Computational Identification of MicroRNAs and Their Targets in Perennial Ryegrass (Lolium perenne)

MicroRNAs (miRNAs) are small non-coding RNA molecules of 22 nucleotides in length that have been characterized as regulators of messenger RNA (mRNA) regulating a number of developmental processes in plants and animals by silencing genes using multiple mechanisms. miRNAs have been extensively studied in various plant species; however, few information are available about miRNAs in perennial ryegrass, animal feed, and industrial raw materials. In this study, the 12 potential perennial ryegrass miRNAs were identified for the first time by computational approach. Using the newly identified miRNA sequences, the perennial ryegrass mRNA database was further used for BLAST search and detected 33 potential targets of miRNAs. Prediction of potential miRNA target genes revealed their functions involved in various important plant biological processes. Our result should be useful for further investigation into the biological functions of miRNAs in perennial ryegrass. The selected miRNAs representing four families were verified by RT-PCR experiment, indicating that the prediction method that we used to identify the miRNAs was effective.

[1]  Duangdao Wichadakul,et al.  C-mii: a tool for plant miRNA and target identification , 2012, BMC Genomics.

[2]  Chen Wang,et al.  Computational identification of MicroRNAs in strawberry expressed sequence tags and validation of their precise sequences by miR-RACE. , 2012, The Journal of heredity.

[3]  O. Voinnet.  Origin, Biogenesis, and Activity of Plant MicroRNAs , 2009, Cell.

[4]  Anders Krogh,et al.  Computational evidence for hundreds of non-conserved plant microRNAs , 2005, BMC Genomics.

[5]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[6]  Yunbo Luo,et al.  Computational identification of microRNAs and their targets in wheat (Triticum aestivum L.) , 2009, Science in China Series C: Life Sciences.

[7]  Qiang Xu,et al.  Selection and validation of suitable reference genes for miRNA expression normalization by quantitative RT-PCR in citrus somatic embryogenic and adult tissues , 2012, Plant Cell Reports.

[8]  L. Delaby,et al.  Effect of perennial ryegrass (Lolium perenne L.) cultivars on the milk yield of grazing dairy cows. , 2013, Animal : an international journal of animal bioscience.

[9]  Hyun-Jin Kim,et al.  In silico identification and characterization of microRNAs and their putative target genes in Solanaceae plants. , 2011, Genome.

[10]  Ramanjulu Sunkar,et al.  In silico identification of conserved microRNAs in large number of diverse plant species , 2008, BMC Plant Biology.

[11]  W. Cooper,et al.  SCIENCE IN CHINA. , 1940, Science.

[12]  Terry Gaasterland,et al.  Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets , 2004, Genome Biology.

[13]  Javier F. Palatnik,et al.  Functional Specialization of the Plant miR396 Regulatory Network through Distinct MicroRNA–Target Interactions , 2012, PLoS genetics.

[14]  Guohui Zhou,et al.  Evaluation of Three RT-qPCR-Based miRNA Detection Methods Using Seven Rice miRNAs , 2013, Bioscience, biotechnology, and biochemistry.

[15]  Fei Li,et al.  Identification of MicroRNA Precursors with Support Vector Machine and String Kernel , 2008, Genom. Proteom. Bioinform..

[16]  C. X. Qiu,et al.  Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. , 2007, Gene.

[17]  Ehsan Mostafavi,et al.  Development of a robust, low cost stem-loop real-time quantification PCR technique for miRNA expression analysis , 2012, Molecular Biology Reports.

[18]  Guiling Sun.  MicroRNAs and their diverse functions in plants , 2011, Plant Molecular Biology.

[19]  H. Vaucheret,et al.  Functions of microRNAs and related small RNAs in plants , 2006, Nature Genetics.

[20]  Wenwei Zhang,et al.  Computational identification of 48 potato microRNAs and their targets , 2009, Comput. Biol. Chem..

[21]  Jing Chen,et al.  A potential role of microRNAs in plant response to metal toxicity. , 2013, Metallomics : integrated biometal science.

[22]  HighWire Press.  Philosophical Transactions of the Royal Society of London , 1781, The London Medical Journal.

[23]  Jon S. Robertson,et al.  Inference of subgenomic origin of BACs in an interspecific hybrid sugarcane cultivar by overlapping oligonucleotide hybridizations. , 2011, Genome.

[24]  R. Sunkar,et al.  Functions of microRNAs in plant stress responses. , 2012, Trends in plant science.

[25]  D. Bartel,et al.  Criteria for Annotation of Plant MicroRNAs , 2008, The Plant Cell Online.

[26]  O. Patanun,et al.  Computational Identification of MicroRNAs and Their Targets in Cassava (Manihot esculenta Crantz.) , 2013, Molecular Biotechnology.

[27]  R. Sunkar,et al.  The role of microRNAs and other endogenous small RNAs in plant stress responses. , 2008, Biochimica et biophysica acta.

[28]  R. Sunkar.  MicroRNAs with macro-effects on plant stress responses. , 2010, Seminars in cell & developmental biology.

[29]  Daniel H. Huson,et al.  Identification of plant microRNA homologs , 2006, Bioinform..

[30]  Guilherme Loss-Morais,et al.  MicroRNAs play critical roles during plant development and in response to abiotic stresses , 2012, Genetics and molecular biology.

[31]  L. Shalloo,et al.  Development and application of an economic ranking index for perennial ryegrass cultivars. , 2011, Journal of dairy science.

[32]  S. Kauppinen,et al.  Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissues. , 2006, The Plant journal : for cell and molecular biology.

[33]  Gang Wu.  Plant microRNAs and development. , 2013, Journal of genetics and genomics = Yi chuan xue bao.

[34]  Weixiong Zhang,et al.  Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants , 2009, Nucleic acids research.

[35]  R. Giegerich,et al.  Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.

[36]  M. Nei,et al.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.

[37]  Baohong Zhang,et al.  Identification and characterization of new plant microRNAs using EST analysis , 2005, Cell Research.

[38]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[39]  A. Naqvi,et al.  Biogenesis, functions and fate of plant microRNAs , 2012, Journal of cellular physiology.

[40]  Sunil Archak,et al.  Computational Prediction of Rice (Oryza sativa) miRNA Targets , 2008, Genom. Proteom. Bioinform..

[41]  D. O. Wijnands,et al.  Identification of plants , 1997 .

[42]  G. Tang.  Plant microRNAs: an insight into their gene structures and evolution. , 2010, Seminars in cell & developmental biology.

[43]  V. Baev,et al.  miRTour: Plant miRNA and target prediction tool , 2011, Bioinformation.

[44]  J. Vielle-Calzada,et al.  A Family of MicroRNAs Present in Plants and Animals[W][OA] , 2006, The Plant Cell Online.

[45]  C. Scutt,et al.  The evolutionary-developmental analysis of plant microRNAs , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.