Abstract
Salinization poses an increasingly serious problem in coastal and agricultural areas with negative effects on plant productivity and yield. Avicennia marina is a pantropical mangrove species that can survive in highly saline conditions. As a first step towards the characterization of genes that contribute to combating salinity stress, the construction of a cDNA library of A. marina genes is reported here. Random expressed sequence tag (EST) sequencing of 1,841 clones produced 1,602 quality reads. These clones were classified into functional categories, and blast comparisons revealed that 113 clones were homologous to genes earlier implicated in stress responses, of which the dehydrins are the most predominant in this category. Of the ESTs analyzed, 30% showed homology to previously uncharacterized genes in the public plant databases. Of these 30%, 52 clones were selected for reverse Northern analysis: 26 were shown to be up-regulated and five shown to be down-regulated. The results obtained by reverse Northern analysis were confirmed by Northern analysis for three clones.
Similar content being viewed by others
References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Bausher M, Shatters R, Chaparro J, Dang P, Hunter W, Niedz R (2003) An expressed sequence tag (EST) set from Citrus sinensis L. Osbeck whole seedling and the implications of further perennial source investigations. Plant Sci 165:415–422
Boon PI, Allaway WG (1982) Assessment of leaf-washing techniques for measuring salt secretion in Avicennia marina (Forsk.) Vierh. Aust J Plant Physiol 9:725–734
Chauhan S, Forsthoefel N, Ran Y, Quigley F, Nelson DE, Bohnert HJ (2000) Na+/myo-inositol symporters and Na+/H+-antiporter in Mesembryanthemum crystallinum. Plant J 24:511–522
Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156–159
Cushman JC, Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 3:117–124
Feliciello I, Chinali G (1993) A modified alkaline lysis method for the preparation of highly purified plasmid DNA from Escherichia coli. Anal Biochem 212:394–401
Garay-Arroyo A, Colmenero-Flores JM, Garciarrubio A, Covarrubias AA (1999) Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit. J Biol Chem 275:5668–5674
Gyorgyey J, Vaubert D, Jimenez-Zurdo JI, Charon C, Troussard L, Kondorosi A, Kondorosi E (2000) Analysis of Medicago truncatula nodule expressed sequence tags. Mol Plant Microbe Interact 13:62–71
Hall JL (2002) Cellular mechanisms for heavy metal detoxification and tolerance. J Exp Bot 53:1–11
Hibino T, Meng YL, Kawamitsu Y, Uehara N, Matsuda N, Tanaka Y, Ishikawa H, Baba S, Takabe T, Wada K, Ishii T, Takabe T (2001) Molecular cloning and functional characterization of two kinds of betaine-aldehyde dehydrogenase in betaine-accumulating mangrove Avicennia marina (Forsk.) Vierh. Plant Mol Biol 45:353–363
Huang X, Madan A (1999) caps3: a DNA sequence assembly program. Genome Res 9:868–77
Koag MC, Fenton RD, Wilkens S, Close TJ (2003) The binding of maize DHN 1 to lipid vesicles. Gain of structure and lipid specificity. Plant Physiol 131:309–316
Kosarev P, Mayer KFX, Hardtke CS (2002) Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome. Genome Biol 3:r0016.1–0016.12
Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P (2004) smart 4.0: towards genomic data integration. Nucleic Acids Res 32:D142–D144
Matsubayashi Y, Sakagami Y (1996) Phytosulfokine, sulfated peptides that induce the proliferation of single mesophyll cells of Asparagus officinalis L. Proc Natl Acad Sci USA 93:7623–7627
Matsubayashi Y, Ogawa M, Morita A, Sakagami Y (2002) An LRR receptor kinase involved in perception of a peptide plant hormone, phytosulfokine. Science 24:1470–1472
Molnar G, Bancos S, Nagy F, Szekeres M (2002) Characterisation of BRH1, a brassinosteroid-responsive RING-H2 gene from Arabidopsis thaliana. Planta 215:127–133
Munns R, Husain S, Rivelli AR, James RA, Condon AG, Lindsay MP, Lagudah ES, Schachtman DP, Hare RA (2002) Avenues for increasing salt tolerance of crops, and the role of physiologically based selection traits. Plant Soil 247:93–105
Murashige T, Skoog F (1962) A revised method for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497
Ozturk ZN, Talame V, Deyholos M, Michalowski CB, Galbraith DW, Gozukirmizi N, Tuberosa R, Bohnert HJ (2002) Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol Biol 48:551–573
Parani M (1999) Isolation of salt tolerance genes from mangroves: characterization of betaine aldehyde dehydrogenase (BADH) gene from Avicennia marina and its expression in tobacco transgenic system. PhD thesis, Anna University, India
Rao AN (1987) Mangrove ecosystems of Asia and the Pacific. In: Umali RM, Zamora PM, Gotera RR, Jara RS, Camacho AS (eds) Mangroves of Asia and the Pacific: status and management. UNDP-UNESCO Technical Report, pp 1–41
Rose A, Manikantan S, Schraegle SJ, Maloy MA, Stahlberg EA, Meier I (2004) Genome-wide identification of Arabidopsis coiled-coil proteins and establishment of the ARABI-COIL database. Plant Physiol 134:927–939
Ryan CA, Pearce G, Scheer J, Moura DS (2002) Polypeptide hormones. Plant Cell 14:S251–S264
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Laboratory Press, Plainview
Schultz J, Milpetz F, Bork P, Ponting CP (1998) smart, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA 95:5857–5864
Shimony C, Fahn A, Reinhold L (1973) Ultrastructure and ion gradients in the salt glands of Avicennia marina (Forsk.) Vierh. New Phytol 72:27–36
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
The International Human Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Tompa P (2002) Intrinsically unstructured proteins. Trends Biochem Sci 27:527–533
Waditee R, Hibino T, Tanaka Y, Nakamura T, Incharoensakdi A, Hayakawa S, Suzuki S, Futsuhara Y, Kawamitsu Y, Takabe T, Takabe T (2002) Functional characterization of betaine/proline transporters in betaine-accumulating mangrove. J Biol Chem 277:18373–18382
Xu R, Li QQ (2003) A RING-H2 zinc finger protein gene RIE1 is essential for seed development in Arabidopsis. Plant Mol Biol 53:37–50
Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35:135–144
Yang H, Matsubayashi Y, Nakamura K, Sakagami Y (2001) Diversity of Arabidopsis genes encoding precursors for phytosulfokine, a peptide growth factor. Plant Physiol 127:842–851
Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273
Acknowledgements
We are grateful to the Department of Biotechnology and Department of Atomic Energy, Government of India for financial support. The help and support provided by Ms. Y. Dilhara Begam in EST analysis is gratefully acknowledged.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by P. Langridge
Rights and permissions
About this article
Cite this article
Mehta, P.A., Sivaprakash, K., Parani, M. et al. Generation and analysis of expressed sequence tags from the salt-tolerant mangrove species Avicennia marina (Forsk) Vierh.. Theor Appl Genet 110, 416–424 (2005). https://doi.org/10.1007/s00122-004-1801-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-004-1801-y