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Analysis of ESTs generated from inner bark tissue of an Acacia auriculiformis x Acacia mangium hybrid

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Abstract

The majority of plant expressed sequence tags (ESTs) available in the public databases are from non-woody species such as Arabidopsis, maize, soybean, and rice, with the exception of the model tree species, Populus. In this study, we report the first EST database constructed from the commercially important tree species Acacia. ESTs were generated from pooled RNA extracted from the mature, intermediate, and young inner bark tissues of an Acacia auriculiformis x Acacia mangium hybrid. Finally, 3,182 high-quality ESTs were analyzed representing a total of 1,982 unique transcripts (663 contigs and 1,319 singletons) for the inner bark cDNA library. A total of 1,053 unigenes (1,750 ESTs) showed similarities with protein sequences in public database where 867 were significant matches (E value ≤ e−10). Further analysis performed on unigenes with significant matches and known functions identified 231 genes including genes involved in cellulose, lignin, and hemicellulose biosynthesis. For cDNA library validation, quantitative real-time RT-PCR was performed to study the expression levels of the cellulose and lignin genes identified from this EST database in the phloem tissue of A. mangium, A. auriculiformis, and A. auriculiformis x A. mangium hybrid. All the seven candidate genes were expressed in all the individuals studied confirming the dependability of the EST database. The cDNA library and the EST database constructed are valuable resources for forest tree research aiming towards understanding the genetic control of wood formation and in the future endeavors to modify wood and fiber profile through marker-assisted breeding programs.

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References

  • Adam MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropulus MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656

    Article  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  PubMed  Google Scholar 

  • Bao W, O’Malley DM, Whetten R, Sederoff RR (1993) A laccase associated with lignifications in loblolly pine xylem. Science 260:672–674

    Article  CAS  PubMed  Google Scholar 

  • 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 seedlings and the implications of further perennial source invstigations. Plant Sci 165:415–422

    Article  CAS  Google Scholar 

  • Bevan M, Shufflebottom D, Edwards K, Jefferson R, Schuch W (1989) Tissue and cell specific activity of a phenylalanine ammonia lyase promoter in transgenic plants. EMBO 8:1899–1906

    CAS  Google Scholar 

  • Blee KA, Choi JW, O’Connel AP (2003) A lignin specific peroxidase in tobacco whose antisense suppression leads to vascular tissue modification. Phytochem 64:163–176

    Article  CAS  Google Scholar 

  • Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546

    Article  CAS  PubMed  Google Scholar 

  • Bradley DJ, Kjellborn PC, Lamb J (1992) Elicitor and wound induced oxidative cross linking of a proline rich plant cell-wall protein: a novel, rapid defense response. Cell 70:21–30

    Article  CAS  PubMed  Google Scholar 

  • Burger A, Seth AK (2004) The ubiquitin-mediated protein degradation pathway in cancer therapeutic implications. EJC 40(15):2217–2229

    Article  CAS  Google Scholar 

  • Canovas F, Dumas-Gaudot E, Recorbet E, Jorrin J, Mock HP, Rossignol M (2004) Plant proteome analysis. Proteomics 4:285–298

    Article  CAS  PubMed  Google Scholar 

  • Chapple CCS, Vogt T, Ellis BE, Somerville CR (1992) An Arabidopsis mutant defective in the general phenylpropanoid pathway. Plant Cell 4:1413–1424

    Article  CAS  PubMed  Google Scholar 

  • Chow KS, Wan KL, Isa MNM, Bahari A, Tan SH, Harikrishna K, Yeang YH (2007) Insights into rubber biosynthesis from transcriptome analysis of Hevea brasiliensis latex. J Exp Bot 58(10):2429–2440

    Article  CAS  PubMed  Google Scholar 

  • Delseny M, Cooke R, Raynal M, Grellet F (1997) The Arabidopsis thaliana cDNA sequencing projects. FEBS Lett 403:221–224

    Article  CAS  PubMed  Google Scholar 

  • Dvorakova L, Cvrckova F, Fischer L (2007) Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns. BMC Genomics 8:412–427

    Article  PubMed  Google Scholar 

  • Ewing B, Hillier L, Wendl MC, Green P (1998) Basic-calling of automated sequencer traces using phred I. Accuracy assesement. Genome Res 8:175–185

    CAS  PubMed  Google Scholar 

  • Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie JM (1999) Large scale statistical analyies of rice ESTs reveal correlated patterns of gene expression. Genome Res 9:950–959

    Article  CAS  PubMed  Google Scholar 

  • Grima-Pettenati J, Campargue JC, Boudet AM (1994) Purification and characterization of cinnamyl alcohol dehydrogenase isoform from Phaseolus vulgaris. Phyto 37:941–947

    Article  CAS  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hauffe KD, Lee SP, Subramaniam R, Douglas CJ (1993) Combinatorial interaction between positive and negative cis-acting elements control spatial pattern of 4CL-1 expression I transgenic tobacco. Plant J 4:235–253

    Article  CAS  PubMed  Google Scholar 

  • Hays DB, Skinner DZ (2002) Development of an expressed sequence tag (EST) library for Medicago sativa. Plant Sci 161(3):517–526

    Article  Google Scholar 

  • Hiraga S, Sasaki K, Ito H, Ohashi Y, Matsui H (2001) A large family of class III plant peroxidases. Plant Cell Physiol 42(5):462–268

    Article  CAS  PubMed  Google Scholar 

  • Hrubcova M, Cvikrova M, Eder J, Zon J, Machackova I (2000) Effect of exhibition of phenylpropanoid biosynthesis on peroxidase and IAA-oxidase activities and auxin contentin alfalfa suspension cultures. Plant Physiol Biochem 38(12):949–956

    Article  CAS  Google Scholar 

  • Hu WJ, Harding SA, Lung J, Popko JL, Ralph J, Stokke DD, Chung JT, Chiang LV (1999) Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nat Biotechnol 17:808–812

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Madan A (1999) A DNA sequence assembly proram. Genome Res 9:868–877

    Article  CAS  PubMed  Google Scholar 

  • Huggett J, Dheda K, Bustin S, Zumla A (2005) Real time RT-PCR normalization; strategies and considerations. Genes Immun 6:284–289

    Article  Google Scholar 

  • Johnson-Flanagan AM, Owens JN (1985) Peroxidase activity in relation to suberization and respiration in white spruce (Picea glauca [Moench] Voss) sedling roots. Plant Physiol 79:103–107

    Article  CAS  PubMed  Google Scholar 

  • Lal S, Ravi V, Khurana JP, Khurana P (2009) Repertoire of leaf expressed sequence tags (ESTs) and partial characterization of stress-related and membrane transporter genes from mulberry (Morus indica L.). Tree Genet Genomes 5:359–374

    Article  Google Scholar 

  • Mader M, Fussl R (1982) Role of peroxidases in lignifications of tobacco cells. Plant Physiol 70:1132–1134

    Article  CAS  PubMed  Google Scholar 

  • Maslin BR, Miller DS, Seigler JT (2003) Overview of the generic status of Acacia (Leguminosae: Mimosoideae). Austral Syst Bot 16(1):1–18

    Article  Google Scholar 

  • Mellerowicz EJ, Bausher M, Sundberg B, Boerjan W (2001) Unravelling cell wall formation in the woody dicot stem. Plant Mol Biol 47:239–274

    Article  CAS  PubMed  Google Scholar 

  • Minibaeva FV, Gordon LK, Kolesnikov OP (2001) Role of extracellular peroxidase in the superoxide production by wheat root cells. Protoplasma 217:125–128

    Article  Google Scholar 

  • Nguyen PD, Ho CL, Harikrishna JA, Wong MCVL, Rahim RA (2006) Generation and analysis of expressed sequence tags from the mangrove plant, Acanthus ebracteatus Vahl. Tree Genet Genomes 2:196–201

    Article  Google Scholar 

  • O’Malley DM, Whetten R (1993) The role of laccase in lignifications. Plant J 4:751–757

    Article  Google Scholar 

  • Oh S, Park S, Han KH (2003) Transcriptional regulation of secondary growth in Arabidopsis thaliana. J Exp Bot 127:1513–1523

    Google Scholar 

  • Pang SL (2007) Characterization and down regulation of lignin genes from Acacia auriculiformis x Acacia mangium hybrid. Ph.D. Dissertation. Universiti Kebangsaan Malaysia

  • Paux E, Tamasloukht M, Ladouce N, Sivadon P, Grima-Pettenati J (2004) Identification of genes preferentially expressed during wood formation in Eucalyptus. Plant Mol Biol 55:63–280

    Article  Google Scholar 

  • Pavy N, Johnson JJ, Crow JA, Paule C, Kunau T, Mackay J, Retzel EF (2007) ForestTreeDB: a database dedicated to the mining of tree transcriptomes. Nucl Acids Res 35:888–894

    Article  Google Scholar 

  • Saxena IM, Brown RM (2005) Cellulose biosynthesis: current views and evolving concepts. Ann Bot 96:9–21

    Article  CAS  PubMed  Google Scholar 

  • Schoof H, Ersnt R, Nazarov V, Pfeifer L, Mewes H-W, Mayer KFX (2004) MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucl Acids Res 32:373–372

    Article  Google Scholar 

  • Tian AG, Wang J, Cui P, Han YJ, Xu H, Cong LJ, Huang XG, Wang XL, Jiao YZ, Wang BJ, Wang YJ, Zhang JS, Chen SY (2004) Characterization of soybean genomic features by analysis of its expressed sequence tags. Theor Appl Genet 108:903–913

    Article  PubMed  Google Scholar 

  • Ujino-Ihara T, Yoshimura K, Ugawa Y, Yoshimaru H, Nagasaka K, Tsumura Y (2000) Expression analysis of ESTs derived from the inner bark of Crytomeria japonica. Plant Mol Biol 43:451–457

    Article  CAS  PubMed  Google Scholar 

  • Vandesompele JO, Preter KD, Pattyn F, Poppe B, Roy NV, Paepe AD, Speleman F (2002) Accurate normalization of real time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3(34):1–11

    Google Scholar 

  • Wagner WL, Herbst DR, Sohmer SH (1999) Manual of the Flowering Plants of Hawaii, vol. 2. Bishop Muzium Special Publication 83. University of Hawaii and Bishop Museum Press, Honolulu, HI

  • Wagner A, Donaldson L, Kim H, Phillips L, Flint H, Steward D, Torr K, Koch G, Schmitt U, Ralph J (2009) Lignin manipulationin the coniferous gymnosperm Pinus radiata. Plant Physiol 149:370–383

    Article  CAS  PubMed  Google Scholar 

  • Whetten R, Sederof R (1992) Phenylalanine ammonia lyase from loblolly pine: purification of the enzymes and isolation of complementary cDNA clones. Plant Physiol 98:380–386

    Article  CAS  PubMed  Google Scholar 

  • Wickneswari R, Cheong PL, Pang SL, Choong CY, Harikrishna JA, Elliott RC, Vaillancourt RE (2004) Analysis of one set of expressed tagged sequences sequence tags from cDNA library of the inner bark tissues of A. mangium x A. auriculiformis interspecific hybrid (in Malay). In: Asmat A, Farah DAB, Munir AAM, Hasidah AS, Norela S, Marina Z (eds) Prosiding Simposium Biologi Kebangsaan Ke-7, Awana Genting Highlands Golf and Country Resort, Malaysia, 18–20 May 2004. pp. 477–480

  • Wong HC, Fear AL, Calhoon RD, Eichinger GH, Mayer R, Amikam D, Benziman M, Gelfand DH, Meade JH, Emerick AW (1990) Genetic organization of the cellulose synthase operon in Acetobacter xylinum. Proc Natl Acad Sci USA 87:8130–8134

    Article  CAS  PubMed  Google Scholar 

  • Yamada N, Khoo KC, Nor MY (1990) Sulphate pulping characteristic of Acacia hybrid, Acacia mangium and Acacia auriculiformis from Sabah. J Trop For Sci 3:206–214

    Google Scholar 

  • Ye ZH, Varner JE (1991) Tissue specific expression of cell wall proteins in developing soybean tissues. Plant Cell 3:23–37

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This research was funded by a Priority Research Grant under the Intensified Research Project Area Scheme to Universiti Kebangsaan Malaysia from the Ministry of Science, Technology & Innovation, Malaysia. We also acknowledge the help of Robert C. Elliott and the Cooperative Research Centre for Forestry (Hobart, Australia).

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Authors and Affiliations

  1. School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia

    S. Y. C. Yong, C. Y. Choong, P. L. Cheong, S. L. Pang, R. Nor Amalina & R. Wickneswari

  2. Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia

    J. A. Harikrishna

  3. Interim Laboratory, The National Institute for Genomics and Molecular Biology, UKM-MTDC Smart Technology Centre, 43600, Bangi, Selangor Darul Ehsan, Malaysia

    M. N. Mat-Isa

  4. Programme of Genetics, SCRI, Dundee, UK

    P. Hedley & L. Milne

  5. School of Plant Science, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia

    R. Vaillancourt

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  1. S. Y. C. Yong
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  2. C. Y. Choong
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Correspondence to R. Wickneswari.

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Communicated by J. Dean

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Yong, S.Y.C., Choong, C.Y., Cheong, P.L. et al. Analysis of ESTs generated from inner bark tissue of an Acacia auriculiformis x Acacia mangium hybrid. Tree Genetics & Genomes 7, 143–152 (2011). https://doi.org/10.1007/s11295-010-0321-y

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