Abstract
Camellia sinensis is an important economic crop worldwide since this plant is used to make one of the most popular non-alcoholic beverages, tea. Salinity together with drought pose a serious threat to the production and qualities of C. sinensis. However, the transcriptome dynamics occurring in response to drought stress and salt stress in tea plants are poorly understood at the molecular level. We reported the first large-coverage transcriptome datasets for C. sinensis under drought and salt stress using next-generation sequencing technology. Using a high-throughput Illumina sequencing platform, approximately 398.95 million high-quality paired-end reads were generated from young leaves of C. sinensis subjected to drought stress and salt stress, and these reads were used for de novo assembly. The transcripts with further processing and filtering yielded a set of 64,905 coding DNA sequences (CDSs) with an average length of 710 bp and an N50 of 933 bp. In total, 3936 and 3715 differentially expressed genes (DEGs) were identified from all analyzed time points of drought stress and salt stress, respectively. Identified in drought and salt stress were 2131 overlap** DEGs, and these are involved in galactosyltransferase activity, tetrapyrrole binding, and hydrolase activity, indicating that C. sinensis has a similar molecular response to these two stresses. We clustered the above DEGs from both sets into four clusters according to their expression dynamics, with the genes in each cluster showing enrichment for particular functional categories. We also found that under salt stress, most DEGs showed down-regulation at early time points and their expression levels were elevated after 48 h, whereas under drought stress most DEGs were down-regulated in all time points. The DEGs relative to pathways of osmotic product such as proline, sugar, and GABA were identified in C. sinensis. Noteworthy, among the identified DEGs are genes involved in the biosynthetic pathways of polyphenol and caffeine, providing evidence at the molecular level that salt and drought affect tea qualities. In addition, we analyzed the differential expression of transcription factors and revealed a large amount of crosstalk between the metabolic pathways of drought and salt stress. All findings suggest that gene expression exhibits rapid and coordinated changes during C. sinensis adaptations to drought stress and salt stress, and common themes in the response to both stresses were identified.
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References
Abe H, Urao T, Ito T et al (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15(1):63–78. doi:10.1105/tpc.006130
Abe H, Yamaguchi-Shinozaki K, Urao T et al (1997) Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell 9(10):1859–1868. doi:10.1105/tpc.9.10.1859
Allakhverdiev SI, Sakamoto A, Nishiyama Y et al (2000) Ionic and osmotic effects of NaCl-induced inactivation of photosystems I and II in Synechococcus sp. Plant Physiol 123(3):1047–1056. doi:10.1104/pp.123.3.1047
Anthony Y (1998) Predicting the interaction between the effects of salinity and climate change on crop plants. Sci Hortic 78(1–4):159–174. doi:10.1016/S0304-4238(98)00193-9
Arbona V, Manzi M, Cd O, Gómez-Cadenas A (2013) Metabolomics as a tool to investigate abiotic stress tolerance in plants. Int J Mol Sci 14(3):4885–4911. doi:10.3390/ijms14034885
Ashraf M, Foolad MR (2007) Roles of glycine betaine and proline in improving plant abiotic stress resistance. Environ Exp Bot 59(2):206–216. doi:10.1016/j.envexpbot.2005.12.006
Bahieldin A, Atef A, Sabir JS (2013) Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq. C R Biol 35(6):1915–1924. doi:10.1016/j.crvi.2015.03.010
Beritognolo I, Harfouche A et al (2011) Comparative study of transcriptional and physiological responses to salinity stress in two contrasting Populus alba L. genotypes. Tree Physiol 31(12):1335–1355. doi:10.1093/treephys/tpr083
Berteli F, Corrales E, Guerrero C et al (2008) Salt stress increases ferredoxin-dependent glutamate synthase activity and protein level in the leaves of tomato. Physiol Plantarum 93(2):259–264. doi:10.1111/j.1399-3054.1995.tb02226.x
Binzel M, Ratajczak R (2002) Function of membrane transport systems under salinity: tonoplast. Springer, Netherlands
Bohnert HJ, Nelson DE, Jensen RG (1995) Adaptations to environmental stresses. Plant Cell 7(7):1099–1111. doi:10.1105/tpc.7.7.1099
Boyer JS (1982) Plant productivity and environment. Science 218(4571):443–448. doi:10.1126/science.218.4571.443
Bown AW, Shelp BJ (1999) Metabolism and functions of gamma-aminobutyric acid. Plant Physiol 115(1):1–5. doi:10.1104/pp.115.1.1
Bullard JH, Purdom E, Hansen KD, Dudoit S (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11:94. doi:10.1186/1471-2105-11-94
Chen C, Khaleel SS, Huang H, Wu CH (2015) NGS QC toolkit: a platform for quality control of next-generation sequencing data. Source Code Biol Med 7(2):1–5. doi:10.1186/1751-0473-9-8
Chinnusamy V, Stevenson B, Lee BH, Zhu JK (2002) Screening for gene regulation mutants by bioluminescence imaging. Sci STKE 2002(140):l10. doi:10.1126/stke.2002.140.pl10
Conesa A, Götz S, García-Gómez JM et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676. doi:10.1093/bioinformatics/bti610
Delauney AJ, Verma DPS (2002) Proline biosynthesis and osmoregulation in plants. Plant J 4(2):215–223. doi:10.1046/j.1365-313X.1993.04020215.x
Eiji O, Yuki M, Yasuaki S et al (2004) Effects of exogenous application of proline and betaine on the growth of tobacco cultured cells under saline conditions. Soil Science and Plant Nutrition 50(8):1301–1305. doi:10.1080/00380768.2004.10408608
Goode JA,Organizers DC (2007) Improving plant drought, salt and freezing tolerance by gene transfer of a single stress-inducible transcription factor. John Wiley & Sons, Ltd. doi:10.1002/9780470515778.ch13
Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652. doi:10.1038/nbt.1883
Haas BJ, Papanicolaou A, Yassour M et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8(8):1494–1512. doi:10.1038/nprot.2013.084
Hasegawa PM, Bressan RA, Zhu JK, Bohnert HJ (2000) Plant cellular and molecular responses to high salinity. Annu Rev Plant Physiol Plant Mol Biol 51:463–499. doi:10.1146/annurev.arplant.51.1.463
Hoque MA, Okuma E, Banu MN et al (2007) Exogenous proline mitigates the detrimental effects of salt stress more than exogenous betaine by increasing antioxidant enzyme activities. J Plant Physiol 164(5):553–561. doi:10.1016/j.jplph.2006.03.010
Jaglo-Ottosen KR, Gilmour SJ, Zarka DG et al (1998) Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science 280(5360):104–106. doi:10.1126/science.280.5360.104
Kanak V, Arpita G, Vinay K et al (2012) De novo transcriptome sequencing in L. to identify genes involved in the biosynthesis of diosgenin. Plant Genome 6(2):1–11. doi:10.3835/plantgenome2012.08.0021
Kanehisa M, Goto S, Kawashima S et al (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(Database issue):277–280. doi:10.1093/nar/gkh063
Kempa S, Krasensky J, Dal Santo S et al (2008) A central role of abscisic acid in stress-regulated carbohydrate metabolism. PLoS One 3(12):e3935. doi:10.1371/journal.pone.0003935
Krasensky J, Jonak C (2012) Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks. J Exp Bot 63(4):1593–1608. doi:10.1093/jxb/err460
Kristiansson E, Asker N, Förlin L, Larsson DG (2009) Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics 10(1):345. doi:10.1186/1471-2164-10-345
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(3):1–10. doi:10.1186/gb-2009-10-3-r25
Li P, Ponnala L, Gandotra N et al (2010) The developmental dynamics of the maize leaf transcriptome. Nat Genet 42(12):1060–1067. doi:10.1038/ng.703
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13):1658–1659. doi:10.1093/bioinformatics/btl158
Liu M, Qiao G, Jiang J et al (2012) Transcriptome sequencing and de novo analysis for ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform. PLoS One 7(10):136–136. doi:10.1371/journal.pone.0046766
Liu Q, Kasuga M, Sakuma Y et al (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10(8):1391–1406. doi:10.1105/tpc.10.8.1391
Livak KJ, Schmittgen TD et al (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt method. Methods 25:402–408
Lugan R, Niogret MF, Leport L et al (2010) Metabolome and water homeostasis analysis of Thellungiella salsuginea suggests that dehydration tolerance is a key response to osmotic stress in this halophyte. Plant J 64(2):215. doi:10.1111/j.1365-313X.2010.04323.x
Mahajan S, Tuteja N (2005) Cold, salinity and drought stresses: an overview. Arch Biochem Biophys 444(2):139–158. doi:10.1016/j.abb.2005.10.018
Meyer E, Aglyamova GV, Wang S et al (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10(1):219. doi:10.1186/1471-2164-10-219
Monte E, Tepperman JM, Al-Sady B et al (2004) The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Proc Natl Acad Sci U S A 101(46):16091–16098. doi:10.1073/pnas.0407107101
Pires N, Dolan L (2010) Origin and diversification of basic-helix-loop-helix proteins in plants. Mol Biol Evol 27(27):862–874. doi:10.1093/molbev/msp288
Rabbani MA, Maruyama K, Abe H et al (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. doi:10.1104/pp.103.025742
Renault H, Roussel V, El Amrani A et al (2010) The Arabidopsis pop2-1 mutant reveals the involvement of GABA transaminase in salt stress tolerance. BMC Plant Biol 10(1):20. doi:10.1186/1471-2229-10-20
Rhodes D, Handa S, Bressan RA (1986) Metabolic changes associated with adaptation of plant cells to water stress. Plant Physiol 82(4):890–903. doi:10.1104/pp.82.4.890
Robert DF, Bateman A, Clements J et al (2014) Pfam: the protein families database. Nucleic Acids Res 42(Database issue):D222–D230. doi:10.1093/nar/gkt1223
Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 10(1):71–73. doi:10.1038/nmeth.2251
Rogers PJ, Smith JE, Heatherley SV, Pleydell-Pearce CW (2008) Time for tea: mood, blood pressure and cognitive performance effects of caffeine and theanine administered alone and together. Psychopharmacology 195(4):569–577. doi:10.1007/s00213-007-0938-1
Rus AM, Bressan RA, Hasegawa PM (2005) Unraveling salt tolerance in crops. Nat Genet 37(10):1029–1030. doi:10.1038/ng1005-1029
Sakuma Y, Liu Q, Dubouzet JG et al (2002) DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. Biochem Biophys Res Commun 290(3):998–1009. doi:10.1006/bbrc.2001.6299
Sanchez DH, Siahpoosh MR, Roessner U et al (2008) Plant metabolomics reveals conserved and divergent metabolic responses to salinity. Physiol Plant 132(2):209–219. doi:10.1111/j.1399-3054.2007.00993.x
Seki M, Narusaka M, Ishida J et al (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(31):279–292. doi:10.1046/j.1365-313X.2002.01359.x
Seo JS, Joo J, Kim MJ et al (2011) OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice. Plant J 65(6):907–921. doi:10.1111/j.1365-313X.2010.04477.x
Shi CY,Wan XC,Jiang CJ, et al. (2007) Method for high-quality total RNA isolation from tea plants [Camellia sinensis (L.) O. Kuntze)]. Journal of Anhui Agricultural University.
Shi CY, Yang H, Wei CL et al (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 12(1):131. doi:10.1186/1471-2164-12-131
Shinozaki K, Yamaguchi-Shinozaki K (2000) Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 3(3):217–223. doi:10.1016/S1369-5266(00)80068-0
Singh K, Foley RC, Oñate-Sánchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5(5):430–436. doi:10.1016/S1369-5266(02)00289-3
Subramanian N, Venkatesh P, Ganguli S, Sinkar VP (1999) Role of polyphenol oxidase and peroxidase in the generation of black tea theaflavins. J Agric Food Chem 47(7):2571. doi:10.1021/jf981042y
Sun C, Gao X, Fu J et al (2015) Metabolic response of maize ( Zea mays L.) plants to combined drought and salt stress. Plant Soil 388(1):99–117. doi:10.1007/s11104-014-2309-0
Suresh I, Allan C (1998) Products of proline catabolism can induce osmotically regulated genes in rice. Plant Physiol 116(1):203–211. doi:10.1104/pp.116.1.203
Takasaki H, Maruyama K, Kidokoro S et al (2010) The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Mol Gen Genomics 284(3):173–183. doi:10.1007/s00438-010-0557-0
Teixeira J, Fidalgo F (2009) Salt stress affects glutamine synthetase activity and mRNA accumulation on potato plants in an organ-dependent manner. Plant Physiol Bioch 47(9):807. doi:10.1016/j.plaphy.2009.05.002
Terol J, Bargues M, Pérez-Alonso M (2001) ZFWD: a novel subfamily of plant proteins containing a C3H zinc finger and seven WD40 repeats. Gene 260(1–2):45–53. doi:10.1016/S0378-1119(00)00446-7
Tuteja N (2007) Mechanisms of high salinity tolerance in plants. Methods Enzymol 428:419–438. doi:10.1016/S0076-6879(07)28024-3
Urano K, Kurihara Y, Seki M, Shinozaki K (2010) ‘Omics’ analyses of regulatory networks in plant abiotic stress responses. Curr Opin Plant Biol 13(2):132–138. doi:10.1016/j.pbi.2009.12.006
Usadel B, Bläsing OE, Gibon Y et al (2008) Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range. Plant Cell Environ 31(4):518–547. doi:10.1111/j.1365-3040.2007.01763.x
Vera JC, Wheat CW, Fescemyer HW et al (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17(7):1636–1647. doi:10.1111/j.1365-294X.2008.03666.x
Vinay K, Sudesh K (2009) Proline and betaine provide protection to antioxidant and methylglyoxal detoxification systems during cold stress in Camellia sinensis (L.) O. Kuntze. Acta Physiol Plant 31(2):261–269. doi:10.1007/s11738-008-0227-6
Wang XC, Zhao QY, Ma CL et al (2013) Global transcriptome profiles of Camellia sinensis during cold acclimation. BMC Genomics 14(1):1–15. doi:10.1186/1471-2164-14-415
Wang Y, Li E, Yu N et al (2012) Characterization and expression of glutamate dehydrogenase in response to acute salinity stress in the Chinese mitten crab, Eriocheir sinensis. PLoS One 7(5):e37316. doi:10.1371/journal.pone.0037316
Wong CE, Li Y, Labbe A et al (2006) Transcriptional profiling implicates novel interactions between abiotic stress and hormonal responses in Thellungiella, a close relative of Arabidopsis. Plant Physiol 140(140):1437–1450. doi:10.1104/pp.105.070508
Wu ZJ, Li XH, Liu ZW et al (2015) Transcriptome-based discovery of AP2/ERF transcription factors related to temperature stress in tea plant (Camellia sinensis). Funct Integr Genomics 15(6):741. doi:10.1007/s10142-015-0457-9
**e C, Mao X, Huang J et al (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39(Web Server issue):W316–W322. doi:10.1093/nar/gkr483
Yamaguchi-Shinozaki K, Shinozaki K (2005) Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters. Trends Plant Sci 10(2):88–94. doi:10.1016/j.tplants.2004.12.012
Ye J, Fang L, Zheng H et al (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(Web Server issue):W293–W297. doi:10.1093/nar/gkl031
Yeung KY, Haynor DR, Ruzzo WL (2001) Validating clustering for gene expression data. Bioinformatics 17(4):309–318. doi:10.1093/bioinformatics/17.4.309
Zhang HB, **a EH, Huang H et al (2015) De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response. BMC Genomics 16:298. doi:10.1186/s12864-015-1494-4
Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53(53):247–273. doi:10.1146/annurev.arplant.53.091401.143329
Acknowledgements
This project was supported by grants from the 863 program (2013AA102604) and the funding from the Fujian Agriculture and Forestry University.
Data archiving statement
The Illumina sequencing datasets are available from the European Nucleotide Archive database (ENA; http://www.ebi.ac.uk/ena) under project number accession PRJEB11522. The experiment accession numbers of cDNA libraries obtained from the control tea plants for 0, 24, 48, and 72 h in cultivation nutrient solution only are ERX1180353, ERX1180350, ERX1180351, and ERX1180352, respectively. The samples from plant cuttings exposed to salt stress or drought stress for 24, 48, and 72 h were ERX1180347, ERX1180348, ERX1180349, ERX1180344, ERX1180345, and ERX1180346, respectively.
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Zhang, Q., Cai, M., Yu, X. et al. Transcriptome dynamics of Camellia sinensis in response to continuous salinity and drought stress. Tree Genetics & Genomes 13, 78 (2017). https://doi.org/10.1007/s11295-017-1161-9
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DOI: https://doi.org/10.1007/s11295-017-1161-9