Abstract
Glycophytic plants suffer from severe stress and injury when roots are exposed to high salinity in the rhizosphere. In contrast, the euhalophyte Salicornia europaea grows well at 200 mM NaCl and can withstand up to 1000 mM NaCl in the root zone. Analysis of gene expression profiles and the underlying molecular mechanisms responsible for this tolerance have been largely overlooked. Using the Illumina sequencing platform and the short-reads assembly programme Trinity, we generated a total of 40 and 39 million clean reads and further 140,086 and 122,728 unigenes from the 200 mM NaCl and 0 mM NaCl treated tissues of S. europaea roots, respectively. All unigenes in this study were functionally annotated within context of the COG, GO and KEGG pathways. Unigene functional annotation analysis allowed us to identify hundreds of ion transporters related to homeostasis and osmotic adaptation as well as a variety of proteins related to cation, amino acid, lipid and sugar transport. We found significant enrichment in response to stress including the functional categories of “antioxidant activity”, “catalytic activity” and “response to stimuli”. These findings represent for a useful resource for the scientific community working on salt tolerance mechanisms. Conversely, a total of 8639 EST-SSRs from 131,594 unigenes were identified and 4539 non-redundant SSRs primers pairs were developed. These data provide a good foundation for future studies on molecular adaptation mechanisms of euhalophytes roots under saline environments and will likely facilitate the identification of critical salt tolerance traits to be transferred in economically important crops.
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References
Abogadallah GM (2010) Insights into the significance of antioxidative defense under salt stress. Plant Signal Behav 5:369–374. https://doi.org/10.4161/psb.5.4.10873
Al-Sadi AM, Al-Masoudi RS, Al-Habsi N et al (2010) Effect of salinity on pythium damping-off of cucumber and on the tolerance of Pythium aphanidermatum. Plant Pathol 59:112–120. https://doi.org/10.1111/j.1365-3059.2009.02176.x
Barthakur S, Babu V, Bansa KC (2001) Over-expression of osmotin induces proline accumulation and confers tolerance to osmotic stress in transgenic tobacco. J Plant Biochem Biotechnol 10:31–37. https://doi.org/10.1007/BF03263103
Butt A, Mousley C, Morris K et al (1998) Differential expression of a senescence-enhanced metallothionein gene in Arabidopsis in response to isolates of Peronospora parasitica and Pseudomonas syringae. Plant J 16:209–221. https://doi.org/10.1046/j.1365-313x.1998.00286.x
Carter CT, Ungar IA (2004) Relationships between seed germinability of Spergularia marina (Caryophyllaceae) and the Formation of zonal communities in an inland salt marsh. Ann Bot 93:119–125. https://doi.org/10.1093/aob/mch018
Chaparzadeh N, D’Amico ML, Khavari-Nejad R-A et al (2004) Antioxidative responses of Calendula officinalis under salinity conditions. Plant Physiol Biochem 42:695–701. https://doi.org/10.1016/j.plaphy.2004.07.001
Chen X, Han H, Jiang P et al (2011) Transformation of beta-lycopene cyclase genes from Salicornia europaea and Arabidopsis conferred salt tolerance in Arabidopsis and tobacco. Plant Cell Physiol 52:909–921. https://doi.org/10.1093/pcp/pcr043
Conesa A, Götz S, García-Gómez JM et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676. https://doi.org/10.1093/bioinformatics/bti610
Delauney AJ, Verma DPS (1993) Proline biosynthesis and osmoregulation in plants. Plant J 4:215–223. https://doi.org/10.1046/j.1365-313X.1993.04020215.x
Duarte B, Caetano M, Almeida PR et al (2010) Accumulation and biological cycling of heavy metal in four salt marsh species, from Tagus estuary (Portugal). Environ Pollut 158:1661–1668. https://doi.org/10.1016/j.envpol.2009.12.004
Ellouzi H, Ben Hamed K, Cela J et al (2011) Early effects of salt stress on the physiological and oxidative status of Cakile maritima (halophyte) and Arabidopsis thaliana (glycophyte). Physiol Plant 142:128–143. https://doi.org/10.1111/j.1399-3054.2011.01450.x
Elthon TE, Stewart CR (1981) Submitochondrial location and electron transport characteristics of enzymes involved in proline oxidation. Plant Physiol 67:780–784
Fan P, Nie L, Jiang P et al (2013) Transcriptome analysis of Salicornia europaea under saline conditions revealed the adaptive primary metabolic pathways as early events to facilitate salt adaptation. PLoS One 8:e80595. https://doi.org/10.1371/journal.pone.0080595
Flowers TJ (2004) Improving crop salt tolerance. J Exp Bot 55:307–319. https://doi.org/10.1093/jxb/erh003
Flowers TJ, Colmer TD (2008) Salinity tolerance in halophytes. New Phytol 179:945–963. https://doi.org/10.1111/j.1469-8137.2008.02531.x
Flowers TJ, Hajibagheri MA, Clipson NJW (1986) Halophytes. Q Rev Biol 61:313–337. https://doi.org/10.1086/415032
Flowers TJ, Garcia A, Koyama M, Yeo AR (1997) Breeding for salt tolerance in crop plants—the role of molecular biology. Acta Physiol Plant 19:427–433. https://doi.org/10.1007/s11738-997-0039-0
Flowers TJ, Galal HK, Bromham L (2010) Evolution of halophytes: multiple origins of salt tolerance in land plants. Funct Plant Biol 37:604–612. https://doi.org/10.1071/FP09269
Ghassemi F, Jakeman AJ, Nix HA (1995) Salinisation of land and water resources: human causes, extent, management and case studies. CAB International, Wallingford
Gierth M, Mäser P, Schroeder JI (2005) The potassium transporter AtHAK5 functions in K+ deprivation-induced high-affinity K+ uptake and AKT1 K+ channel contribution to K+ uptake kinetics in Arabidopsis roots. Plant Physiol 137:1105–1114. https://doi.org/10.1104/pp.104.057216
Glenn EP, Brown JJ, Blumwald E (1999) Salt Tolerance and crop potential of halophytes. Crit Rev Plant Sci 18:227–255. https://doi.org/10.1080/07352689991309207
Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29:644–652. https://doi.org/10.1038/nbt.1883
Guo Y-Q, Tian Z-Y, Qin G-Y et al (2009) Gene expression of halophyte Kosteletzkya virginica seedlings under salt stress at early stage. Genetica 137:189–199. https://doi.org/10.1007/s10709-009-9384-9
Guo L, Yang H, Zhang X, Yang S (2013) Lipid transfer protein 3 as a target of MYB96 mediates freezing and drought stress in Arabidopsis. J Exp Bot 64:1755–1767. https://doi.org/10.1093/jxb/ert040
Han H, Li Y, Zhou S (2008) Overexpression of phytoene synthase gene from Salicornia europaea alters response to reactive oxygen species under salt stress in transgenic Arabidopsis. Biotechnol Lett 30:1501–1507. https://doi.org/10.1007/s10529-008-9705-6
Han B, Wang C, Tang Z et al (2015) Genome-wide analysis of microsatellite markers based on sequenced database in Chinese spring wheat (Triticum aestivum L.). PLoS One 10:e0141540. https://doi.org/10.1371/journal.pone.0141540
Hester MW, Mendelssohn IA, McKee KL (2001) Species and population variation to salinity stress in Panicum hemitomon, Spartina patens, and Spartina alterniflora: morphological and physiological constraints. Environ Exp Bot 46:277–297. https://doi.org/10.1016/S0098-8472(01)00100-9
Howitt SM, Udvardi MK (2000) Structure, function and regulation of ammonium transporters in plants. Biochim Biophys Acta (BBA) Biomembr 1465:152–170. https://doi.org/10.1016/S0005-2736(00)00136-X
Hsu SY, Hsu YT, Kao CH (2003) The effect of polyethylene glycol on proline accumulation in rice leaves. Biol Plant 46:73–78. https://doi.org/10.1023/A:1022362117395
Husaini AM, Abdin MZ (2008) Development of transgenic strawberry (Fragaria × ananassa Duch.) plants tolerant to salt stress. Plant Sci 174:446–455. https://doi.org/10.1016/j.plantsci.2008.01.007
Iseli C, Cv J, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In: Proceedings of the international conference on intelligent systems for molecular biology; ISMB international conference on intelligent systems for molecular biology, pp 138–148
Ji H, Pardo JM, Batelli G et al (2013) The salt overly sensitive (SOS) pathway: established and emerging roles. Mol Plant 6:275–286. https://doi.org/10.1093/mp/sst017
Kader J-C (1996) Lipid-transfer proteins in plants. Annu Rev Plant Physiol Plant Mol Biol 47:627–654. https://doi.org/10.1146/annurev.arplant.47.1.627
Kishor PBK, Sangam S, Amrutha RN et al (2005) Regulation of proline biosynthesis, degradation, uptake and transport in higher plants: its implications in plant growth and abiotic stress tolerance. Curr Sci 88:424–438
Li H, Wang Y, Jiang J et al (2009) Identification of genes responsive to salt stress on Tamarix hispida roots. Gene 433:65–71. https://doi.org/10.1016/j.gene.2008.12.007
Li J, Pu L, Han M et al (2014a) Soil salinization research in China: advances and prospects. J Geogr Sci 24:943–960. https://doi.org/10.1007/s11442-014-1130-2
Li J, Sun X, Yu G et al (2014b) Generation and analysis of expressed sequence tags (ESTs) from halophyte Atriplex canescens to explore salt-responsive related genes. Int J Mol Sci 15:11172–11189. https://doi.org/10.3390/ijms150611172
Lv S, Jiang P, Chen X et al (2012) Multiple compartmentalization of sodium conferred salt tolerance in Salicornia europaea. Plant Physiol Biochem 51:47–52. https://doi.org/10.1016/j.plaphy.2011.10.015
Ma J, Zhang M, Xiao X et al (2013) Global transcriptome profiling of Salicornia europaea L. shoots under NaCl treatment. PLoS One 8:e65877. https://doi.org/10.1371/journal.pone.0065877
Maathuis FJM, Sanders D (1996) Mechanisms of potassium absorption by higher plant roots. Physiol Plant 96:158–168. https://doi.org/10.1111/j.1399-3054.1996.tb00197.x
Maathuis FJM, Sanders D (1997) Regulation of K+ absorption in plant root cells by external K+: interplay of different plasma membrane K+ transporters. J Exp Bot 48:451–458
Manousaki E, Kalogerakis N (2009) Phytoextraction of Pb and Cd by the Mediterranean saltbush (Atriplex halimus L.): metal uptake in relation to salinity. Environ Sci Pollut Res 16:844–854. https://doi.org/10.1007/s11356-009-0224-3
Martínez-Atienza J, Jiang X, Garciadeblas B et al (2007) Conservation of the salt overly sensitive pathway in rice. Plant Physiol 143:1001–1012. https://doi.org/10.1104/pp.106.092635
Momonoki YS, Oguri S, Kato S, Kamimura H (1996) Studies on the mechanism of salt tolerance in Salicornia europaea L.: III. Salt accumulation and ACh function. Jpn J Crop Sci 65:693–699. https://doi.org/10.1626/jcs.65.693
Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Meth 5:621–628. https://doi.org/10.1038/nmeth.1226
Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651–681. https://doi.org/10.1146/annurev.arplant.59.032607.092911
Oh D-H, Leidi E, Zhang Q et al (2009) Loss of halophytism by interference with SOS1 expression. Plant Physiol 151:210–222. https://doi.org/10.1104/pp.109.137802
Olías R, Eljakaoui Z, Li J et al (2009) The plasma membrane Na+/H+ antiporter SOS1 is essential for salt tolerance in tomato and affects the partitioning of Na+ between plant organs. Plant Cell Environ 32:904–916. https://doi.org/10.1111/j.1365-3040.2009.01971.x
Öztürk L, Demir Y (2002) In vivo and in vitro protective role of proline. Plant Growth Regul 38:259–264. https://doi.org/10.1023/A:1021579713832
Panta S, Flowers T, Lane P et al (2014) Halophyte agriculture: success stories. Environ Exp Bot 107:71–83. https://doi.org/10.1016/j.envexpbot.2014.05.006
Parida AK, Jha B (2010) Antioxidative defense potential to salinity in the euhalophyte Salicornia brachiata. J Plant Growth Regul 29:137–148. https://doi.org/10.1007/s00344-009-9129-0
Parkhi V, Kumar V, Sunilkumar G et al (2009) Expression of apoplastically secreted tobacco osmotin in cotton confers drought tolerance. Mol Breed 23:625–639. https://doi.org/10.1007/s11032-009-9261-3
Pasapula V, Shen G, Kuppu S et al (2011) Expression of an Arabidopsis vacuolar H+-pyrophosphatase gene (AVP1) in cotton improves drought- and salt tolerance and increases fibre yield in the field conditions. Plant Biotechnol J 9:88–99. https://doi.org/10.1111/j.1467-7652.2010.00535.x
Rodríguez-Navarro A, Rubio F (2006) High-affinity potassium and sodium transport systems in plants. J Exp Bot 57:1149–1160. https://doi.org/10.1093/jxb/erj068
Rubio F, Santa-María GE, Rodríguez-Navarro A (2000) Cloning of Arabidopsis and barley cDNAs encoding HAK potassium transporters in root and shoot cells. Physiol Plant 109:34–43. https://doi.org/10.1034/j.1399-3054.2000.100106.x
Sairam RK, Tyagi A (2004) Physiology and molecular biology of salinity stress tolerance in plants. Curr Sci 86:407–421
Shabala S, Shabala L, Volkenburgh EV (2003) Effect of calcium on root development and root ion fluxes in salinised barley seedlings. Funct Plant Biol 30:507–514. https://doi.org/10.1071/fp03016
Shi H, Ishitani M, Kim C, Zhu J-K (2000) The Arabidopsis thaliana salt tolerance gene SOS1 encodes a putative Na+/H+ antiporter. PNAS 97:6896–6901. https://doi.org/10.1073/pnas.120170197
Shi H, Quintero FJ, Pardo JM, Zhu J-K (2002) The putative plasma membrane Na+/H+ antiporter SOS1 controls long-distance Na+ transport in plants. Plant Cell 14:465–477. https://doi.org/10.1105/tpc.010371
Singh NK, Handa AK, Hasegawa PM, Bressan RA (1985) Proteins associated with adaptation of cultured tobacco cells to NaCl. Plant Physiol 79:126–137. https://doi.org/10.1104/pp.79.1.126
Singh NK, Bracker CA, Hasegawa PM et al (1987) Characterization of osmotin: a thaumatin-like protein associated with osmotic adaptation in plant cells. Plant Physiol 85:529–536. https://doi.org/10.1104/pp.85.2.529
Stewart GR, Lee JA (1974) The role of proline accumulation in halophytes. Planta 120:279–289. https://doi.org/10.1007/BF00390296
Subramanyam K, Arun M, Mariashibu TS et al (2012) Overexpression of tobacco osmotin (Tbosm) in soybean conferred resistance to salinity stress and fungal infections. Planta 236:1909–1925. https://doi.org/10.1007/s00425-012-1733-8
Szabolcs I (1994) Soil and salinization. In: Pessarakli M (ed) Handbook of plant and crop stress, vol 19. Marcell Decker Inc., New York, pp 768–770
Tang R-J, Liu H, Bao Y et al (2010) The woody plant poplar has a functionally conserved salt overly sensitive pathway in response to salinity stress. Plant Mol Biol 74:367–380. https://doi.org/10.1007/s11103-010-9680-x
Tester M, Davenport R (2003) Na+ tolerance and Na+ transport in higher plants. Ann Bot 91:503–527. https://doi.org/10.1093/aob/mcg058
Ungar IA (1996) Effect of salinity on seed germination, growth, and ion accumulation of Atriplex patula (Chenopodiaceae). Am J Bot 83:604–607. https://doi.org/10.2307/2445919
Van Oosten MJ, Maggio A (2015) Functional biology of halophytes in the phytoremediation of heavy metal contaminated soils. Environ Exp Bot 111:135–146. https://doi.org/10.1016/j.envexpbot.2014.11.010
Verma S, Dubey RS (2003) Lead toxicity induces lipid peroxidation and alters the activities of antioxidant enzymes in growing rice plants. Plant Sci 164:645–655. https://doi.org/10.1016/S0168-9452(03)00022-0
Wang X, Fan P, Song H et al (2009) Comparative proteomic analysis of differentially expressed proteins in shoots of Salicornia europaea under different salinity. J Proteome Res 8:3331–3345. https://doi.org/10.1021/pr801083a
Wang F, Zang X, Kabir MR et al (2014) A wheat lipid transfer protein 3 could enhance the basal thermotolerance and oxidative stress resistance of Arabidopsis. Gene 550:18–26. https://doi.org/10.1016/j.gene.2014.08.007
Weaver LM, Gan S, Quirino B, Amasino RM (1998) A comparison of the expression patterns of several senescence-associated genes in response to stress and hormone treatment. Plant Mol Biol 37:455–469. https://doi.org/10.1023/A:1005934428906
Wu S, Su Q, An LJ (2010) Isolation of choline monooxygenase (CMO) gene from Salicornia europaea and enhanced salt tolerance of transgenic tobacco with CMO genes. Indian J Biochem Biophys 47:298–305
Yamanaka T, Miyama M, Tada Y. Bioscience (2009) Transcriptome profiling of the mangrove plant Bruguiera gymnorhiza and identification of salt tolerance genes by agrobacterium functional screening. Biotechnol Biochem 73:304–310. https://doi.org/10.1271/bbb.80513
Yang T, Poovaiah BW (2003) Calcium/calmodulin-mediated signal network in plants. Trends Plant Sci 8:505–512. https://doi.org/10.1016/j.tplants.2003.09.004
Yang X, Ji J, Wang G et al (2011) Over-expressing Salicornia europaea (SeNHX1) gene in tobacco improves tolerance to salt. Afr J Biotechnol 10:16452–16460
Yoshida S, Ito M, Nishida I, Watanabe A (2001) Isolation and RNA gel blot analysis of genes that could serve as potential molecular markers for leaf senescence in Arabidopsis thaliana. Plant Cell Physiol 42:170–178. https://doi.org/10.1093/pcp/pce021
Zhang Y, Lai J, Sun S et al (2008) Comparison analysis of transcripts from the halophyte Thellungiella halophila. J Integr Plant Biol 50:1327–1335. https://doi.org/10.1111/j.1744-7909.2008.00740.x
Zhu J-K (2001) Plant salt tolerance. Trends Plant Sci 6:66–71. https://doi.org/10.1016/S1360-1385(00)01838-0
Zou H-W, Tian X-H, Ma G-H, Li Z-X (2013) Isolation and functional analysis of ZmLTP3, a homologue to Arabidopsis LTP3. Int J Mol Sci 14:5025–5035. https://doi.org/10.3390/ijms14035025
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This work was supported by Natural Science Foundation in China (Grant no. U1703106), Youth Innovation Promotion Association, CAS (2016381), and the Open Fund of the Shanghai Key Laboratory of Bio-Energy Crops.
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Supplementary file S1
: All-Unigene sequences of S. europaea roots (Description: Sequences with no gap and with a length longer than 200 bp were selected from the assembly results) (FA 78994 KB)
Supplementary file S2
: Functional annotation of All-Unigenes, including GO, COG, and KEGG analyses (Description: All-Unigene sequences were searched against protein databases (Nr, Swiss-prot database, KEGG, COG, and GO) using BLASTX (E-value Nr, -5)) (XLS 32526 KB)
Supplementary file S3
: Summary of functional annotation of identified DEGs (Description: Unigenes with an absolute value of |log2Ratio| ≥ 1 and FDR ≤ 0.001 were identified as DEGs. GO and KEGG analyses of DEGs were based on a cutoff E-value of less than or equal to 10-5) (XLS 7464 KB)
Supplementary file S4
: GO categories of DEGs between salt-free and salt-treated roots of S. europaea (Description: DEGs were divided into three major categories: molecular functions, cellular components and biological processes. Gene numbers and gene ID are listed in this file) (XLS 428 KB)
Supplementary file S5
: Summary of DEGs enriched in KEGG pathways (Description: Pathways and backbone gene numbers are given in the table. The q-values for all pathways are less than or equal to 0.05) (XLSX 61 KB)
Supplementary file S6
: The transcriptome data comparison between shoot and root (Description: The gene length, rowreads number, RPKM value, gene annotation were given in form) (XLS 22034 KB)
Supplementary file S7: Summary of SSR primers
(Description: The gene ID and primer pairs were given in form) (XLSX 202 KB)
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Ma, J., Xiao, X., Li, L. et al. Large-scale de novo transcriptome analysis reveals specific gene expression and novel simple sequence repeats markers in salinized roots of the euhalophyte Salicornia europaea. Acta Physiol Plant 40, 140 (2018). https://doi.org/10.1007/s11738-018-2702-z
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DOI: https://doi.org/10.1007/s11738-018-2702-z