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Identification of Conserved miRNAs and Their Target Genes in Faba Bean by EST Based Homology Analysis

Year 2016, Volume: 5 Issue: 9, 1 - 6, 26.12.2016

Abstract

MicroRNAs (miRNAs) are a class of endogenous, non-coding short RNAs, around 21 nucleotides (nt) in length found in eukaryotic cells and some viruses. To date, miRNAs are identified in several plant species through experimental and computational approaches where they play important roles in growth and development, metabolism, stress responses by guiding mRNA cleavage or repressing translation. Although the faba bean (Vicia faba) is an important source of protein widely used for human and animal nutrition, not a single miRNA has been identified in it up till now. Evolutionary conserved characteristics of plant miRNAs allow the identification of conserved plant miRNAs by homology analysis. The aim of this study is the identification and characterization of miRNAs in faba bean using the EST based homology analysis approach. For computational identification of novel miRNAs in faba bean, 8496 known and unique plant miRNAs from 73 plant species were searched for homology against 20697 expressed sequence tags (EST) and 577 genome survey sequences (GSS). Candidate miRNAs including protein coding sequences were recognized following the miRNA criteria of secondary structure and biogenesis. In this study, 262 candidate miRNAs belonging to 143 miRNA families have been identified for the first time in faba bean. Moreover, psRNATarget server predicted 712 potential target genes of these candidate miRNAs from faba bean. Predicted target genes seem to be involved in the regulation of several important biological processes. The results of this study will contribute to further research on miRNAs, leading to an improved understanding of the role miRNAs play in biological processes and the underlying environmental stress related molecular mechanisms of faba bean.

References

  • Ambros, V., Bartel, B., Bartel, D.P., Burge, C.B., Carrington, J.C., Chen, X., Dreyfuss, G., Eddy, S.R., Griffiths-Jones, S., Marshall, M., Matzke, M., Ruvkun, G., Tuschl, T. 2003. A uniform system for microRNA annotation. RNA 9(3), 277-279.
  • Bologna, N.G., Schapire, A.L., Palatnik, J.F. 2013. Processing of plant microRNA precursors. Briefings in Functional Genomics 12(1), 37-45.
  • Cock, P.J.A., Tiago. A., Jeffrey, T.C., Brad, A.C., Cymon, J.C., Andrew, D., Iddo, F., Thomas, H., Frank, K., Bartek, W., Michiel, J.L. de H. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11), 1422-1423.
  • Conesa, A., Götz, S. 2008. Blast2GO: A comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics, 2008, 1-13.
  • Cuperus, J.T., Fahlgren, N., Carrington, J.C. 2011. Evolution and functional diversification of MIRNA genes. The Plant Cell 23(2), 431-442.
  • Dai, X., Zhao, P. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research 39, 155-159.
  • Dhandapani, V., Nirala, R., Parameswari, P., Joonki, K., Sun, H.C., Jeongyeo, L., Yoonkang, H., Yong, P.L. 2011. Identification of potential microRNAs and their targets in Brassica rapa L. Molecules and Cells 32, 21-37.
  • Duc, G. 1997. Faba bean (Vicia faba L.). Field Crops Research 53, 99-109.
  • FAOSTAT, 2015. Food and Agriculture Organizatıon of The United Nations. http://faostat3.fao.org/browse/Q/QC/E.
  • Han, J., Xie, H., Kong, M.L., Sun, Q.P., Li, R.Z., Pan, J.B. 2014. Computational identification of miRNAs and their targets in Phaseolus vulgaris. Genetics and Molecular Research 13(1), 310-322.
  • Hanafy, M.S., El-Banna, A., Schumacher, H.M., Jacobsen, H.S., Hassan, F.S. 2013. Enhanced tolerance to drought and salt stresses in transgenic faba bean (Vicia faba L.) plants by heterologous expression of the PR10a gene from potato. Plant Cell Reports 32(5), 663-674.
  • Hao, Y., Haiyang, Z., Lin, Z., Chenyu, Z., Donghai, L. 2012. Identification and characterization of microRNAs in Macaca fascicularis by EST analysis. Comparative and Functional Genomics ID: 957607. http://dx.doi.org/10.1155/2012/957607.
  • He, P.A., Nie, Z., Chen, J., Chen, J. L.Z., Sheng, Q., Zhou, S., Gao, X., Kong, L., Wu, X., Jin, Y., Zhang, Y. 2008. Identification and characteristics of microRNAs from Bombyx mori. BMC Genomics 9(248), 1-17.
  • Huang, Y., Beifang, N., Ying, G., Limin, F., Weizhong, L. 2010. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26(5), 680-682.
  • Kozomara, A., Griffiths-Jones, S. 2014. MiRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Research 42, 68-73.
  • Lee, R.C., Feinbaum, R.L., Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.
  • Li, T., Li, H., Zhang, Y.X., Liu, J.Y. 2011. Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). Nucleic Acids Research 39, 2821-2833.
  • Li, W., Xiao, C., Zhaolu, M., Xiahe, H., Qi, X., Heng, W., Hailing, J., Dabing, Z., Wanqi, L., 2012. Transcriptional regulation of Arabidopsis MIR168a and argonaute1 homeostasis in abscisic acid and abiotic stress responses. Plant Physiology 158(3), 1279-1292.
  • Liu, Q., Zhang, H., 2012. Molecular identification and analysis of arsenite stress-responsive miRNAs in rice. Journal of Agricultural and Food Chemistry 60, 6524-6536.
  • Meyers, B.C., Axtell, M.J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths-Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qio, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D., Zhu, J.K. 2008. Criteria for annotation of plant MicroRNAs. The Plant Cell 20(12), 3186-3190.
  • miRBase. 2014 miRBase. http://www.mirbase.org.
  • NCBI. 2014. National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov.
  • Nodine, M.D., Bartel, D.P. 2010. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes and Development, 24(23), 2678-2692.
  • Panda. D., Dehury, B., Sahu, J., Barooah, M., Sen, P., Modi, M.K. 2014. Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags. Gene 537(2), 333-342.
  • Park, M.Y., Gang, W., Alfredo, G.S., Hervé, V.R., Scott, P. 2005. Nuclear processing and export of microRNAs in Arabidopsis. PNAS 102, 3691-3696.
  • Park, W., Junjie, L., Rentao, S., Joachim, M., Xuemei, C. 2002. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology 12(17), 1484-1495.
  • Prabu, G.R., Mandal, A.K. 2010. Computational identification of miRNAs and their target genes from expressed sequence tags of tea (Camellia sinensis). Genomics Proteomics and Bioinformatics 8(2), 113-121.
  • Prüfer, K., Stenzel, U., Dannemann, M., Green, R.E., Lachmann, M., Kelso, J. 2008. PatMaN: rapid alignment of short sequences to large databases. Bioinformatics, 24(13), 1530-1531.
  • Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., Bartel, D.P. 2002. MicroRNAs in plants. Genes Development 16: 1616-1626.
  • Song. C., Fang, J., Li. X., Liu, H., Chao, C.T. 2009. Identification and characterization of 27 conserved microRNAs in citrus. Planta 230(4), 671-685.
  • Stocks, M.B., Moxon, S., Mapleson, D., Woolfenden, H.C., Mohorianu, I., Folkes, L., Schwach, F., Dalmay, T., Moulton, V. 2012. The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics 28(15), 2059-2061.
  • Supek, F., Bosnjak, M., Skunca, N., Smuc, T. 2011. REVIGO Summarizes and visualizes long lists of gene ontology terms. PLoS One 6(7), e21800. http://dx.doi.org/10.1371/journal.pone.0021800
  • Voinnet, O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136(4), 669-687.
  • Wightman, B., Ha, I., Ruykun, G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862.
  • Xie, F.L., Huang, S.Q., Guo, K., Xiang, A.L., Zhu, Y.Y, Nie, L., Yang, Z.M. 2007. Computational identification of novel microRNAs and targets in Brassica napus. FEBS Letters 581(7), 1464-1474.
  • Yang, G.D., Yan, K., Wu, B.J., Wang, Y.H., Gao, Y.X., Zheng, C.C. 2012. Genomewide analysis of intronic microRNAs in rice and Arabidopsis. Journal of Genetics 91(3), 313-324.
  • Zhang, B.H., Pan, X.P., Wang, Q.L., Cobb, G.P., Anderson, T.A. 2005. Identification and characterization of new plant microRNAs using EST analysis. Cell Research 15(5), 336-360.
  • Zhang, B., Pan, X., Cox, S. 2006. Evidence that miRNAs are different from other RNAs. Cellular and Molecular Life Sciences 63, 246-254.
  • Zhang, B.H., Pan, X.P., Stellwag, E.J. 2008. Identification of soybean microRNAs and their targets. Planta 229, 161-182.
  • Zhi-Liang, H,. Bao, J., Reecy, J.M. 2008. CateGOrizer: A web-based program to batch analyze gene ontology classification categories. Online Journal of Bioinformatics 9(2), 108-112.

Identification of Conserved miRNAs and Their Target Genes in Faba Bean by EST Based Homology Analysis

Year 2016, Volume: 5 Issue: 9, 1 - 6, 26.12.2016

Abstract

MicroRNAs (miRNAs) are a class of endogenous, non-coding short RNAs, around 21 nucleotides (nt) in length found in eukaryotic cells and some viruses. To date, miRNAs are identified in several plant species through experimental and computational approaches where they play important roles in growth and development, metabolism, stress responses by guiding mRNA cleavage or repressing translation. Although the faba bean (Vicia faba) is an important source of protein widely used for human and animal nutrition, not a single miRNA has been identified in it up till now. Evolutionary conserved characteristics of plant miRNAs allow the identification of conserved plant miRNAs by homology analysis. The aim of this study is the identification and characterization of miRNAs in faba bean using the EST based homology analysis approach. For computational identification of novel miRNAs in faba bean, 8496 known and unique plant miRNAs from 73 plant species were searched for homology against 20697 expressed sequence tags (EST) and 577 genome survey sequences (GSS). Candidate miRNAs including protein coding sequences were recognized following the miRNA criteria of secondary structure and biogenesis. In this study, 262 candidate miRNAs belonging to 143 miRNA families have been identified for the first time in faba bean. Moreover, psRNATarget server predicted 712 potential target genes of these candidate miRNAs from faba bean. Predicted target genes seem to be involved in the regulation of several important biological processes. The results of this study will contribute to further research on miRNAs, leading to an improved understanding of the role miRNAs play in biological processes and the underlying environmental stress related molecular mechanisms of faba bean.

References

  • Ambros, V., Bartel, B., Bartel, D.P., Burge, C.B., Carrington, J.C., Chen, X., Dreyfuss, G., Eddy, S.R., Griffiths-Jones, S., Marshall, M., Matzke, M., Ruvkun, G., Tuschl, T. 2003. A uniform system for microRNA annotation. RNA 9(3), 277-279.
  • Bologna, N.G., Schapire, A.L., Palatnik, J.F. 2013. Processing of plant microRNA precursors. Briefings in Functional Genomics 12(1), 37-45.
  • Cock, P.J.A., Tiago. A., Jeffrey, T.C., Brad, A.C., Cymon, J.C., Andrew, D., Iddo, F., Thomas, H., Frank, K., Bartek, W., Michiel, J.L. de H. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11), 1422-1423.
  • Conesa, A., Götz, S. 2008. Blast2GO: A comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics, 2008, 1-13.
  • Cuperus, J.T., Fahlgren, N., Carrington, J.C. 2011. Evolution and functional diversification of MIRNA genes. The Plant Cell 23(2), 431-442.
  • Dai, X., Zhao, P. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research 39, 155-159.
  • Dhandapani, V., Nirala, R., Parameswari, P., Joonki, K., Sun, H.C., Jeongyeo, L., Yoonkang, H., Yong, P.L. 2011. Identification of potential microRNAs and their targets in Brassica rapa L. Molecules and Cells 32, 21-37.
  • Duc, G. 1997. Faba bean (Vicia faba L.). Field Crops Research 53, 99-109.
  • FAOSTAT, 2015. Food and Agriculture Organizatıon of The United Nations. http://faostat3.fao.org/browse/Q/QC/E.
  • Han, J., Xie, H., Kong, M.L., Sun, Q.P., Li, R.Z., Pan, J.B. 2014. Computational identification of miRNAs and their targets in Phaseolus vulgaris. Genetics and Molecular Research 13(1), 310-322.
  • Hanafy, M.S., El-Banna, A., Schumacher, H.M., Jacobsen, H.S., Hassan, F.S. 2013. Enhanced tolerance to drought and salt stresses in transgenic faba bean (Vicia faba L.) plants by heterologous expression of the PR10a gene from potato. Plant Cell Reports 32(5), 663-674.
  • Hao, Y., Haiyang, Z., Lin, Z., Chenyu, Z., Donghai, L. 2012. Identification and characterization of microRNAs in Macaca fascicularis by EST analysis. Comparative and Functional Genomics ID: 957607. http://dx.doi.org/10.1155/2012/957607.
  • He, P.A., Nie, Z., Chen, J., Chen, J. L.Z., Sheng, Q., Zhou, S., Gao, X., Kong, L., Wu, X., Jin, Y., Zhang, Y. 2008. Identification and characteristics of microRNAs from Bombyx mori. BMC Genomics 9(248), 1-17.
  • Huang, Y., Beifang, N., Ying, G., Limin, F., Weizhong, L. 2010. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26(5), 680-682.
  • Kozomara, A., Griffiths-Jones, S. 2014. MiRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Research 42, 68-73.
  • Lee, R.C., Feinbaum, R.L., Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.
  • Li, T., Li, H., Zhang, Y.X., Liu, J.Y. 2011. Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). Nucleic Acids Research 39, 2821-2833.
  • Li, W., Xiao, C., Zhaolu, M., Xiahe, H., Qi, X., Heng, W., Hailing, J., Dabing, Z., Wanqi, L., 2012. Transcriptional regulation of Arabidopsis MIR168a and argonaute1 homeostasis in abscisic acid and abiotic stress responses. Plant Physiology 158(3), 1279-1292.
  • Liu, Q., Zhang, H., 2012. Molecular identification and analysis of arsenite stress-responsive miRNAs in rice. Journal of Agricultural and Food Chemistry 60, 6524-6536.
  • Meyers, B.C., Axtell, M.J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths-Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qio, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D., Zhu, J.K. 2008. Criteria for annotation of plant MicroRNAs. The Plant Cell 20(12), 3186-3190.
  • miRBase. 2014 miRBase. http://www.mirbase.org.
  • NCBI. 2014. National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov.
  • Nodine, M.D., Bartel, D.P. 2010. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes and Development, 24(23), 2678-2692.
  • Panda. D., Dehury, B., Sahu, J., Barooah, M., Sen, P., Modi, M.K. 2014. Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags. Gene 537(2), 333-342.
  • Park, M.Y., Gang, W., Alfredo, G.S., Hervé, V.R., Scott, P. 2005. Nuclear processing and export of microRNAs in Arabidopsis. PNAS 102, 3691-3696.
  • Park, W., Junjie, L., Rentao, S., Joachim, M., Xuemei, C. 2002. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology 12(17), 1484-1495.
  • Prabu, G.R., Mandal, A.K. 2010. Computational identification of miRNAs and their target genes from expressed sequence tags of tea (Camellia sinensis). Genomics Proteomics and Bioinformatics 8(2), 113-121.
  • Prüfer, K., Stenzel, U., Dannemann, M., Green, R.E., Lachmann, M., Kelso, J. 2008. PatMaN: rapid alignment of short sequences to large databases. Bioinformatics, 24(13), 1530-1531.
  • Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., Bartel, D.P. 2002. MicroRNAs in plants. Genes Development 16: 1616-1626.
  • Song. C., Fang, J., Li. X., Liu, H., Chao, C.T. 2009. Identification and characterization of 27 conserved microRNAs in citrus. Planta 230(4), 671-685.
  • Stocks, M.B., Moxon, S., Mapleson, D., Woolfenden, H.C., Mohorianu, I., Folkes, L., Schwach, F., Dalmay, T., Moulton, V. 2012. The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics 28(15), 2059-2061.
  • Supek, F., Bosnjak, M., Skunca, N., Smuc, T. 2011. REVIGO Summarizes and visualizes long lists of gene ontology terms. PLoS One 6(7), e21800. http://dx.doi.org/10.1371/journal.pone.0021800
  • Voinnet, O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136(4), 669-687.
  • Wightman, B., Ha, I., Ruykun, G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862.
  • Xie, F.L., Huang, S.Q., Guo, K., Xiang, A.L., Zhu, Y.Y, Nie, L., Yang, Z.M. 2007. Computational identification of novel microRNAs and targets in Brassica napus. FEBS Letters 581(7), 1464-1474.
  • Yang, G.D., Yan, K., Wu, B.J., Wang, Y.H., Gao, Y.X., Zheng, C.C. 2012. Genomewide analysis of intronic microRNAs in rice and Arabidopsis. Journal of Genetics 91(3), 313-324.
  • Zhang, B.H., Pan, X.P., Wang, Q.L., Cobb, G.P., Anderson, T.A. 2005. Identification and characterization of new plant microRNAs using EST analysis. Cell Research 15(5), 336-360.
  • Zhang, B., Pan, X., Cox, S. 2006. Evidence that miRNAs are different from other RNAs. Cellular and Molecular Life Sciences 63, 246-254.
  • Zhang, B.H., Pan, X.P., Stellwag, E.J. 2008. Identification of soybean microRNAs and their targets. Planta 229, 161-182.
  • Zhi-Liang, H,. Bao, J., Reecy, J.M. 2008. CateGOrizer: A web-based program to batch analyze gene ontology classification categories. Online Journal of Bioinformatics 9(2), 108-112.
There are 40 citations in total.

Details

Primary Language English
Subjects Engineering
Journal Section Articles
Authors

Dilek Koptekin This is me

Lale Yildiz Aktaş

Publication Date December 26, 2016
Published in Issue Year 2016 Volume: 5 Issue: 9

Cite

APA Koptekin, D., & Aktaş, L. Y. (2016). Identification of Conserved miRNAs and Their Target Genes in Faba Bean by EST Based Homology Analysis. Avrupa Bilim Ve Teknoloji Dergisi, 5(9), 1-6.