Login Register Cart 0
Generic placeholder image

Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Research Article

Whole Aegilops tauschii Transcriptome Investigation Revealed Nine Novel miRNAs Involved in Stress Response

Author(s): Behnam Bakhshi* and Ehsan Mohseni Fard

Volume 15, Issue 5, 2020

Page: [455 - 462] Pages: 8

DOI: 10.2174/1574893614666191017151708

Price: $65

Abstract

Background: Aegilops tauschii is a wild relative of bread wheat. This species has been reported as the donor of bread wheat D genome. There are also several reports that mentioned the importance of Ae. tauschii in biotic and abiotic stress tolerance. On the other hands, miRNAs have been reported as the essential regulatory elements in stress response.

Objective: Therefore, it is important to discover novel miRNAs involved in stress tolerance in this species. The aim of the current study was to predict novel miRNAs in Ae. tauschii and also uncover their potential role in stress response.

Methods: For this purpose, ESTs, TSAs, and miRBase databases were obtained and used to predict new miRNAs.

Results: Our results discovered nine novel stem-loop miRNAs. These predicted miRNAs could be introduced as the new members of previously identified miRNA families in Ae. tauschii, including miR156, miR168, miR169, and miR319. The result indicating that miR397 and miR530 are novel families in this species. Furthermore, several novel stem-loop miRNAs predicted for T. aestivum showed remarkable similarities to novel Ae. tauschii stem-loops.

Conclusion: Our results demonstrated that predicted novel miRNAs could play a significant role in stress response.

Keywords: Ae. tauschii, wheat, microRNAs, EST, TSA, transcriptome.

« Previous Next »
Graphical Abstract

[1]
Matsuoka Y, Aghaei MJ, Abbasi MR, Totiaei A, Mozafari J, Ohta S. Durum wheat cultivation associated with Aegilops tauschii in northern Iran. Genet Resour Crop Evol 2008; 55(6): 861-8.
[http://dx.doi.org/10.1007/s10722-007-9290-x]
[2]
Aghaei MJ, Mozafari J, Taleei AR, Naghavi MR, Omidi M. Distribution and diversity of Aegilops tauschii in Iran. Genet Resour Crop Evol 2008; 55(3): 341-9.
[http://dx.doi.org/10.1007/s10722-007-9239-0]
[3]
Bakhshi B, Aghaei M, Bihamta M, Darvish F, Zarifi E. Ploidy determination of Aegilops cylindrica Host accessions of Iran by using flow cytometry and chromosome counting. Iran J Bot 2010; 16(2): 258-66.
[4]
Jia J, Zhao S, Kong X, et al. International Wheat Genome Sequencing Consortium. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 2013; 496(7443): 91-5.
[http://dx.doi.org/10.1038/nature12028] [PMID: 23535592]
[5]
Huang S, Sirikhachornkit A, Su X, et al. Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 2002; 99(12): 8133-8.
[http://dx.doi.org/10.1073/pnas.072223799] [PMID: 12060759]
[6]
Mujeeb-Kazi A, Rosas V, Roldan S. Conservation of the genetic variation of Triticum tauschii (Coss.) Schmalh.(Aegilops squarrosa auct. non L.) in synthetic hexaploid wheats (T. turgidum L. s. lat. x T. tauschii; 2n= 6x= 42, AABBDD) and its potential utilization for wheat improvement. Genet Resour Crop Evol 1996; 43(2): 129-34.
[http://dx.doi.org/10.1007/BF00126756]
[7]
Miranda LM, Murphy JP, Marshall D, Leath S. Pm34: a new powdery mildew resistance gene transferred from Aegilops tauschii Coss. to common wheat (Triticum aestivum L.). Theor Appl Genet 2006; 113(8): 1497-504.
[http://dx.doi.org/10.1007/s00122-006-0397-9] [PMID: 16953419]
[8]
Huang L, Gill B. An RGA–like marker detects all known Lr21 leaf rust resistance gene family members in Aegilops tauschii and wheat. Theor Appl Genet 2001; 103(6-7): 1007-13.
[http://dx.doi.org/10.1007/s001220100701]
[9]
Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009; 136(4): 669-87.
[http://dx.doi.org/10.1016/j.cell.2009.01.046] [PMID: 19239888]
[10]
Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, et al. Widespread translational inhibition by plant miRNAs and siRNAs. Science 2008; 320(5880): 1185-90.
[http://dx.doi.org/10.1126/science.1159151] [PMID: 18483398]
[11]
Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116(2): 281-97.
[http://dx.doi.org/10.1016/S0092-8674(04)00045-5] [PMID: 14744438]
[12]
Ding Y, Tao Y, Zhu C. Emerging roles of microRNAs in the mediation of drought stress response in plants. J Exp Bot 2013; 64(11): 3077-86.
[http://dx.doi.org/10.1093/jxb/ert164] [PMID: 23814278]
[13]
Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA. Identification and characterization of new plant microRNAs using EST analysis. Cell Res 2005; 15(5): 336-60.
[http://dx.doi.org/10.1038/sj.cr.7290302] [PMID: 15916721]
[14]
Dezulian T, Remmert M, Palatnik JF, Weigel D, Huson DH. Identification of plant microRNA homologs. Bioinformatics 2006; 22(3): 359-60.
[http://dx.doi.org/10.1093/bioinformatics/bti802] [PMID: 16317073]
[15]
Pani A, Mahapatra RK. Computational identification of microRNAs and their targets in Catharanthus roseus expressed sequence tags. Genom Data 2013; 1: 2-6.
[http://dx.doi.org/10.1016/j.gdata.2013.06.001] [PMID: 26484050]
[16]
Gupta H, Tiwari T, Patel M, Mehta A, Ghosh A. An approach to identify the novel miRNA encoded from H. Annuus EST sequences. Genom Data 2015; 6: 139-44.
[http://dx.doi.org/10.1016/j.gdata.2015.09.005] [PMID: 26697356]
[17]
Khraiwesh B, Zhu J-K, Zhu J. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 2012; 1819(2): 137-48.
[http://dx.doi.org/10.1016/j.bbagrm.2011.05.001] [PMID: 21605713]
[18]
Shui X-R, Chen Z-W, Li J-X. MicroRNA prediction and its function in regulating drought-related genes in cowpea. Plant Sci 2013; 210: 25-35.
[http://dx.doi.org/10.1016/j.plantsci.2013.05.002] [PMID: 23849110]
[19]
Nishijima R, Yoshida K, Motoi Y, Sato K, Takumi S. Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions. Mol Genet Genomics 2016; 291(4): 1681-94.
[http://dx.doi.org/10.1007/s00438-016-1211-2] [PMID: 27142109]
[20]
Qibin L, Jiang W. MIREAP: microRNA discovery by deep sequencing 2008.
[21]
Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003; 31(13): 3406-15.
[http://dx.doi.org/10.1093/nar/gkg595] [PMID: 12824337]
[22]
Wang L, Liu H, Li D, Chen H. Identification and characterization of maize microRNAs involved in the very early stage of seed germination. BMC Genomics 2011; 12(1): 154.
[http://dx.doi.org/10.1186/1471-2164-12-154] [PMID: 21414237]
[23]
Dai X, Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 2011; 39(Suppl. 2). W155-9
[24]
Wang J-W, Czech B, Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 2009; 138(4): 738-49.
[http://dx.doi.org/10.1016/j.cell.2009.06.014] [PMID: 19703399]
[25]
Wu G, Poethig RS. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 2006; 133(18): 3539-47.
[http://dx.doi.org/10.1242/dev.02521] [PMID: 16914499]
[26]
Li W-X, Oono Y, Zhu J, et al. The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscrip-tionally to promote drought resistance. Plant Cell 2008; 20(8): 2238-51.
[http://dx.doi.org/10.1105/tpc.108.059444] [PMID: 18682547]
[27]
Ni Z, Hu Z, Jiang Q, Zhang H. GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress. Plant Mol Biol 2013; 82(1-2): 113-29.
[http://dx.doi.org/10.1007/s11103-013-0040-5] [PMID: 23483290]
[28]
Schommer C, Palatnik JF, Aggarwal P, et al. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol 2008; 6(9) e230
[http://dx.doi.org/10.1371/journal.pbio.0060230] [PMID: 18816164]
[29]
Dong C-H, Pei H. Over-expression of miR397 improves plant tolerance to cold stress in Arabidopsis thaliana. J Plant Biol 2014; 57(4): 209-17.
[http://dx.doi.org/10.1007/s12374-013-0490-y]
[30]
Stief A, Altmann S, Hoffmann K, Pant BD, Scheible W-R, Bäurle I. Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors. Plant Cell 2014; 26(4): 1792-807.
[http://dx.doi.org/10.1105/tpc.114.123851] [PMID: 24769482]
[31]
Cui LG, Shan JX, Shi M, Gao JP, Lin HX. The miR156-SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants. Plant J 2014; 80(6): 1108-17.
[http://dx.doi.org/10.1111/tpj.12712] [PMID: 25345491]
[32]
Koyama T, Furutani M, Tasaka M, Ohme-Takagi M. TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell 2007; 19(2): 473-84.
[http://dx.doi.org/10.1105/tpc.106.044792] [PMID: 17307931]
[33]
Schommer C, Debernardi JM, Bresso EG, Rodriguez RE, Palatnik JF. Repression of cell proliferation by miR319-regulated TCP4. Mol Plant 2014; 7(10): 1533-44.
[http://dx.doi.org/10.1093/mp/ssu084] [PMID: 25053833]
[34]
Thiebaut F, Rojas CA, Almeida KL, et al. Regulation of miR319 during cold stress in sugarcane. Plant Cell Environ 2012; 35(3): 502-12.
[http://dx.doi.org/10.1111/j.1365-3040.2011.02430.x] [PMID: 22017483]
[35]
Zhou M, Li D, Li Z, et al. Constitutive expression of a miR319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. Plant Physiol 2013; 161(3): 1375-91.
[http://dx.doi.org/10.1104/pp.112.208702] [PMID: 23292790]
[36]
Bakhshi B, Fard EM, Gharechahi J, et al. The contrasting microRNA content of a drought tolerant and a drought susceptible wheat cultivar. J Plant Physiol 2017; 216: 35-43.
[http://dx.doi.org/10.1016/j.jplph.2017.05.012] [PMID: 28575745]
[37]
Bakhshi B, Mohseni Fard E, Nikpay N, et al. MicroRNA signatures of drought signaling in rice root. PLoS One 2016; 11(6) e0156814
[http://dx.doi.org/10.1371/journal.pone.0156814] [PMID: 27276090]
[38]
Fard EM, Bakhshi B, Farsi M, et al. MicroRNAs regulate the main events in rice drought stress response by manipulating the water supply to shoots. Mol Biosyst 2017; 13(11): 2289-302.
[http://dx.doi.org/10.1039/C7MB00298J] [PMID: 28872648]
[39]
Fard EM, Bakhshi B, Keshavarznia R, Nikpay N, Shahbazi M, Salekdeh GH. Drought responsive microRNAs in two barley cultivars differing in their level of sensitivity to drought stress. Plant Physiol Biochem 2017; 118: 121-9.
[http://dx.doi.org/10.1016/j.plaphy.2017.06.007] [PMID: 28624683]

Rights & Permissions Print Cite
Article Metrics
28
© 2024 Bentham Science Publishers | Privacy Policy