Skip to main content
SpringerLink
Log in

De novo transcriptome assembly and variable salinity induced differential biochemical and transcript responses in Kappaphycus alvarezii, a red carrageenophyte

  • Research
  • Published:
Journal of Applied Phycology Aims and scope Submit manuscript

Abstract

Kappaphycus alvarezii is an important kappa-carrageenan producer. Fluctuating environmental conditions, especially seawater salinity, significantly affect the cultivation of K. alvarezii. To assess the variable salinity-induced responses, biochemical responses and gene expressions via high throughput RNA sequencing were studied in K. alvarezii under hypo- [3.25 practical salinity units (psu)] and hyper- (65 psu) salinity conditions. Under variable salinity, the influx of Na+ and efflux of K+ ions resulted in a lower K+/Na+ ratio. Both salinity levels had differential effect on accumulation of different solutes and photosynthetic pigments. Superoxide dismutase, ascorbate peroxidase and glutathione peroxidase exhibited higher activity under stress. The RNA sequencing revealed the differential gene expression in K. alvarezii at variable salinity. In this study, 52,875 CDS were predicted, and most of these showed a match with Chondrus crispus. At hypo-salinity, 246 and 171 genes exhibited up- and down-regulation, respectively. At hyper-salinity, 457 and 1,008 exhibited up- and down-regulation, respectively. Transcriptome data revealed differential expression of genes encoding components of photosynthetic, signal transduction, fatty acid and amino acid metabolism, energy metabolism and redox homeostasis machineries under stress. Differential expression of ubiquitin-mediated proteolytic genes and heat shock proteins indicated the important role of these genes under studied strengths of salinity. The differentially expressed genes showed a correlation with biochemical responses and ion accumulation. The study identified numerous key genes regulating different metabolic pathways and antioxidant machinery. The results would facilitate insights into the molecular mechanism underlying the salinity stress adaptation in K. alvarezii and studies on the gene discoveries for subsequent strain improvement.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

Data Availability

Transcriptome data are available on NCBI domain with accession number PRJNA661401. This information may please be provided as data availability statement.

References

  • Agrawal S, Siddiqui SA, Chaudhary DR, Rathore MS (2022) Bio-prospection and compositional multivariate analysis revealed the industrial potential of selected seaweeds along Gujarat seacoast. Bioresour Technol Rep 19:101130

  • Beyer WF, Fridovich I (1987) Assaying for superoxide dismutase activity: some large consequences of minor changes in conditions. Ana Biochem 161:559–566

    CAS  Google Scholar 

  • Bischof K, Rautenberger R (2012) Seaweed responses to environmental stress: reactive oxygen and antioxidative strategies. In: Bishof K, Wiencke C (eds) Seaweed Biology. Springer, Heidelberg, pp 109–132

    Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    CAS  PubMed  PubMed Central  Google Scholar 

  • Collén J, Guisle-Marsollier I, Léger JJ, Boyen C (2007) Response of the transcriptome of the intertidal red seaweed Chondrus crispus to controlled and natural stresses. New Phytol 176:45–55

    PubMed  Google Scholar 

  • Collén J, Pedersén M, Bornman CH (1994) A stress-induced oxidative burst in Eucheuma platycladum (Rhodophyta). Physiol Plant 92:417–422

    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

    CAS  PubMed  Google Scholar 

  • Contreras-Porcia L, López-Cristoffanini C, Lovazzano C, Flores-Molina MR, Thomas D, Núñez A, Fierro C, Guajardo E, Correa JA, Kube M, Reinhardt R (2013) Differential gene expression in Pyropia columbina (Bangiales, Rhodophyta) under natural hydration and desiccation conditions. Lat Am J Aquat Res 41:933–958

    Google Scholar 

  • Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11:163

    PubMed  PubMed Central  Google Scholar 

  • Das P, Mondal D, Maiti S (2017) Thermochemical conversion pathways of Kappaphycus alvarezii granules through study of kinetic models. Bioresour Technol 234:233–242

    CAS  PubMed  Google Scholar 

  • De Marsac NT, Houmard J (1988) Complementary chromatic adaptation: Physiological conditions and action spectra. Meth Enzymol 167:318–328

    Google Scholar 

  • Dittami SM, Scornet D, Petit JL, Ségurens B, da Silva C, Corre E, Dondrup M, Glatting KH, König R, Sterck L, Rouzé P, van de Peer Y, Cock JM, Boyen C, Tonon T (2009) Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol 10:R66

    PubMed  PubMed Central  Google Scholar 

  • Dring MJ (2006) Stress resistance and disease resistance in seaweeds: the role of reactive oxygen metabolism. Adv Bot Res 43:175–207

    CAS  Google Scholar 

  • Fattorusso E, Piatelli M (1980) Amino acids from marine algae. In: Scheuer PJ (ed) Marine natural products: Chemical and biological perspectives, Vol III. Academic Press, Toronto pp 95–140

  • Gao S, Niu J, Chen W, Wang G, Xie X, Pan G, Gu W, Zhu D (2013) The physiological links of the increased photosystem II activity in moderately desiccated Porphyra haitanensis (Bangiales, Rhodophyta) to the cyclic electron flow during desiccation and re-hydration. Photosynth Res 116:45–54

    CAS  PubMed  Google Scholar 

  • Gigon A, Matos AR, Laffray D, Zuily-Fodil Y, Pham-Thi AT (2004) Effect of drought stress on lipid metabolism in the leaves of Arabidopsis thaliana (ecotype Columbia). Ann Bot 94:345–351

    CAS  PubMed  PubMed Central  Google Scholar 

  • Góes HG, Reis RP (2011) An initial comparison of tubular netting versus tie-tie methods of cultivation for Kappaphycus alvarezii (Rhodophyta, Solieriaceae) on the south coast of Rio de Janeiro State, Brazil. J Appl Phycol 23:607–613

    Google Scholar 

  • Goyal A (2007) Osmoregulation in Dunaliella, Part II: Photosynthesis and starch contribute carbon for glycerol synthesis during a salt stress in Dunaliella tertiolecta. Plant Physiol Biochem 45:705–710

    CAS  PubMed  Google Scholar 

  • Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, ouger MB, Eccles D, Li B, Lieber M, MacManes MD (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Prot 8:1494

  • Jacob PT, Siddiqui SA, Rathore MS (2020) Seed germination, seedling growth and seedling development associated physio-chemical changes in Salicornia brachiata (Roxb.) under salinity and osmotic stress. Aquat Bot 166:103272

  • Jebara S, Jebara M, Limam F, Aouani ME (2005) Changes in ascorbate peroxidase, catalase, guaiacol peroxidase and superoxide dismutase activities in common bean (Phaseolus vulgaris) nodules under salt stress. J Plant Physiol 162:929–936

    CAS  PubMed  Google Scholar 

  • Ji Z, Zou D, Gong J, Liu C, Ye C, Chen Y (2019) The different responses of growth and photosynthesis to NH4+ enrichments between Gracilariopsis lemaneiformis and its epiphytic alga Ulva lactuca grown at elevated atmospheric CO2. Mar Pollut Bull 144:173–180

    CAS  PubMed  Google Scholar 

  • Jia Z, Niu J, Huan L, Wu X, Wang G, Hou Z (2013) Cyclophilin participates in responding to stress situations in Porphyra haitanensis (Bangiales, Rhodophyta). J Phycol 49:194–201

    CAS  PubMed  Google Scholar 

  • Junglee S, Urban L, Sallanon H, Lopez-Lauri F (2014) Optimized assay for hydrogen peroxide determination in plant tissue using potassium iodide. Am J Anal Chem 5:730–736

    CAS  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280

    CAS  PubMed  PubMed Central  Google Scholar 

  • Karsten U (2007) Salinity tolerance of Arctic kelps from Spitsbergen. Phycol Res 55:257–262

    Google Scholar 

  • Kerjean V, Morel B, Stiger V, Bessieres MA, Simon-Colin C, Magné C, Deslandes E (2007) Optimization of floridoside production in the red alga Mastocarpus stellatus: Pre treatment, extraction and seasonal variations. Bot Mar 50:59–64

  • Khatri K, Rathore MS (2022) Salt and osmotic stress-induced changes in physio-chemical responses, PSII photochemistry and chlorophyll a fluorescence in peanut. Plant Stress 3:100063

  • Kim JG, Back K, Lee HY, Lee HJ, Phung TH, Grimm B, Jung S (2014) Increased expression of Fe-chelatase leads to increased metabolic flux into heme and confers protection against photodynamically induced oxidative stress. Plant Mol Biol 86:271–287

    CAS  Google Scholar 

  • Kumar M, Kumari P, Gupta V, Reddy CR, Jha B (2010) Biochemical responses of red alga Gracilaria corticata (Gracilariales, Rhodophyta) to salinity induced oxidative stress. J Exp Mar Biol Ecol 391:27–34

    CAS  Google Scholar 

  • Kumari J, Haque M, Jha RK, Rathore MS (2022) The red seaweed Kappaphycus alvarezii antiporter gene (KaNa+/H+) confers abiotic stress tolerance in transgenic tobacco. Mol Biol Rep 49:3729–3743

    CAS  PubMed  Google Scholar 

  • Lalegerie F, Gager L, Stiger-Pouvreau V, Connan S (2020) The stressful life of red and brown seaweeds on the temperate intertidal zone: Effect of abiotic and biotic parameters on the physiology of macroalgae and content variability of particular metabolites. Adv Bot Res 95:247–287

    CAS  Google Scholar 

  • Lee WK, Namasivayam P, Ong Abdullah J, Ho CL (2017) Transcriptome profiling of sulfate deprivation responses in two agarophytes Gracilaria changii and Gracilaria salicornia (Rhodophyta). Sci Rep 7: srep46563.

  • Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform 12:323

    CAS  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li Q, Zhang L, Pang T, Liu J (2019) Comparative transcriptome profiling of Kappaphycus alvarezii (Rhodophyta, Gigartinales) in response to two extreme temperature treatments: an RNA-seq-based resource for photosynthesis research. Eur J Phycol 54:162–174

    CAS  Google Scholar 

  • Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659

    CAS  PubMed  Google Scholar 

  • Liu CL, Wang XL, Huang XH, Liu J (2011) Identification of hypo-osmotically induced genes in Kappachycus alvarezii (Solieriaceae, Rhodophyta) through expressed sequence tag analysis. Bot Mar 54:557–562

  • Lu IF, Sung MS, Lee TM (2006) Salinity stress and hydrogen peroxide regulation of antioxidant defense system in Ulva fasciata. Mar Biol 150:1–15

    CAS  Google Scholar 

  • Lu X, Huan L, Gao S, He L, Wang G (2016) NADPH from the oxidative pentose phosphate pathway drives the operation of cyclic electron flow around photosystem I in high-intertidal macroalgae under severe salt stress. Physiol Plant 156:397–406

    CAS  PubMed  Google Scholar 

  • Luo MB, Liu F (2011) Salinity-induced oxidative stress and regulation of antioxidant defense system in the marine macroalga Ulva prolifera. J Exp Mar Biol Ecol 409:223–228

    CAS  Google Scholar 

  • Macler BA (1988) Salinity effects on photosynthesis, carbon allocation and nitrogen assimilation in the red alga Gelidium coulteri. Plant Physiol 88:690–694

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mandal SK, Ajay G, Monisha N, Malarvizhi J, Temkar G, Mantri VA (2015) Differential response of varying temperature and salinity regimes on nutrient uptake of drifting fragments of Kappaphycus alvarezii: implication on survival and growth. J Appl Phycol 27:1571–1581

    CAS  Google Scholar 

  • Miyagawa Y, Tamoi M, Shigeoka S (2000) Evaluation of the defense system in chloroplasts to photooxidative stress caused by paraquat using transgenic tobacco plants expressing catalase from Escherichia coli. Plant Cell Physiol 41:311–320

    CAS  PubMed  Google Scholar 

  • Mohanty B, Kitazumi A, Cheung CM, Lakshmanan M, Benildo G, Jang IC, Lee DY (2016) Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network. Plant Sci 242:224–239

    CAS  PubMed  Google Scholar 

  • Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185

    PubMed  PubMed Central  Google Scholar 

  • Muzi C, Camoni L, Visconti S, Aducci P (2016) Cold stress affects H+-ATPase and phospholipase D activity in Arabidopsis. Plant Physiol Biochem 108:328–336

    CAS  PubMed  Google Scholar 

  • Nakano Y, Asada K (1981) Hydrogen peroxide is scavenged by ascorbate-specific peroxidase in spinach chloroplasts. Plant Cell Physiol 22:867–880

    CAS  Google Scholar 

  • Narusak Y, Narusaka M, Seki M, Umezawa T, Ishida J, Nakajima M, Enju A, Shinozaki K (2004) Crosstalk in the responses to abiotic and biotic stresses in Arabidopsis: analysis of gene expression in cytochrome P450 gene superfamily by cDNA microarray. Plant Mol Biol 55:327–342

    Google Scholar 

  • Obata T, Fernie AR (2012) The use of metabolomics to dissect plant responses to abiotic stresses. Cell Mol Life Sci 69:3225–3243

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pan L, Zhang X, Wang J, Ma X, Zhou M, Huang L, Nie G, Wang P, Yang Z, Li J (2016) Transcriptional profiles of drought-related genes in modulating metabolic processes and antioxidant defenses in Lolium multiflorum. Front Plant Sci 7:519

    PubMed  PubMed Central  Google Scholar 

  • Pereira DT, Simioni C, Filipin EP, Bouvie F, Ramlov F, Maraschin M, Bouzon ZL, Schmidt ÉC (2017) Effects of salinity on the physiology of the red macroalga, Acanthophora spicifera (Rhodophyta, Ceramiales). Acta Bot Bras 31:555–565

    Google Scholar 

  • Pliego-Cortés H, Caamal-Fuentes E, Montero-Muñoz J, Freile-Pelegrín Y, Robledo D (2017) Growth, biochemical and antioxidant content of Rhodymenia pseudopalmata (Rhodymeniales, Rhodophyta) cultivated under salinity and irradiance treatments. J Appl Phycol 29:2595–2603

    Google Scholar 

  • Reed RH, Collins JC, Russell G (1981) The Effects of Salinity upon Ion Content and Ion Transport of the Marine Red Alga Porphyra purpurea (Roth) C. Ag J Exp Bot 32:347–367

    CAS  Google Scholar 

  • Samanta P, Shin S, Jang S, Kim JK (2019) Comparative assessment of salinity tolerance based on physiological and biochemical performances in Ulva australis and Pyropia yezoensis. Algal Res 42:101590

  • Sampath-Wiley P, Neefus CD (2007) An improved method for estimating R-phycoerythrin and R-phycocyanin contents from crude aqueous extracts of Porphyra (Bangiales, Rhodophyta). J Appl Phycol 19:123–129

    CAS  PubMed  Google Scholar 

  • Scherer GE (2010) Phospholipase A in plant signal transduction. In: Munnik T (ed) Lipid Signaling in Plants. Springer, Heidelberg pp 3–22

  • Schopfer P, Plachy C, Frahry G (2001) Release of reactive oxygen intermediates (superoxide radicals, hydrogen peroxide, and hydroxyl radicals) and peroxidase in germinating radish seeds controlled by light, gibberellin, and abscisic acid. Plant Physiol 125:1591–1602

    CAS  PubMed  PubMed Central  Google Scholar 

  • Siddiqui SA, Agrawal S, Brahmbhatt H, Rathore MS (2022) Metabolite expression changes in Kappaphycus alvarezii (a red alga) under hypo-and hyper-saline conditions. Algal Res 63:102650

  • Smirnoff N, Arnaud D (2018) Hydrogen peroxide metabolism and functions in plants. New Phytol 221:1197–1214

    PubMed  Google Scholar 

  • Smith IK, Vierheller TL, Thorne CA (1988) Assay of glutathione reductase in crude tissue homogenates using 5,5′-dithiobis(2-nitrobenzoic acid). Anal Biochem 175:408–413

    CAS  PubMed  Google Scholar 

  • Song L, Wu S, Sun J, Wang L, Liu T, Chi S, Liu C, Li X, Yin J, Wang X, Yu J (2014) De novo sequencing and comparative analysis of three red algal species of family Solieriaceae to discover putative genes associated with carrageenan biosynthesis. Acta Oceanol Sin 33:45–53

    CAS  Google Scholar 

  • Sun P, Mao Y, Li G, Cao M, Kong F, Wang L, Bi G (2015) Comparative transcriptome profiling of Pyropia yezoensis (Ueda) M.S. Hwang and H.G. Choi in response to temperature stresses. BMC Genom 16:463

  • Sung MS, Hsu YT, Hsu YT, Wu TM, Lee TM (2009) Hypersalinity and hydrogen peroxide upregulation of gene expression of antioxidant enzymes in Ulva fasciata against oxidative stress. Mar Biotechnol 11:199–209

    CAS  Google Scholar 

  • Surget G, Le Lann K, Delebecq G, Kervarec N, Donval A, Poullaouec MA, Bihannic I, Poupart N, Stiger-Pouvreau V (2017) Seasonal phenology and metabolomics of the introduced red macroalga Gracilaria vermiculophylla, monitored in the Bay of Brest (France). J Appl Phycol 29:2651–2666

    CAS  Google Scholar 

  • Sweetlove LJ, Beard KF, Nunes-Nesi A, Fernie AR, Ratcliffe RG (2010) Not just a circle: flux modes in the plant TCA cycle. Trends Plant Sci 15:462–470

    CAS  PubMed  Google Scholar 

  • Tammam AA, Fakhry EM, El-Sheekh M (2011) Effect of salt stress on antioxidant system and the metabolism of the reactive oxygen species in Dunaliella salina and Dunaliella tertiolecta. Afr J Biotechnol 10:3795–3808

    CAS  Google Scholar 

  • Teo SS, Ho CL, Teoh S, Rahim RA, Phang SM (2009) Transcriptomic analysis of Gracilaria changii (Rhodophyta) in response to hyper- and hypoosmotic stresses. J Phycol 45:1093–1099

    CAS  PubMed  Google Scholar 

  • Thalmann M, Santelia D (2017) Starch as a determinant of plant fitness under abiotic stress. New Phytol 214:943–951

    CAS  PubMed  Google Scholar 

  • Thien VY, Rodrigues KF, Voo CLY, Wong CMVL, Yong WTL (2021) Comparative transcriptome profiling of Kappaphycus alvarezii (Rhodophyta, Solieriaceae) in response to light of different wavelengths and carbon dioxide enrichment. Plants 10:1236

    CAS  PubMed  PubMed Central  Google Scholar 

  • Touchette BW (2007) Seagrass-salinity interactions: Physiological mechanisms used by submersed marine angiosperms for a life at sea. J Exp Mar Biol Ecol 350:194–215

    Google Scholar 

  • Vairappan C, Chung C, Hurtado A, Soya F, Lhonneur G, Critchley A (2008) Distribution and symptoms of epiphyte infection in major carrageenophyte-producing farms. J Appl Phycol 20:477–483

    Google Scholar 

  • van Ginneken V (2018) Some mechanism seaweeds employ to cope with salinity stress in the harsh euhaline oceanic environment. Am J Plant Sci 9:1191–1211

    Google Scholar 

  • Vorphal MA, Gallardo-Escárate C, Valenzuela-Muñoz V, Dagnino-Leone J, Vásquez JA, Martínez-Oyanedel J, Bunster M (2017) De novo transcriptome analysis of the red seaweed Gracilaria chilensis and identification of linkers associated with phycobilisomes. Mar Genom 31:17–19

    Google Scholar 

  • Wang W, Lin Y, Teng F, Ji D, Xu Y, Chen C, Xie C (2018) Comparative transcriptome analysis between heat-tolerant and sensitive Pyropia haitanensis strains in response to high temperature stress. Algal Res 29:104–112

    Google Scholar 

  • Wang W, Shen Z, Sun X, Liu F, Liang Z, Wang F, Zhu J (2019a) De novo transcriptomics analysis revealed a global reprogramming towards dehydration and hyposalinity in Bangia fuscopurpurea gametophytes (Rhodophyta). J Appl Phycol 31:637–651

    CAS  Google Scholar 

  • Wang W, Vinocur B, Shoseyov O, Altman A (2004) Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends Plant Sci 9:244–252

  • Wang W, Xing L, Xu K, Ji D, Xu Y, Chen C, Xie C (2020) Salt stress-induced H2O2 and Ca2+ mediate K+/Na+ homeostasis in Pyropia haitanensis. J Appl Phycol 32:4199–4210

    CAS  Google Scholar 

  • Wang WJ, Li XL, Zhu JY, Liang ZR, Liu FL, Sun XT, Wang FJ, Shen ZG (2019b) Antioxidant response to salinity stress in freshwater and marine Bangia (Bangiales, Rhodophyta). Aquat Bot 154:35–41

    Google Scholar 

  • Wu Y, Jin X, Liao W, Hu L, Dawuda MM, Zhao X, Tang Z, Gong T, Yu J (2018) 5-Aminolevulinic acid (ALA) alleviated salinity stress in cucumber seedlings by enhancing chlorophyll synthesis pathway. Front Plant Sci 9:635

    PubMed  PubMed Central  Google Scholar 

  • Xu K, Xu Y, Ji D, Xie J, Chen C, Xie C (2016) Proteomic analysis of the economic seaweed Pyropia haitanensis in response to desiccation. Algal Res 19:198–206

    Google Scholar 

  • Yadav SK, Khatri K, Rathore MS, Jha B (2018) Introgression of UfCyt c6, a thylakoid lumen protein from a green seaweed Ulva fasciata Delile enhanced photosynthesis and growth in tobacco. Mole Biol Rep 45:1745–1758

    CAS  Google Scholar 

  • Yadav SK, Khatri K, Rathore MS, Jha B (2020) Ectopic Expression of a Transmembrane protein KaCyt b6 from a red seaweed Kappaphycus alvarezii in transgenic tobacco augmented the photosynthesis and growth. DNA Cell Biol. https://doi.org/10.1089/dna.2020.5479

    Article  PubMed  Google Scholar 

  • Yamasaki T, Yamakawa T, Yamane Y, Koike H, Satoh K. Katoh S (2002) Temperature acclimation of photosynthesis and related changes in photosystem II electron transport in winter wheat. Plant Physiol 128:1087–1097

  • 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:W293–W297

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yee TV, Rodrigues KF, Lym WYT, Ling CMWV (2017) Comparison of gene expression patterns of Kappaphycus alvarezii (Rhodophyta, Solieriaceae) under different light wavelengths and CO2 enrichment. bioRxiv 188250

  • Yu L, Nie J, Cao C, Jin Y, Yan M, Wang F, Liu J, Xiao Y, Liang Y, Zhang W (2010) Phosphatidic acid mediates salt stress response by regulation of MPK6 in Arabidopsis thaliana. New Phytol 188:762–773

    CAS  PubMed  Google Scholar 

  • Yunque DAT, Tibubos KR, Hurtado AQ, Critchley AT (2011) Optimization of culture conditions for tissue culture production of young plantlets of carrageenophyte Kappaphycus. J Appl Phycol 23:433–438

    Google Scholar 

  • Zhang H, Li W, Li J, Fu W, Yao J, Duan D (2012) Characterization and expression analysis of hsp70 gene from Ulva prolifera J. Agardh (Chlorophycophyta, Chlorophyceae). Mar Genom 5:53–58

    CAS  Google Scholar 

  • Zhang Z, Pang T, Li Q, Zhang L, Li L, Liu J (2015) Transcriptome sequencing and characterization for Kappaphycus alvarezii. Eur J Phycol 50:400–407

    CAS  Google Scholar 

Download references

Acknowledgment

CSIR-CSMCRI PRIS: 129/2022

Authors are thankful to CSIR (Government of India), New Delhi for financial support under different plan projects. The authors are thankful to analytical facility of CSMCRI institute. KK thanks CSIR (Government of India), New Delhi for Junior/Senior Research Fellowship (JRF/SRF) and Academy of Scientific and Innovative Research (AcSIR), Ghaziabad for registration in Ph.D. program.

Author information

Author notes

  1. Kusum Khatri

    Present address: Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, 8499000, Be’er Sheva, Israel

  2. Sandeep Sharma

    Present address: Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India

Authors and Affiliations

  1. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Kusum Khatri, Sandeep Sharma & Mangal S. Rathore

  2. Applied Phycology and Biotechnology Division, Council of Scientific and Industrial Research - Central Salt and Marine Chemicals Research (CSIR - CSMCRI), Bhavnagar, Gujarat, 364002, India

    Kusum Khatri, Sandeep Sharma & Mangal S. Rathore

Authors
  1. Kusum Khatri
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sandeep Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mangal S. Rathore
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

MSR and SS- Conceptualization, fund raising, experimental design, editing and finalization of manuscript; KK- designing and execution of experiments, data analyses, drafting and editing of manuscript.

Corresponding author

Correspondence to Mangal S. Rathore.

Ethics declarations

Competing interests

The authors declare no competing interests.

Competing interest

Authors declare no potential conflict of interest.

Additional information

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

10811_2023_3006_MOESM1_ESM.pptx

Fig. S1 Ion (a) and chlorophyll and carotenoids (b) contents in K. alvarezii under hypo- and hyper-saline conditions (PPTX 52.5 KB)

Fig. S2 Flow chart of transcriptome experimental procedure (PPTX 184 KB)

Fig. S3 Top blast hit species distribution of pooled CDS of K. alvarezii (PPTX 195 KB)

10811_2023_3006_MOESM4_ESM.pptx

Fig. S4 GO term distribution for biological functions (a), cellular components (b) and molecular functions (c) in pooled CDS of K. alvarezii (PPTX 58.6 KB)

Fig. S5 KEGG pathway of K. alvarezii transcriptome (PPTX 50.8 KB)

Fig. S6 The COG distribution in K. alvarezii. (PPTX 48 KB)

Table S1 List of primers used for transcriptome characterization study (DOCX 18.8 KB)

10811_2023_3006_MOESM8_ESM.pdf

Table S2 Correlation matrix of different physio-biochemical activities and contents observed in Kappaphycus alvarezii under hypo- and hyper-saline conditions (PDF 138 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Khatri, K., Sharma, S. & Rathore, M.S. De novo transcriptome assembly and variable salinity induced differential biochemical and transcript responses in Kappaphycus alvarezii, a red carrageenophyte. J Appl Phycol 35, 1847–1864 (2023). https://doi.org/10.1007/s10811-023-03006-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10811-023-03006-y

Keywords

Search

Navigation