Abstract
Aeluropus lagopoides sequesters excess salt on its leaf surface via salt glands to maintain osmotic and ionic balance during salt stress. The present study aimed to identify the molecular responses involved in salt excretion, osmotic adjustment, and transcriptional regulation during NaCl treatment at different time points using RNA-seq analysis. In total, 460.8 million raw reads were generated, resulting in the de novo assembly of 592,893 transcripts. Differential expression analysis revealed 3150 and 6548 unique differentially expressed genes (DEGs) in shoot and root samples, respectively. Gene ontology (GO) enrichment analysis revealed that genes involved in kinase activity and calcium transport activity were regulated at 2 h, while genes related to phosphatase activity, ATP-dependent transport, water transport, and potassium transport were regulated at 24 h and 48 h of salt stress. DEGs associated with kinases (CIPK6, CIPK23, and CIPK29), transcription factors (ERF RAP2-13, WRKY 33, ZFP 52), and transporters (NHX2, KUP19, KUP9) were significantly up-regulated at different time points. Additionally, genes related to osmoprotectant biosynthesis, antioxidative enzymes, and late embryogenesis abundant family (LEA) were found up-regulated. The RNA-seq data were correlated with qPCR analysis of 12 stress-responsive DEGs. Further, the qPCR expression analysis revealed up-regulation of trichome initiation genes during salt stress, shedding light on the development of salt glands. Overall, these results provide valuable insights into the molecular mechanisms underlying the salt stress response of A. lagopoides.
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Agarwal P, Dabi M, Kinhekar K, Gangapur DR, Agarwal PK (2020) Special adaptive features of plant species In response to salinity. Salt Drought Stress Toler Plants: Signal Netw Adapt Mech. https://doi.org/10.1007/978-3-030-40277-8_3
Aliakbari M, Razi H, Alemzadeh A, Tavakol E (2021) RNA-seq transcriptome profiling of the halophyte Salicornia persica in response to salinity. J Plant Growth Regul 40:707–721. https://doi.org/10.1007/s00344-020-10134-z
Barajas-Lopez JD, Moreno JR, Gamez-Arjona FM, Pardo JM, Punkkinen M, Zhu JK, Quintero FJ, Fujii H (2018) Upstream kinases of plant SnRKs are involved in salt stress tolerance. Plant J 93(1):107–118. https://doi.org/10.1111/tpj.13761
Barhoumi Z, Djebali W, Smaoui A, Chaïbi W, Abdelly C (2007) Contribution of NaCl excretion to salt resistance of Aeluropus littoralis (Willd) Parl. J Plant Physiol 164(7):842–850. https://doi.org/10.1016/j.jplph.2006.05.008
Barros NL, Marques DN, Tadaiesky LB, de Souza CR (2021) Halophytes and other molecular strategies for the generation of salt-tolerant crops. Plant Physiol Biochem 162:581–591. https://doi.org/10.1016/j.plaphy.2021.03.028
Bigeard J, Hirt H (2018) Nuclear signaling of plant MAPKs. Front Plant Sci 11(9):469. https://doi.org/10.3389/fpls.2018.00469
Bosamia TC, Gangapur DR, Agarwal P, Agarwal PK. (2022) Deciphering the Molecular Mechanism of Salinity Tolerance in Halophytes Using Transcriptome Analysis. InAdvancements in Developing Abiotic Stress-Resilient Plants 2022 Jun 20 (pp. 237–254). CRC Press. doi: https://doi.org/10.3390/plants11030291
Bushmanova E, Antipov D, Lapidus A, Prjibelski AD (2019) rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. GigaScience 8(9):giz100. https://doi.org/10.1093/gigascience/giz100
Butcher K, Wick AF, DeSutter T, Chatterjee A, Harmon J (2016) Soil salinity: a threat to global food security. Agron J 108(6):2189–2200. https://doi.org/10.2134/agronj2016.06.0368
Cackett L, Cannistraci CV, Meier S, Ferrandi P, Pěnčík A, Gehring C, Novák O, Ingle RA, Donaldson L (2022) Salt-specific gene expression reveals elevated auxin levels in Arabidopsis thaliana plants grown under saline conditions. Front Plant Sci 13:15. https://doi.org/10.3389/fpls.2022.804716
Cai H, Chen H, Yi T, Daimon CM, Boyle JP, Peers C, Maudsley S, Martin B (2013) VennPlex–a novel Venn diagram program for comparing and visualizing datasets with differentially regulated datapoints. PLoS ONE 8(1):e53388. https://doi.org/10.1371/journal.pone.0053388
Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J (2021) eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 38(12):5825–5829. https://doi.org/10.1093/molbev/msab293
Che-Othman MH, Millar AH, Taylor NL (2017) Connecting salt stress signalling pathways with salinity-induced changes in mitochondrial metabolic processes in C3 plants. Plant Cell Environ 40(12):2875–2905. https://doi.org/10.1111/pce.13034
Dassanayake M, Larkin JC (2017) Making plants break a sweat: the structure, function, and evolution of plant salt glands. Front Plant Sci 8:406. https://doi.org/10.3389/fpls.2017.00406
Dave A, Sanadhya P, Joshi PS, Agarwal P, Agarwal PK (2021) Molecular cloning and characterization of high-affinity potassium transporter (AlHKT2;1) gene promoter from halophyte Aeluropus lagopoides. Int J Biol Macromol 181:1254–1264. https://doi.org/10.1016/j.ijbiomac.2021.05.038
Diray-Arce J, Clement M, Gul B, Khan MA, Nielsen BL (2015) Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. BMC Genom 16(1):1–24. https://doi.org/10.1186/s12864-015-1553-x
Do TH, Martinoia E, Lee Y, Hwang JU (2021) update on ATP-binding cassette (ABC) transporters: how they meet the needs of plants. Plant Physiol 187(4):1876–1892. https://doi.org/10.1093/plphys/kiab193
Feng W, Kita D, Peaucelle A, Cartwright HN, Doan V, Duan Q, Liu MC, Maman J, Steinhorst L, Schmitz-Thom I, Yvon R (2018) The FERONIA receptor kinase maintains cell-wall integrity during salt stress through Ca2+ signaling. Curr Biol 28(5):666–675. https://doi.org/10.1016/j.cub.2018.01.023
Flowers TJ, Colmer TD (2008) Salinity tolerance in halophytes. New Phytol 1:945–963. https://doi.org/10.1111/j.1469-8137.2008.02531.x
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652. https://doi.org/10.1038/nbt.1883
Han G, Wang M, Yuan F, Sui N, Song J, Wang B (2014) The CCCH zinc finger protein gene AtZFP1 improves salt resistance in Arabidopsis thaliana. Plant Mol Biol 86:237–253. https://doi.org/10.1007/s11103-014-0226-5
Han G, Li Y, Qiao Z, Wang C, Zhao Y, Guo J, Chen M, Wang B (2021) Advances in the regulation of epidermal cell development by C2H2 zinc finger proteins in plants. Front Plant Sci 12:754512. https://doi.org/10.3389/fpls.2021.754512
Hao S, Wang Y, Yan Y, Liu Y, Wang J, Chen S (2021) A review on plant responses to salt stress and their mechanisms of salt resistance. Horticulturae 7(6):132. https://doi.org/10.3390/horticulturae7060132
Hellsberg E, Montanari F, Ecker GF (2015) The ABC of phytohormone translocation. Planta Med 81(06):474–487. https://doi.org/10.1055/s-0035-1545880
Joshi PS, Agarwal P, Agarwal PK (2021) Overexpression of AlNAC1 from recretohalophyte Aeluropus lagopoides alleviates drought stress in transgenic tobacco. Environ Exp Bot 181:104277. https://doi.org/10.1016/j.envexpbot.2020.104277
Khedia J, Agarwal P, Agarwal PK (2018) AlNAC4 transcription factor from halophyte Aeluropus lagopoides mitigates oxidative stress by maintaining ROS homeostasis in transgenic tobacco. Front Plant Sci 9:1522. https://doi.org/10.3389/fpls.2018.01522
Krueger F, James F, Ewels P, Afyounian E, Schuster-Boeckler BF (2021) trimgalore: v0. 6.7-doi via zenodo. Zenodo10. 2021:5281
Kumar P, Sharma PK (2020) Soil salinity and food security in India. Front Sustain Food Syst 4:533781. https://doi.org/10.1016/j.jenvman.2020.111736
Larkin JC, Brown ML, Schiefelbein J (2003) How do cells know what they want to be when they grow up? Lessons from epidermal patterning in Arabidopsis. Annu Rev Plant Bio 54(1):403–430. https://doi.org/10.1146/annurev.arplant.54.031902.134823
Li J, Long Y, Qi GN, Li J, Xu ZJ, Wu WH, Wang Y (2014) The Os-AKT1 channel is critical for K+ uptake in rice roots and is modulated by the rice CBL1-CIPK23 complex. Plant Cell 26(8):3387–3402. https://doi.org/10.1105/tpc.114.123455
Li C, Qi Y, Zhao C, Wang X, Zhang Q (2021) Transcriptome profiling of the salt stress response in the leaves and roots of halophytic Eutrema salsugineum. Front Genet 2021:2117. https://doi.org/10.3389/fgene.2021.770742
Liu Y, Liu D, Hu R, Hua C, Ali I, Zhang A, Liu B, Wu M, Huang L, Gan Y (2017) AtGIS, a C2H2 zinc-finger transcription factor from Arabidopsis regulates glandular trichome development through GA signaling in tobacco. Biochem Biophys Res Commun 483(1):209–215. https://doi.org/10.1016/j.bbrc.2016.12.164
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods 25(4):402–408. https://doi.org/10.1006/meth.2001.1262
Ma X, Li QH, Yu YN, Qiao YM, Haq SU, Gong ZH (2020) The CBL–CIPK pathway in plant response to stress signals. Int J Mol Sci 21(16):5668. https://doi.org/10.3390/ijms21165668
Nayak SS, Pradhan S, Sahoo D, Parida A (2020) De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance. Sci Rep 10(1):5192. https://doi.org/10.1038/s41598-020-61857-8
Nikalje GC, Srivastava AK, Pandey GK, Suprasanna P (2018) Halophytes in biosaline agriculture: mechanism, utilization, and value addition. Land Degrad Dev 29(4):1081–1095. https://doi.org/10.1002/ldr.2819
Nishimura O, Hara Y, Kuraku S (2017) gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics 33(22):3635–3637. https://doi.org/10.1093/bioinformatics/btx445
Parida AK, Veerabathini SK, Kumari A, Agarwal PK (2016) Physiological, anatomical and metabolic implications of salt tolerance in the halophyte Salvadora persica under hydroponic culture condition. Front Plant Sci 7:351. https://doi.org/10.3389/fpls.2016.00351
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14(4):417–419. https://doi.org/10.1038/nmeth.4197
Pyvovarenko T, Lopato S (2011) Isolation of plant transcription factors using a yeast one-hybrid system. Plant Trans Factors: Methods Protoc. https://doi.org/10.1007/978-1-61779-154-3_3
Ragel P, Ródenas R, García-Martín E, Andrés Z, Villalta I, Nieves-Cordones M, Rivero RM, Martínez V, Pardo JM, Quintero FJ, Rubio F (2015) The CBL-interacting protein kinase CIPK23 regulates HAK5-mediated high-affinity K+ uptake in Arabidopsis roots. Plant Physiol 169(4):2863–2873. https://doi.org/10.1104/pp.15.01401
Rajan N, Agarwal P, Patel K, Sanadhya P, Khedia J, Agarwal PK (2015) Molecular characterization and identification of target protein of an important vesicle trafficking gene AlRab7 from a salt excreting halophyte Aeluropus lagopoides. DNA Cell Biol 34(2):83–91. https://doi.org/10.1089/dna.2014.2592
Rajappa S, Krishnamurthy P, Kumar PP (2020) Regulation of AtKUP2 expression by bHLH and WRKY transcription factors helps to confer increased salt tolerance to Arabidopsis thaliana plants. Front Plant Sci 11:1311. https://doi.org/10.3389/fpls.2020.01311
Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140. https://doi.org/10.1093/bioinformatics/btp616
Sadat-Hosseini M, Bakhtiarizadeh MR, Boroomand N, Tohidfar M, Vahdati K (2020) Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut. PLoS ONE 15(4):e0232005. https://doi.org/10.1371/journal.pone.0232005
Sami F, Yusuf M, Faizan M, Faraz A, Hayat S (2016) Role of sugars under abiotic stress. Plant Physiol Biochem 109:54–61. https://doi.org/10.1016/j.plaphy.2016.09.005
Sanadhya P, Agarwal P, Agarwal PK (2015) Ion homeostasis in a salt-secreting halophytic grass. AoB Plants 1:7. https://doi.org/10.1093/aobpla/plv055
Shabala S, Bose J, Hedrich R (2014) Salt bladders: do they matter? Trends Plant Sci 19(11):687–691. https://doi.org/10.1016/j.tplants.2014.09.001
Sheikh-Assadi M, Naderi R, Salami SA, Kafi M, Fatahi R, Shariati V, Martinelli F, Cicatelli A, Triassi M, Guarino F, Improta G (2022) Normalized workflow to optimize hybrid de novo transcriptome assembly for non-model species: a case study in Lilium ledebourii (Baker) boiss. Plants 11(18):2365. https://doi.org/10.3390/plants11182365
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31(19):3210–3212. https://doi.org/10.1093/bioinformatics/btv351
Sui N, Wang Y, Liu S, Yang Z, Wang F, Wan S (2018) Transcriptomic and physiological evidence for the relationship between unsaturated fatty acid and salt stress in peanut. Front Plant Sci 9:7. https://doi.org/10.3389/fpls.2018.00007
Sun L, Zhang A, Zhou Z, Zhao Y, Yan A, Bao S, Yu H, Gan Y (2015) GLABROUS INFLORESCENCE STEMS 3 (GIS 3) regulates trichome initiation and development in Arabidopsis. New Phytol 206(1):220–230. https://doi.org/10.1111/nph.13218
Tripathi V, Parasuraman B, Laxmi A, Chattopadhyay D (2009) CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plants. Plant J 58(5):778–790. https://doi.org/10.1111/j.1365-313X.2009.03812.x
Vaziriyeganeh M, Khan S, Zwiazek JJ (2021) Transcriptome and metabolome analyses reveal potential salt tolerance mechanisms contributing to maintenance of water balance by the halophytic grass Puccinellia nuttalliana. Front Plant Sci 12:760863. https://doi.org/10.3389/fpls.2021.760863
Wang D, Yang N, Zhang C, He W, Ye G, Chen J, Wei X (2022a) Transcriptome analysis reveals molecular mechanisms underlying salt tolerance in halophyte Sesuvium portulacastrum. Front Plant Sci 13:973419. https://doi.org/10.3389/fpls.2022.973419
Wang L, Du M, Wang B, Duan H, Zhang B, Wang D, Li Y, Wang J (2022b) Transcriptome analysis of halophyte Nitraria tangutorum reveals multiple mechanisms to enhance salt resistance. Sci Rep 12(1):14031. https://doi.org/10.1038/s41598-022-17839-z
Xie Z, Nolan TM, Jiang H, Yin Y (2019) AP2/ERF transcription factor regulatory networks in hormone and abiotic stress responses in Arabidopsis. Front Plant Sci 10:228. https://doi.org/10.3389/fpls.2019.00228
Yamamoto N, Takano T, Tanaka K, Ishige T, Terashima S, Endo C, Kurusu T, Yajima S, Yano K, Tada Y (2015) Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus. Front Plant Sci 6:241. https://doi.org/10.3389/fpls.2015.00241
Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(suppl_2):293–297. https://doi.org/10.1093/nar/gkl031
Younesi-Melerdi E, Nematzadeh GA, Pakdin-Parizi A, Bakhtiarizadeh MR, Motahari SA (2020) De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress. Sci Rep 10(1):9148. https://doi.org/10.1038/s41598-020-65947-5
Yu G, Wang LG, Han Y, He QY (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS J Integr Biol 16(5):284–287. https://doi.org/10.1089/omi.2011.0118
Yuan F, Leng B, Wang B (2016) Progress in studying salt secretion from the salt glands in recretohalophytes: how do plants secrete salt? Front Plant Sci 7:977. https://doi.org/10.3389/fpls.2016.00977
Yuan F, Wang X, Zhao B, Xu X, Shi M, Leng B, Dong X, Lu C, Feng Z, Guo J, Han G (2022) The genome of the recretohalophyte Limonium bicolor provides insights into salt gland development and salinity adaptation during terrestrial evolution. Mol Plant 15(6):1024–1044. https://doi.org/10.1016/j.molp.2022.04.011
Zhang X, Liao M, Chang D, Zhang F (2014) Comparative transcriptome analysis of the Asteraceae halophyte Karelinia caspica under salt stress. BMC Res Notes 7:1–9. https://doi.org/10.1186/1756-0500-7-927
Zhou Z, Wei X, Lan H (2023) CgMYB1, an R2R3-MYB transcription factor, can alleviate abiotic stress in an annual halophyte Chenopodium glaucum. Plant Physiol Biochem 196:484–496. https://doi.org/10.1016/j.plaphy.2023.01.055
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CSIR communication is no. 72/2023. The authors are thankful to CSIR, New Delhi for providing the funds under Agriculture Nutrition Biotech theme (MLP 0057).
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The study was supported by CSIR, New Delhi under Agriculture Nutrition Biotech theme (MLP 0057).
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PKA conceptualized the experiment. TCB and NM involved in experiments. TCB, PKA, PA, and HKP analyzed and infer the data. PKA, DRG, and HKP overall coordinated the study. TCB and PKA prepared the manuscript. All authors reviewed the manuscript and agreed to the published version of the manuscript.
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Bosamia, T.C., Agarwal, P., Gangapur, D.R. et al. Transcriptome Sequencing of Rectretohalophyte Aeluropus lagopoides Revealed Molecular Insight of Salt Stress Adaptation. J Plant Growth Regul (2024). https://doi.org/10.1007/s00344-023-11222-6
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DOI: https://doi.org/10.1007/s00344-023-11222-6