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Computational Identification of MicroRNAs and Their Targets in Cassava (Manihot esculenta Crantz.)

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Abstract

MicroRNAs (miRNAs) are a newly discovered class of noncoding endogenous small RNAs involved in plant growth and development as well as response to environmental stresses. miRNAs have been extensively studied in various plant species, however, only few information are available in cassava, which serves as one of the staple food crops, a biofuel crop, animal feed and industrial raw materials. In this study, the 169 potential cassava miRNAs belonging to 34 miRNA families were identified by computational approach. Interestingly, mes-miR319b was represented as the first putative mirtron demonstrated in cassava. A total of 15 miRNA clusters involving 7 miRNA families, and 12 pairs of sense and antisense strand cassava miRNAs belonging to six different miRNA families were discovered. Prediction of potential miRNA target genes revealed their functions involved in various important plant biological processes. The cis-regulatory elements relevant to drought stress and plant hormone response were identified in the promoter regions of those miRNA genes. The results provided a foundation for further investigation of the functional role of known transcription factors in the regulation of cassava miRNAs. The better understandings of the complexity of miRNA-mediated genes network in cassava would unravel cassava complex biology in storage root development and in coping with environmental stresses, thus providing more insights for future exploitation in cassava improvement.

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Acknowledgments

This research was financially supported by Mahidol University. OP was partially supported by Center of Excellence on Agricultural Biotechnology, Science and Technology Postgraduate Education and Research Development Office, Commission on Higher Education, Ministry of Education (AG-BIO/PERDO-CHE), Thailand.

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Authors and Affiliations

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

    Onsaya Patanun, Manassawe Lertpanyasampatha, Punchapat Sojikul & Jarunya Narangajavana

  2. Center of Excellence on Agricultural Biotechnology, Science and Technology Postgraduate Education and Research Development Office, Commission on Higher Education, Ministry of Education (AG-BIO/PERDO-CHE), Bangkok, Thailand

    Onsaya Patanun & Jarunya Narangajavana

  3. Department of Plant Science, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand

    Unchera Viboonjun

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  1. Onsaya Patanun
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  2. Manassawe Lertpanyasampatha
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  3. Punchapat Sojikul
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  4. Unchera Viboonjun
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  5. Jarunya Narangajavana
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Correspondence to Jarunya Narangajavana.

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12033_2012_9521_MOESM3_ESM.pdf

Supplement Figure S1 Predicted secondary hairpin structure for 169 cassava miRNAs identified in this study. (PDF 2073 kb)

12033_2012_9521_MOESM4_ESM.tif

Supplement Figure S2 Relative transcript abundance of miR159 in the fibrous and storage root. The relative expression corresponds to the ratio of the transcript abundance of miR159 gene/transcript abundance of the small RNA U6 control gene. Data are means of three independent experiments and SE (n = 9). Different letters indicate values that are significantly different between the transcripts of the fibrous and storage root cDNA samples (Tukey’s test, one-way ANOVA; P < 0.05). (TIFF 677 kb)

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Patanun, O., Lertpanyasampatha, M., Sojikul, P. et al. Computational Identification of MicroRNAs and Their Targets in Cassava (Manihot esculenta Crantz.). Mol Biotechnol 53, 257–269 (2013). https://doi.org/10.1007/s12033-012-9521-z

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