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De novo characterization of the Rehmannia glutinosa leaf transcriptome and analysis of gene expression associated with replanting disease

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Abstract

The perennial herbaceous plant, Rehmannia glutinosa Libosch, is a traditional Chinese medicine because of the active extracts from its dried tuberous roots. However, R. glutinosa productivity and quality has been seriously affected by replanting (continuous monoculture) disease, which cannot at present be effectively prevented or controlled. Since very little is known about the molecular mechanism of replanting disease, we aimed to investigate transcriptional changes in replanted R. glutinosa leaves and identify genes responding to the disease. Here, we constructed a cDNA library from total RNA isolated from the mixture of leaves of the first year planted (L1) and the second year replanted R. glutinosa (L2) at the tuberous root expansion stage. We generated about 37 million high-quality reads from the cDNA library using deep sequencing and obtained 94,544 distinct sequences by de novo assembly and gap-filling. From this set, a total of 54,490 transcripts containing a complete or partial encoding region was annotated in public protein databases. Based on this resource, we screened differentially expressed genes in the L1 and L2 libraries by the digital gene expression (DGE) technique. Finally, a set of 1,954 genes was found to be differentially expressed in L2. Using bioinformatics and qRT-PCR, the 117 most strongly differentially expressed genes were considered to be prime candidates responsible for replanting disease. Functional analysis of the candidates showed that ethylene signaling was exaggerated and the genes in key metabolism pathways were abnormally expressed in L2. The study provides an important resource for further investigating the cause of replanting disease and developing methods to control or reduce its harmful effects.

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References

  • Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995

    CAS  PubMed  Google Scholar 

  • Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125:279–284

    Article  CAS  PubMed  Google Scholar 

  • Bürstenbinder K, Savchenko T, Müller J, Adamson AW, Stamm G, Kwong R, Zipp BJ, Dinesh DC, Abel S (2013) Arabidopsis calmodulin-binding protein IQ67-domain 1 localizes to microtubules and interacts with kinesin light chain-related protein-1. J Biol Chem 288:1871–1882

    Article  PubMed Central  PubMed  Google Scholar 

  • Chen L, Song Y, Li S, Zhang L, Zou C, Yu D (2012) The role of WRKY transcription factors in plant abiotic stresses. Biochim Biophys Acta 1819:120–128

    Article  CAS  PubMed  Google Scholar 

  • Choi D, Lee Y, Cho HT, Kende H (2003) Regulation of expansin gene expression affects growth and development in transgenic rice plants. Plant Cell 15:1386–1398

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Cui MH, Yoo KS, Hyoung S, Nguyen HT, Kim YY, Kim HJ, Ok SH, Yoo SD, Shin JS (2013) An Arabidopsis R2R3-MYB transcription factor, AtMYB20, negatively regulates type 2C serine/threonine protein phosphatases to enhance salt tolerance. FEBS Lett 587:1773–1778

    Article  CAS  PubMed  Google Scholar 

  • Dang ZH, Zheng LL, Wang J, Gao Z, Wu SB, Qi Z, Wang YC (2013) Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna. BMC Genom. doi:10.1186/1471-2164-14-29

    Google Scholar 

  • Dietz KJ, Oliver M, Viehhauser VA (2010) AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signaling. Protoplasma 245:3–14

    Article  CAS  PubMed  Google Scholar 

  • Du JF, Yin WJ, Zhang ZY, Hou J, Huang J, Li J (2009) Autotoxicity and phenolic acids content in soils with different planting interval years of Rehmannia glutinosa. Chin J Ecol 28:445–450 (in Chinese)

    CAS  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  PubMed  Google Scholar 

  • Durrant WE, Rowland O, Piedras P, Hammond-Kosack KE, Jones JDG (2000) cDNA-AFLP reveals a striking overlap in race-specific resistance and wound response gene expression profiles. Plant Cell 12:963–977

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ellis CM, Nagpal P, Young JC, Hagen G, Guilfoyle TJ, Reed JW (2005) AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana. Development 132:4563–4574

    Article  CAS  PubMed  Google Scholar 

  • Gupta P, Goel R, Pathak S, Srivastava A, Singh SP, Sangwan RS, Asif MH, Trivedi PK (2013) De novo assembly, functional annotation and comparative analysis of Withania somnifera leaf and root transcriptomes to identify putative genes involved in the withanolides biosynthesis. PLoS ONE 8:e62714

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • He R, Kim MJ, Nelson W, Balbuena TS, Kim R, Kramer R, Crow JA, May GD, Thelen JJ, Soderlund CA, Gang DR (2012) Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity. Am J Bot 99(2):232–247. doi:10.3732/ajb.1100429

    Article  CAS  PubMed  Google Scholar 

  • Hemmerich P, von Mikecz A, Neumann F, Sozeri O, Wolff-Vorbeck G, Zoebelein R, Krawinkel U (1993) Structural and functional properties of ribosomal protein L7 from humans and rodents. Nucleic Acids Res 21:223–231

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hwang HY, Olson SK, Brown JR, Esko JD, Horvitz HR (2003) The caenorhabditis elegans genes sqv-2 and sqv-6, which are required for vulval morphogenesis, encode glycosaminoglycan galactosyltransferase II and xylosyltransferase. J BiolChem 278:11735–11738

    CAS  Google Scholar 

  • Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proceedings of the international conference in intelligence systems for molecular biology, pp 138–148

  • Jafari Z, Haddad R, Hosseini R, Garoosi G (2013) Cloning, identification and expression analysis of ACC oxidase gene involved in ethylene production pathway. Mol Biol Rep 40:1341–1350

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M et al (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kao CC, Singh P, Ecker DJ (2001) De novo initiation of viral RNA-dependent RNA synthesis. Virology 287:251–260

    Article  CAS  PubMed  Google Scholar 

  • Kühn U, Wahle E (2004) Structure and function of poly(A) binding proteins. Biochim Biophys Acta 1678:67–84

    Article  PubMed  Google Scholar 

  • Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967

    Article  CAS  PubMed  Google Scholar 

  • Li ZF, Yang YQ, Xie DF, Zhu LF, Zhang ZG, Lin WX (2012) Identification of autotoxic compounds in fibrous roots of Rehmannia (Rehmannia glutinosa Libosch). PLoS ONE 7:e28806

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Liang C, Liu X, Yiu SM, Lim BL (2013) De novo assembly and characterization of Camelina sativa transcriptome by paired-end sequencing. BMC Genom. doi:10.1186/1471-2164-14-146

    Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2 (−Delta Delta C (T)). Method 25:402–408

    Article  CAS  Google Scholar 

  • Maitra U, Chaudhuri J, Chaudhuri J, Si K (2012) Function of eukaryotic translation initiation factor 1A (eIF1A) (formerly called eIF-4C) in initiation of protein synthesis. J BiolChem 272:7883–7891

    Google Scholar 

  • Mazzola M, Manici LM (2012) Apple replant disease: role of microbial ecology in cause and control. Annu Rev Phytopathol 50:45–65

    Article  CAS  PubMed  Google Scholar 

  • Meluh PB, Rose MD (1990) KAR3, a kinesin-related gene required for yeast nuclear fusion. Cell 60:1029–1041

    Article  CAS  PubMed  Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wrold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Meth 5:621–628

    Article  CAS  Google Scholar 

  • Nekrasov V, Ludwig AA, Jones JD (2006) CITRX thioredoxin is a putative adaptor protein connecting Cf-9 and the ACIK1 protein kinase during the Cf-9/Avr9-induced defence response. FEBS Lett 580:4236–4241

    Article  CAS  PubMed  Google Scholar 

  • Pandey SP, Somssich IE (2009) The role of WRKY transcription factors in plant immunity. Plant Physiol 150:1648–1655

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Reed JW (2001) Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci 6:420–425

    Article  CAS  PubMed  Google Scholar 

  • Rowland O, Ludwig AA, Merrick CJ, Baillieul F, Tracy FE, Durrant WE, Fritz-Laylin L, Nekrasov V, Sjölander K, Yoshioka H, Jones JD (2005) Functional analysis of Avr9/Cf-9 rapidly elicited genes identifies a protein kinase, ACIK1, that is essential for full Cf-9–dependent disease resistance in tomato. Plant Cell 17:295–310

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Schönfeld C, Wobbe L, Borgstädt R, Kienast A, Nixon PJ, Kruse O (2004) The nucleus-encoded protein MOC1 is essential for mitochondrial light acclimation inChlaydomonas reinhardtii. J Biol Chem 279:50366–50374

    Article  PubMed  Google Scholar 

  • Stone JM, Walker JC (1995) Plant protein kinase families and signal transduction. Plant Physiol 108:451–457

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sun P, Song S, Zhou L, Zhang B, Qi J, Li X (2012) Transcriptome analysis reveals putative genes involved in iridoid biosynthesis in Rehmannia glutinosa. Int J MolSci 13:13748–13763

    Article  CAS  Google Scholar 

  • Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Taybi T, Nimmo HG, Borland AM (2004) Expression of phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxylase kinase genes. Implications for genotypic capacity and phenotypic plasticity in the expression of crassulacean acid metabolism. Plant Physiol 135:587–598

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wang QQ, Fei L, Chen XS, Ma JX, Zeng QH, Yang ZM (2010) Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics 96:369–376

    Article  CAS  PubMed  Google Scholar 

  • Wang YB, Liu YF, Lu XT, Yan FF, Wang B, Bai WW, Zhao YX (2013) Rehmannia glutinosa extract activates endothelial progenitor cells in a rat model of myocardial infarction through a SDF-1 α/CXCR4 cascade. PLoS ONE 8:e54303

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wei M, Song M, Fan S, Yu S (2013) Transcriptomic analysis of differentially expressed genes during anther development in genetic male sterile and wild type cotton by digital gene-expression profiling. BMC Genom 14:97. doi:10.1186/1471-2164-14-97

    Article  CAS  Google Scholar 

  • Wen XS, Yang SL, Wei JH, Zheng JH (2002) Textual research on planting history of Rehmannia glutinosa and its cultivated varieties. Chinese Traditional and Herbal Drugs 33:946–949 (in Chinese)

    Google Scholar 

  • Wu LK, Wang HB, Zhang ZX, Lin R, Zhang ZY, Lin WX (2011) Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil. PLoS ONE 6:e20611

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Xu Q, Morgan RD, Roberts RJ, Xu SY, van Doorn LJ, Donahue JP, Miller GG, Blaser MJ (2002) Functional analysis of iceA1, a CATG-recognizing restriction endonuclease gene in Helicobacter pylori. Nucleic Acids Res 30:3839–3847

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yan X, Dong C, Yu J, Liu W, Jiang C, Liu J, Hu Q, Fang X, Wei W (2013) Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus. BMC Genom. doi:10.1186/1471-2164-14-29

    Google Scholar 

  • Yang Y, Smith SA (2013) Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genom 14:328. doi:10.1186/1471-2164-14-328

    Article  CAS  Google Scholar 

  • Yang JT, Laymon RA, Goldstein LS (1989) A three-domain structure of kinesin heavy chain revealed by DNA sequence and microtubule binding analyses. Cell 56:879–889

    Article  CAS  PubMed  Google Scholar 

  • Yang JI, Ruegger PM, McKenry MV, Becker JO, Borneman J (2012) Correlations between root-associated microorganisms and peach replant disease symptoms in a California soil. PLoS ONE 7:e46420

  • Yang YH, Zhang ZY, Fan HM, Zhao YD, Li MJ, Li J, Chen JY, Lin WX, Chen XJ (2013) Construction and analysis of a different expression cDNA library in Rehmannia glutinosa plants subjected to continuous cropping. Acta Physiol Plant 35:645–655

  • Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L (2006a) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ye J, McGinnis S, Madden TL (2006b) BLAST: improvements for better sequence analysis. Nucleic Acids Res 34:W6–W9

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yu FP, Yang L (1994) Preliminary study of Rehmannia mosaic virus. Acta Phytopathol Sinica 24:310 (in Chinese)

    Google Scholar 

  • Yu Y, Wang J, Wang H, Zhang Z, Liu J (2010) Relationship between Rh-RTH1 and ethylene receptor gene expression in response to ethylene in cut rose. Plant Cell Rep 29:895–904

    Article  CAS  PubMed  Google Scholar 

  • Zhang G, Gao HW, Wang Z, Yang X, Sun GZ, Guan N (2007) Studies on screening identification indexes of salt tolerance and comprehensive evaluation at seedling stage of elytrigia. Acta Prataculturae Sinica 16:55–61 (in Chinese)

    Google Scholar 

  • Zhang Z, Lin W, Yang Y, Chen H, Chen X (2011) Effects of continuous cropping Rehmannia glutinosa L. on diversity of fungal community in rhizospheric soil. Agric Sci China 10:1374–1384

    Article  Google Scholar 

  • Zhang X, Hao L, Meng L, Liu M, Zhao L et al (2013) Digital gene expression tag profiling analysis of the gene expression patterns regulating the early stage of mouse spermatogenesis. PLoS ONE 8:e58680

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhao YJ, Chen Z (1991) Effect of N, P and K supply on dry matter accumulation and nutrient contents of Rehmannia glutinosa Libosch. J Chin Med Mater 14:3–6 (in Chinese)

    Google Scholar 

Download references

Acknowledgments

This work was supported by grants from the National Natural Science Foundation of China (Nos. 81072983, 31271674 and 81274022) and the Science and Technology Research Key Project of Henan Educational Committee (No. 13A180160).

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Authors and Affiliations

  1. College of Bioengineering, Henan University of Technology, Zhengzhou City, 450001, China

    Yan Hui Yang, Yan Jie Yi & Zong Wu Zhang

  2. College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou City, 450002, Henan Province, China

    Ming Jie Li, Xin Jian Chen, Peng Fei Wang & Feng Qing Wang

  3. College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Wen Xiong Lin & Zhong Yi Zhang

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  1. Yan Hui Yang
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  2. Ming Jie Li
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Correspondence to Xin Jian Chen or Zhong Yi Zhang.

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Yang, Y.H., Li, M.J., Chen, X.J. et al. De novo characterization of the Rehmannia glutinosa leaf transcriptome and analysis of gene expression associated with replanting disease. Mol Breeding 34, 905–915 (2014). https://doi.org/10.1007/s11032-014-0084-5

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