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Genome-wide identification of drought-responsive microRNAs and their target genes in Chinese jujube by deep sequencing

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Abstract

Background

MicroRNAs (miRNAs) are about 21 snucleotide (nt) long, non-coding RNAs that play an important role in plant abiotic stress responses. Chinese jujube is a native fruit tree in China, which is also an admittedly drought-resistant plant. But the drought-related miRNAs have little been reported in jujube.

Objective

To identify possibly drought-responsive microRNAs and their target genes in Chinese Jujube.

Methods

Twelve small RNA libraries were constructed from two jujube genotypes both drought treated and control samples with three replicates to identify known and novel miRNAs in Chinese Jujube, DESeq2 was used to identify expression pattern of miRNAs between drought treatment and control samples, TargetFinder program was used to predict potential target genes of conserved and novel miRNAs, RT-qPCR were used to analysis the expression levels of drought-related miRNAs and their potential targets. The RNA ligase-mediated RLM-5′ RACE experiments were performed to validate predicted target genes of drought-related miRNAs.

Results

43 known miRNAs and 431 novel miRNAs were identified in Chinese jujube. Expression analysis showed that 28 miRNAs were differential expressed under drought stress in jujube variety “Dongzao”, including 21 up-regulated miRNAs and 7 down-regulated miRNAs, 61 miRNAs were differential expressed under drought stress in Chinese jujube variety “Zanhuangdazao”, including 23 up-regulated miRNAs and 37 down-regulated miRNAs. Depend on miRNAs target prediction, functional annotation and expression analysis, we identified 9 drought-related miRNAs, and 7 target genes of 6 miRNAs were confirmed using the modified 5′-RACE method. Also, RT-qPCR analyses revealed that relative expression of those miRNAs and their targets have negative tendency.

Conclusion

We identified 6 drought-related miRNAs by high-throughout sequencing and target gene annotation from Chinese jujube, and targets of those miRNAs were confirmed by the modified 5′-RACE method. These findings provide molecular evidence for enhancing drought tolerance in Chinese jujube and other plants.

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References

  • Akdogan G, Tufekci ED, Uranbey S, Unver T (2016) miRNA-based drought regulation in wheat. Funct Integr Genomics 16(3):221–233

    Article  CAS  Google Scholar 

  • Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221

    Article  CAS  Google Scholar 

  • Apweiler R, Bairoch A, Wu CH (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32:D115–D119

    Article  CAS  Google Scholar 

  • Ashraf M (2010) Inducing drought tolerance in plants: recent advances. Biotechnol Adv 28:169–183

    Article  CAS  Google Scholar 

  • Balusamy SR, Rahimi S, Yang DC (2019) Characterization of squalene-induced PgCYP736B involved in salt tolerance by modulating key genes of abscisic acid biosynthesis. Int J Biol Macromol 121:796–805

    Article  CAS  Google Scholar 

  • Barrera-Figueroa BE, Gao L, Diop NN, Wu Z, Ehlers JD, Roberts PA, Close TJ, Zhu JK, Liu R (2011) Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes. BMC Plant Biol 11:127

    Article  CAS  Google Scholar 

  • Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233

    Article  CAS  Google Scholar 

  • Bechtold U, Albihlal WS, Lawson T, Michael JF, Sparrow PA, Richard F, Persad R et al (2013) Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b overexpression enhances water productivity, resistance to drought, and infection. J Exp Bot 64:3467–3481

    Article  CAS  Google Scholar 

  • Bu J, Zhao J, Liu ML (2016) Expression stabilities of candidate reference genes for RT-qPCR in Chinese jujube (Ziziphus jujuba Mill.) under a variety of conditions. PLoS ONE 11(4):e0154212

    Article  Google Scholar 

  • Cao ZH, Zhang SZ, Wang RK, Zhang RF, Hao YJ (2013) Genome wide analysis of the apple MYB transcription factor family allows the identification of MdoMYB121 gene conferring abiotic stress tolerance in plants. PLoS ONE 8:e69955

    Article  CAS  Google Scholar 

  • Chaves MM, Oliveira MM (2004) Mechanisms underlying plant resilience to water deficits: prospects for water-saving agriculture. J Exp Bot 55(407):2365–2384

    Article  CAS  Google Scholar 

  • Cheng XW, Ma YP, Xu CX (2013) Absorption, translocation and distribution characteristics of salt ions of Chinese jujube and sour jujube under iso-osmotic potential drought, salt, and alkaline stresses. J Cent South Univ Fore Technol 33:20–25

    Google Scholar 

  • Ci D, Song YP, Tian M, Zhang DQ (2015) Methylation of miRNA genes in the response to temperature stress in Populus simonii. Front Plant Sci 6:921

    Article  Google Scholar 

  • Cuming AC, Cho SH, Kamisugi Y, Graham H, Quatrano RS (2007) Microarray analysis of transcriptional responses to abscisic acid and osmotic, salt, and drought stress in the moss, Physcomitrella patens. New Phytol 176:275–287

    Article  CAS  Google Scholar 

  • Deng YY, Li JQ, Wu SF (2006) Integrated nr database in protein annotation system and its localization. Comput Eng 32(5):71–74

    Google Scholar 

  • Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15:573–581

    Article  CAS  Google Scholar 

  • Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14(9):755–763

    Article  CAS  Google Scholar 

  • Eldem V (2012) Genome-wide identifification of miRNAs responsive to drought in peach (Prunus persica) by high-throughput deep sequencing. PLoS ONE 7:e50298

    Article  CAS  Google Scholar 

  • Fedoroff NV, Battisti DS, Beachy RN, Cooper PJ, Fischhoff DA, Hodges CN, Knauf VC, Lobell D, Mazur BJ, Molden D (2010) Radically rethinking agriculture for the 21st century. Science 327:833–834

    Article  CAS  Google Scholar 

  • Friedlander MR, Mackowiak SD, Li N, Chen W, Rajewsky N (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40:37–52

    Article  Google Scholar 

  • Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to down regulate auxin signals for Arabidopsis lateral root development. Plant Cell 17:1376–1386

    Article  CAS  Google Scholar 

  • Guo M, Liu JH, Ma X, Luo DX, Gong ZH, Lu MH (2016) The plant heat stress transcription factors (HSFs): structure, regulation, and function in response to abiotic stresses. Front Plant Sci 7:114

    Article  Google Scholar 

  • Hackenberg M, Gustafson P, Langridge P, Shi BJ (2015) Differential expression of microRNAs and other small RNAs in barley between water and drought conditions. Plant Biotechnol J 13:2–13

    Article  CAS  Google Scholar 

  • Hartl FU (1996) Molecular chaperones in cellular protein folding. Nature 381(6583):571–579

    Article  CAS  Google Scholar 

  • Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (2007) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17:287–291

    Article  Google Scholar 

  • Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R et al (2004) A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 5(2):R7

    Article  Google Scholar 

  • Kropat J (2005) A regulator of nutritional copper signaling in Chlamydomonas is an SBP domain protein that recognizes the GTAC core of copper response element. Proc Natl Acad Sci USA 102:18730–18735

    Article  CAS  Google Scholar 

  • Kurihara Y, Watanabe Y (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci USA 101(34):12753–12758

    Article  CAS  Google Scholar 

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  Google Scholar 

  • Lauter N, Kampani A, Carlson S, Goebel M, Moose SP (2005) MicroRNA172 down-regulates glossy 15 to promote vegetative phase change in maize. Proc Natl Acad Sci 102:9412–9417

    Article  CAS  Google Scholar 

  • Li G, Niu JF (2006) Study on building jujube plantation using wild jujube seeds in the middle barren areas of Ningxia province. China Fruits 2:58

    Google Scholar 

  • Li JW, Fan LP, Ding SD, Ding XL (2007) Nutritional composition of five cultivars of Chinese jujube. Food Chem 103:454–460

    Article  CAS  Google Scholar 

  • Li BS, Qin YR, Duan H, Yin WL, Xia XL (2011) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J Exp Bot 62:3765–3779

    Article  CAS  Google Scholar 

  • Liu J, Liu H, Ma L, Wang S, Gao J, Li Y (2014) A Chinese jujube (Ziziphus jujuba Mill.) fruit-expressed sequence tag (EST) library: annotation and EST-SSR characterization. Sci Hortic 165:99–105

    Article  CAS  Google Scholar 

  • Liu H, Able AJ, Able JA (2016) SMARTER de-stressed cereal breeding. Trends Plant Sci 21:909–925

    Article  CAS  Google Scholar 

  • Long SP, Ort DR (2010) More than taking the heat: crops and global change. Curr Opin Plant Biol 13(3):241–248

    Article  Google Scholar 

  • Long RC, Li MN, Kang JM, Zhang TJ, Sun Y, Yang QC (2015) Small RNA deep sequencing identififies novel and salt-stress-regulated microRNAs from roots of Medicago sativa and Medicago truncatula. Physiol Plant 154:13–27

    Article  CAS  Google Scholar 

  • Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550

    Article  Google Scholar 

  • Ma F, Huang J, Yang J, Zhou J, Sun Q, Sun J (2020) Identification, expression and miRNA targeting of auxin response factor genes related to phyllody in the witches’ broom disease of jujube. Gene 746:144656

    Article  CAS  Google Scholar 

  • Mallory AC, Dugas DV, Bartel DP, Bartel B (2004) MicroRNA regulation of NAC domaintargets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol 14:1035–1046

    Article  CAS  Google Scholar 

  • Manassero NU, Viola IL, Welchen E, Gonzalez DH (2013) TCP transcription factors: architectures of plant form. Biomol Concepts 4:111–127

    Article  CAS  Google Scholar 

  • Mao G, Seebeck T, Schrenker D, Yu O (2013) CYP709B3, a cytochrome P450 monooxygenase gene involved in salt tolerance in Arabidopsis thaliana. BMC Plant Biol 13:169–182

    Article  Google Scholar 

  • Martin-Trillo M, Cubas P (2009) TCP genes: a family snapshot ten years later. Trends Plant Sci 15:31–39

    Article  Google Scholar 

  • Michael A, Catherine AB, Judith AB (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-C29

    Article  Google Scholar 

  • Minoru K, Susumu G, Shuichi K (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(277):D280

    Google Scholar 

  • Moldovan D, Spriggs A, Yang J, Pogson BJ, Dennis ES, Wilson IW (2010) Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. J Exp Bot 61:165–177

    Article  CAS  Google Scholar 

  • Moxon S, Jing R, Szittya G, Schwach F, Rusholme-Pilcher RL (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 18:1602–1609

    Article  CAS  Google Scholar 

  • Mukhopadhyay P, Tyagi AK (2015) OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways. Sci Rep 5:9998

    Article  CAS  Google Scholar 

  • Niu CD, Li HY, Jiang LJ, Yan MJ, Li CY, Geng D, Xie YP, Yan Y, Shen XX, Chen PX, Dong J, Ma FW, Guan QM (2019) Genome-wide identification of drought responsive microRNAs in two sets of Malus from interspecific hybrid progenies. Hortic Res-Englang 6:75

    Article  Google Scholar 

  • Palatnik JF, Allen E, Wu X, Schommer C, Schwab R (2003) Control of leaf morphogenesis by microRNAs. Nature 425:257–263

    Article  CAS  Google Scholar 

  • Paul S, Datta SK, Datta K (2015) miRNA regulation of nutrient homeostasis in plants. Front Plant Sci 6:232

    Article  Google Scholar 

  • Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133(4):1755–1767

    Article  CAS  Google Scholar 

  • Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B (2002) Prediction of plant microRNA targets. Cell 110:513–520

    Article  CAS  Google Scholar 

  • Roman LT, Michael YG, Darren AN (2000) The COG database: a tool for genome scale analysis of protein functions and evolution. Nucleic Acids Res 128(1):33–36

    Google Scholar 

  • Sahi C, Singh A, Kumar K, Blumwald E, Grover A (2006) Salt stress response in rice: genetics, molecular biology, and comparative genomics. Funct Integr Genomics 6:263–284

    Article  CAS  Google Scholar 

  • Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31(3):279–292

    Article  CAS  Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58:221–227

    Article  CAS  Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozakiy K, Sekiz M (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol 6:410–417

    Article  CAS  Google Scholar 

  • Shiu SH, Bleecker AB (2003) Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis. Plant Physiol 132(2):530–543

    Article  CAS  Google Scholar 

  • Stief A (2014) Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors. Plant Cell 26:1792–1807

    Article  CAS  Google Scholar 

  • Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019

    Article  CAS  Google Scholar 

  • Umezawa T, Fujita M, Fujita Y, Yamaguchi-Shinozaki K, Shinozaki K (2006) Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future. Curr Opin Biotechnol 17(2):113–122

    Article  CAS  Google Scholar 

  • Wang TZ, Chen L, Zhao MG, Tian QY, Zhang WH (2011) Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics 12:367

    Article  CAS  Google Scholar 

  • Wang C, Yang Y, Wang H, Ran X, Li B, Zhang J, Zhang H (2016) Ectopic expression of a cytochrome P450 monooxygenase gene PtCYP714A3 from Populus trichocarpa reduces shoot growth and improves tolerance to salt stress in transgenic rice. Plant Biotechnol J 14:1838–1851

    Article  CAS  Google Scholar 

  • Wu B, Wang M, Ma Y, Yuan L, Lu S (2012) High-throughput sequencing and characterization of the small RNA transcriptome reveal features of novel and conserved microRNAs in Panax ginseng. PLoS ONE 7:e44385

    Article  CAS  Google Scholar 

  • Yao Y (2010) Non-coding small RNAs responsive to abiotic stress in wheat (Triticum aestivum L.). Funct Integr Genom 10:187–190

    Article  CAS  Google Scholar 

  • Zhang L (2009) A genome-wide characterization of microRNA genes in maize. PLoS Genet 5:e1000716

    Article  Google Scholar 

  • Zhang R, Marshall D, Bryan GJ, Hornyik C (2013) Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS ONE 8:e57233

    Article  CAS  Google Scholar 

  • Zhao B, Liang R, Ge L, Li W, Xiao H (2007) Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun 354:585–590

    Article  CAS  Google Scholar 

  • Zhou LG, Liu YH, Liu ZC, Kong DY, Duan M, Luo LJ (2010) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 61:4157–4168

    Article  CAS  Google Scholar 

  • Zhou ZS, Zeng HQ, Yang ZM (2012) Genome-wide identification of Medicago truncatula microRNAs and their targets reveals their differential regulation by heavy metal. Plant Cell Environ 35:86–99

    Article  Google Scholar 

  • Zhou M, Li D, Li Z, Hu Q, Yang C, Zhu L, Luo H (2013) Constitutive expression of a miR319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. Plant Physiol 161:1375–1391

    Article  CAS  Google Scholar 

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Acknowledgements

This work was sponsored by the Forestry and Grassland Science and Technology Innovation Project of Gansu Province (kjcx202006), National Natural Science Foundation of China (No. 31860400), and the 2021 Subsidy of Gansu Province Woody Oil Engineering Research Center.

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Authors and Affiliations

  1. College of Forestry, Gansu Agricultural University, Lanzhou, 730070, People’s Republic of China

    Luhe Zhang & Yi Li

  2. Gansu Academy of Forestry Sciences, Lanzhou, 730020, People’s Republic of China

    Luhe Zhang, Huali Huang, Junying Zhao, Fang Wang & Duofeng Wang

  3. College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, People’s Republic of China

    Jiangwei Yang

  4. College of Resources and Environment, Gansu Agricultural University, Lanzhou, 730070, People’s Republic of China

    Qian Lu

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  1. Luhe Zhang
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  2. Yi Li
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  3. Jiangwei Yang
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  4. Huali Huang
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  5. Qian Lu
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Contributions

Conceived and designed the experiments: LZ YL JY. Performed the experiments: LZ YL JY. Analyzed the data: LZ YL JY. Contributed reagents/materials/analysis tools: HH QL JZ FW DW. Wrote the paper: LZ YL JY.

Corresponding author

Correspondence to Yi Li.

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Supplementary Information

Below is the link to the electronic supplementary material.

13258_2022_1274_MOESM1_ESM.xls

Supplementary file1 Supplementary Material 1: sRNAs annotation and distribution of twelve Chinese jujube samples (XLS 27 KB)

Supplementary file2 Supplementary Material 2: The novel miRNAs in Chinese jujube (XLS 64 KB)

13258_2022_1274_MOESM3_ESM.xls

Supplementary file3 Supplementary Material 3: Expression analysis of known and novel miRNAs between control and drought treatment in two Chinese jujube varieties (XLS 56 KB)

13258_2022_1274_MOESM4_ESM.docx

Supplementary file4 Supplementary Material 4: The differentially expressed miRNAs between two Chinese jujube varieties (DOCX 39 KB)

Supplementary file5 Supplementary Material 5: Predicted target genes of miRNA in Chinese jujube (XLS 60 KB)

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Zhang, L., Li, Y., Yang, J. et al. Genome-wide identification of drought-responsive microRNAs and their target genes in Chinese jujube by deep sequencing. Genes Genom 45, 231–245 (2023). https://doi.org/10.1007/s13258-022-01274-5

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