miRNAs was significantly higher than other non-coding or coding RNAs. The largest group of miRNA target genes consists of regulatory genes predicted to encode transcription factors, while non-regulatory genes involving in various functions. Some miRNAs contain different targets, suggesting the diverse functions of miRNAs depending on plant species and environmental conditions. The 6 expressed Hbr-miRNAs were verified in rubber tree. Gaining insight into the miRNA targets will help us to understand the range of miRNA expression regulation and to more coherently describe the functional importance of miRNAs. These findings considerably facilitate the basis for broaden future investigation on the role of these miRNAs in the economic important Euphorbiaceous species.

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Abbreviations

AGO1:

ARGONAUTE 1

Ath :

Arabidopsis thaliana

DEPC:

Diethylpyrocarbonate

EST:

Expressed sequenced tag

Hbr :

Hevea brasiliensis

MFE:

Negative folding free energy (ΔG)

MFEI:

Minimal folding free energy index

MIR gene:

microRNA encoding gene

miRNAs:

microRNAs

RT-PCR:

Reverse transcription polymerase chain reaction

Ptc :

Populus trichocarpa

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Acknowledgements

This research was financially supported by National Science and Technology Development Agency, (grant No. BT-B-01-PG-14-5202) and Mahidol University. Lertpanyasampatha M.. was supported by the Royal Golden Jubilee Ph.D. program (no. PHD/0216/2550). Pramoolkit P. was partially supported by Biotech Alumni Scholarship, Department of Biotechnology, Faculty of Science, Mahidol University.

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Authors and Affiliations

  1. Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand

    Manassawe Lertpanyasampatha, Porawee Pramoolkit & Jarunya Narangajavana

  2. Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand

    Panida Kongsawadworakul & Unchera Viboonjun

  3. Institut de Recherche pour le Développement (IRD), Montpellier, France

    Hervé Chrestin

Authors
  1. Manassawe Lertpanyasampatha
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  2. Porawee Pramoolkit
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  3. Panida Kongsawadworakul
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  4. Unchera Viboonjun
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  5. Hervé Chrestin
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  6. Jarunya Narangajavana
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Corresponding author

Correspondence to Jarunya Narangajavana.

Electronic supplementary material

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Supplementary Figure S1

Secondary structures of potential miRNAs in Euphorbiaceous plants. The region of the mature miRNA sequence is shown in CAPITAL letters. (DOC 102 kb)

Supplementary Table S1

The predicted targets of each member of Euphobiaceous miRNAs (DOC 812 kb)

Supplementary Table S2

Multiple alignment of Hevea-miRNA sequences with A. thaliana and P. thichocarpa (DOC 380 kb)

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Lertpanyasampatha, M., Pramoolkit, P., Kongsawadworakul, P. et al. Conserved microRNAs and their targets in rubber tree and the related Euphorbiaceous species. J. Plant Biochem. Biotechnol. 22, 52–61 (2013). https://doi.org/10.1007/s13562-012-0110-9

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  • DOI: https://doi.org/10.1007/s13562-012-0110-9

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