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Identification of novel miRNAs and their target genes from Populus szechuanica infected with Melampsora larici-populina

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Abstract

Two novel miRNAs were selected from a pre-constructed RNA library of Populus szechuanica infected with the foliar rust fungus Melampsora larici-populina in order to detect the genes regulated as targets of the miRNAs novel_mir_11 and novel_mir_357. The novel miRNAs were identified from P. szechuanica using stem-loop methods and their precursors were able to fold into a complete stem loop structure. The predicted target genes of the novel miRNAs were verified with RNA ligase-mediated 5′ rapid amplification of cDNA ends (RLM-5′RACE). The full-length sequences of target genes, RPM1 and RPS2/5, in P. szechuanica were obtained through rapid amplification of cDNA ends (RACE) and officially named PsRPM1 and PsRPS2/5. These genes contain nucleotide binding site-leucine-rich repeats (NBS-LRR) domains typical of resistance genes. The expression levels of miRNAs and their target genes in different periods post infection were analysed with quantitative real-time PCR (qRT-PCR). After infection with the foliar rust fungus, the expression levels of the novel miRNAs and their target genes were dynamic. Both novel_mir_11 and novel_mir_357 negatively regulated the expression of their target genes. In this study, the regulatory effects of two novel miRNAs through their target genes were characterized to provide further mechanistic information regarding the interaction between Populus and a foliar rust fungus. Results of this study improve our understanding of the defence response mechanisms of Populus and will stimulate future work to characterize strategies to prevent and control Populus diseases.

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References

  1. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5(7):522–531

    Article  CAS  PubMed  Google Scholar 

  2. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Bonnet E, Wuyts J, Rouze P, Van de Peer Y (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci 101:11511–11516

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14(6):787–799

    Article  CAS  PubMed  Google Scholar 

  5. Martínez G, Forment J, Llave C, Pallás V, Gómez G (2011) High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs. PLoS ONE 6:e19523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Xie FL, Frazier TP, Zhang BH (2010) Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 232:417–434

    Article  CAS  PubMed  Google Scholar 

  7. Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510

    Article  CAS  PubMed  Google Scholar 

  8. Katiyar-Agarwal S, Jin H (2010) Role of small RNAs in host-microbe interactions. Annu Rev Phytopathol 48:225–246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Vionnet O, Jones JD (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Sci Signal 312(5772):436

    CAS  Google Scholar 

  10. Luan SY, Cui J, Wang WC, Meng J (2016) MiR1918 enhances tomato sensitivity to Phytophthora infestans infection. Sci Rep 6:35858

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Rhoades M, Reinhart B, Lim L, Burge B, Bartel B, Barte D (2002) Prediction of plant microRNA targets. Cell 110:513–520

    Article  CAS  PubMed  Google Scholar 

  12. Chen M, Cao ZM (2015) Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina. BMC Genom 16(1):696

    Article  CAS  Google Scholar 

  13. Ma C, A YL ABSL, Zhang WN, Duan XW, Meng D, Wang ZG, Wang AD, Zhou ZS, Li TZ (2014) Cloning and characterization of miRNAs and their targets, including a novel miRNA-targeted NBS–LRR protein class gene in apple (Golden Delicious). Mol Cell 7(1):218–230

    CAS  Google Scholar 

  14. Liu X, Gorovsky MA (1993) Mapping the 5′ and 3′ ends of Tetrahymena thermophila mRNAs using RNA ligase mediated amplification of cDNA ends (RLM-RACE). Nucleic Acids Res 21(21):4954–4960

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL (2005) Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17(8):2186–2203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297(5589):2053–2056

    Article  CAS  PubMed  Google Scholar 

  17. Brunner AM, Busov VB, Strauss SH (2004) Poplar genome sequence, functional genomics in an ecologically dominant plant species. Trends Plant Sci 9:49–56

    Article  CAS  PubMed  Google Scholar 

  18. Duplessis S, Major I, Martin F, Séguin A (2009) Poplar and pathogen interactions: insights from Populus genome-wide analyses of resistance and defense gene families and gene expression profiling. Crit Rev Plant Sci 28(5):309–334

    Article  CAS  Google Scholar 

  19. Cao ZM, Li ZQ, Hu JJ (1998) Study on physiological differentiation of Melampsora larici-populina Kleb. J Northw For Coll 13(1):53–57 (In Chinese with English)

    Google Scholar 

  20. Rinaldi C, Kohler A, Frey P, Duchaussoy F, Ningre N, Couloux A, Wincker P, Le Thiec D, Fluch S, Martin F, Duplessis S (2007) Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar Rust Melampsora larici-populina. Plant Physiol 144(1):347–366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu N, Mahuvakar VR. Andersen MR, Lao K, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33(20):e179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Dheda K, Huggett JF, Bustin SA, Johnson MA, Rook G, Zumla A (2004) Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 37:112–119

    Article  CAS  PubMed  Google Scholar 

  23. Kohler A, Blaudez D, Chalot M, Martin F (2004) Cloning and expression of multiple metallothioneins from hybrid poplar. New Phytol 164(1):83–93

    Article  CAS  PubMed  Google Scholar 

  24. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2–∆∆Ct method. Methods 25(4):402–408

    Article  CAS  PubMed  Google Scholar 

  25. Chen L, Ren Y, Zhang Y, Xu J, Sun F, Zhang Z, Wang Y (2012) Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa. Gene 504(2):160–165

    Article  CAS  PubMed  Google Scholar 

  26. Chen L, Zhang Y, Ren Y, Xu J, Zhang Z, Wang Y (2012) Genome-wide identification of cold-responsive and new microRNAs in Populus tomentosa by high-throughput sequencing. Biochem Biophys Res Co 417(2):892–896

    Article  CAS  Google Scholar 

  27. Jia X, Ren L, Chen Q, Li R, Tang G (2009) UV-B responsive microRNAs in Populus tremula. J Plant Physiol 166(18):2046–2057

    Article  CAS  PubMed  Google Scholar 

  28. Li B, Yin W, Xia X (2009) Identification of microRNAs and their targets from Populus euphratica. Biochem Bioph Res Co 388(2):272–277

    Article  CAS  Google Scholar 

  29. Li B, Qin Y, Duan H, Yin W, Xia X (2011) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J Exp Bot 62(11):3765–3779

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Lu S, Sun YH, Chiang VL (2008) Stress-responsive microRNAs in Populus. Plant J 55(1):131–151

    Article  CAS  PubMed  Google Scholar 

  31. Qin Y, Duan Y, Xia X, Yin W (2011) Expression profiles of precursor and mature microRNAs under dehydration and high salinity shock in Populus euphratica. Plant Cell Rep 30(10):1893–1907

    Article  CAS  PubMed  Google Scholar 

  32. Ren Y, Chen L, Zhang Y, Kang X, Zhang Z, Wang Y (2012) Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress. Funct Integr Genomic 12(2):327–339

    Article  CAS  Google Scholar 

  33. Zhou J, Zhuo R, Liu M, Qiao G, Jiang J, Li H, Qiu W, Zhang X, Lin S (2011) Identification and characterization of Novel MicroRNAs from Populus cathayana Rehd. Plant Mol Biol Rep 29(1):242–251

    Article  CAS  Google Scholar 

  34. Zhou X, Wang G, Zhang W (2007) UV-B responsive microRNA genes in Arabidopsis thaliana. Mol Syst Biol 3(1):103

    Article  PubMed  PubMed Central  Google Scholar 

  35. Medzihradszky A, Várallyay E, Kauppinen S, Havelda Z (2006) Spatio-temporal accumulation of micro RNAs is highly coordinated in developing plant tissues. Plant J 47(1):140–151

    Article  CAS  Google Scholar 

  36. Khaldun ABM, Huang W, Liao S, Lv H, Wang Y (2015) Identification of microRNAs and target genes in the fruit and shoot tip of Lycium chinense: A traditional chinese medicinal plant. PLoS ONE 10(1):e0116334

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Wang J, Yang X, Xu H, Chi X, Zhang M, Hou X (2012) Identification and characterization of microRNAs and their target genes in Brassica oleracea. Gene 505(2):300–308

    Article  CAS  PubMed  Google Scholar 

  38. Song C, Jia Q, Fang J, Li F, Wang C, Zhang Z (2010) Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags. Plant Biol 12(6):927–934

    Article  CAS  PubMed  Google Scholar 

  39. Zhu Q, Fan L, Liu Y, Xu H, Llewellyn D, Wilson I (2013) miR482 regulation of NBS-LRR defense genes during fungal pathogen infection in cotton. PLoS ONE 8(12):e84390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Marone D, Russo MA, Laidò G, De Leonardis AM, Mastrangelo AM (2013) Plant nucleotide binding site-leucine-rich repeat (NBS-LRR) genes: active guardians in host defense responses. Int J Mol Sci 14(4):7302–7326

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Lu S, Sun YH, Amerson H, Chiang VL (2007) MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development. Plant J 51(6):1077–1098

    Article  CAS  PubMed  Google Scholar 

  42. Klevebring D, Street NR, Fahlgren N, Kasschau KD, Carrington JC, Lundeberg J, Jansson S (2009) Genome-wide profiling of Populus small RNAs. BMC Gemomics 10:620–638

    Article  CAS  Google Scholar 

  43. Gielen H, Remans T, Vangronsveld J, Cuypers A (2012) MicroRNAs in metal stress: Specific roles or secondary responses? Int J Mol Sci 13(12):15826–15847

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Wang B, Sun YF, Song N, Wang XJ, Feng H, Huang LL, Kang ZS (2013) Identification of UV-B induced microRNAs in wheat. Genet Mol Res 12(4):4213–4221

    Article  CAS  PubMed  Google Scholar 

  45. Kumar R (2014) Role of microRNAs in biotic and abiotic stress responses in crop plants. Appl Biochem Biotech 174(1):93–115

    Article  CAS  Google Scholar 

  46. Wang LL, Zhao HS, Chen DL, Li LC, Sun HY, Lou YF, Gao ZM (2016) Characterization and primary functional analysis of a bamboo NAC gene targeted by miR164b. Plant Cell Rep 35:1371–1383

    Article  CAS  PubMed  Google Scholar 

  47. Jiang N, Meng J, Cui J, Sun GX, Luan YS (2018) Function identification of miR482b, a negative regulator during tomato resistance to Phytophthora infestans. Hortic Res 5(1):9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Dugas DV, Bartel B (2004) MicroRNA regulation of gene expression in plants. Curr Opin Plant Biol 7(5):512–520

    Article  CAS  PubMed  Google Scholar 

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Funding

This research was supported by the National Key Research and Development Program project (No. 2017YFD0600103-4-2).

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  1. College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China

    Xin Liu, Min Chen, Xue Zhou & Zhimin Cao

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  1. Xin Liu
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  2. Min Chen
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Correspondence to Zhimin Cao.

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Liu, X., Chen, M., Zhou, X. et al. Identification of novel miRNAs and their target genes from Populus szechuanica infected with Melampsora larici-populina. Mol Biol Rep 46, 3083–3092 (2019). https://doi.org/10.1007/s11033-019-04746-2

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