ORIGINAL PAPER Analysis of ESTs generated from inner bark tissue of an Acacia auriculiformis x Acacia mangium hybrid S. Y. C. Yong & C. Y. Choong & P. L. Cheong & S. L. Pang & R. Nor Amalina & J. A. Harikrishna & M. N. Mat-Isa & P. Hedley & L. Milne & R. Vaillancourt & R. Wickneswari Received: 20 April 2009 / Revised: 15 June 2010 / Accepted: 11 July 2010 / Published online: 12 August 2010 # Springer-Verlag 2010 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 single- tons) 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. Keywords cDNA library . Wood formation genes . Transcript profiling . Library validation . Comparative sequence analysis Introduction Acacia is a genus from the family Fabaceae consisting of around 1,380 species (Maslin et al. 2003). It is globally distributed but the majority of species are located in Australia (Wagner et al. 1999). Acacia mangium and Acacia auriculiformis have been planted commercially in Communicated by J. Dean Electronic supplementary material The online version of this article (doi:10.1007/s11295-010-0321-y) contains supplementary material, which is available to authorized users. S. Y. C. Yong : C. Y. Choong : P. L. Cheong : S. L. Pang : R. Nor Amalina : R. Wickneswari (*) School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia e-mail: wicki@ukm.my J. A. Harikrishna Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia M. N. Mat-Isa Interim Laboratory, The National Institute for Genomics and Molecular Biology, UKM-MTDC Smart Technology Centre, 43600 Bangi, Selangor Darul Ehsan, Malaysia P. Hedley : L. Milne Programme of Genetics, SCRI, Dundee, UK R. Vaillancourt School of Plant Science, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia Tree Genetics & Genomes (2011) 7:143–152 DOI 10.1007/s11295-010-0321-y