Journal of Wood Science

, Volume 57, Issue 1, pp 40–46 | Cite as

Analysis of expressed sequence tags in developing secondary xylem and shoot of Acacia mangium

  • Shiro Suzuki
  • Kunihiro Suda
  • Nozomu Sakurai
  • Yoshiyuki Ogata
  • Takefumi Hattori
  • Hideyuki Suzuki
  • Daisuke Shibata
  • Toshiaki Umezawa
Original Article


Acacia mangium is a fast-growing tree widely planted in tropical countries because of its rapid growth, high wood density, high fiber quality, and good adaptability. Despite its importance as a fiber source in the pulp and paper industry, a large-scale analysis of expressed sequence tags (ESTs) has not been performed in A. mangium. In this study, we sequenced 10 752 clones of a normalized complementary DNA (cDNA) library prepared from A. mangium developing secondary xylem and shoot, and obtained a total of 8963 ESTs. The ESTs were assembled into 6220 unigenes comprising 1614 contigs and 4606 singletons. The unigene set was then subjected to various bioinformatic analyses. BlastN searches of the unigene set against the Gene Index Databases of soybean, Medicago truncatula, Lotus japonicus, grape, poplar, spruce, and pine demonstrated that the largest number of unigenes shared homologies with the soybean Gene Indices. BlastX searches against the TAIR9 peptide database enabled us to annotate the unigenes. Based on the annotation, we discussed whether the unigenes involved in the cell cycle, cell growth, shoot apical meristem development, and cell wall biosynthesis were present. This new genomic resource will accelerate the functional genomics of wood formation and molecular breeding to improve the wood properties of A. mangium.

Key words

Acacia mangium EST Secondary xylem Wood formation 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Zimmerman MH (1983) Conducting units: tracheids and vessels. In: Xylem structure and the ascent of sap. Springer-Verlag, Berlin, pp 4–20Google Scholar
  2. 2.
    Demura T, Fukuda H (2007) Transcriptional regulation in wood formation. Trends Plant Sci 12:64–70CrossRefPubMedGoogle Scholar
  3. 3.
    Higuchi T (1997) Structure and functions of wood. In: Biochemistry and molecular biology of wood. Springer-Verlag, Berlin, pp 1–40Google Scholar
  4. 4.
    Suzuki S, Li L, Sun Y, Chiang VL (2006) The cellulose synthase gene superfamily and biochemical functions of xylem-specific cellulose synthase-like genes in Populus trichocarpa. Plant Physiol 142:1233–1245CrossRefPubMedGoogle Scholar
  5. 5.
    Rengel D, San Clemente H, Servant F, Ladouce N, Paux E, Wincker P, Couloux A, Sivadon P, Grima-Pettenati J (2009) A new genomic resource dedicated to wood formation in Eucalyptus. BMC Plant Biol 9:36–49CrossRefPubMedGoogle Scholar
  6. 6.
    Umezawa T, Suzuki S, Shibata D (2009) Tree biotechnology of tropical Acacia. Plant Biotechnol 25:309–331Google Scholar
  7. 7.
    Xie D, Hong Y (2002) Agrobacterium-mediated genetic transformation of Acacia mangium. Plant Cell Rep 20:917–922CrossRefGoogle Scholar
  8. 8.
    Saito Y, Kojima K, Ide Y, Sasaki S (1993) In vitro propagation from axillary buds of Acacia mangium - a legume tree in the tropics. Plant Tissue Cult Lett 10:163–168Google Scholar
  9. 9.
    Wang XJ, Cao XL, Hong Y (2005) Isolation and characterization of flower-specific transcripts in Acacia mangium. Tree Physiol 25:167–178PubMedGoogle Scholar
  10. 10.
    Bugos RC, Chiang VL, Zhang XH, Campbell ER, Podila GK, Campbell WH (1995) RNA isolation from plant tissues recalcitrant to extraction in guanidine. BioTechniques 19:734–737PubMedGoogle Scholar
  11. 11.
    Tsugane T, Watanabe M, Yano K, Sakurai N, Suzuki H, Shibata D (2005) Expressed sequence tags of full-length cDNA clones from the miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom. Plant Biotechnol 22:161–165Google Scholar
  12. 12.
    Ewing B, Hillier L, Wendl M, Green P (1998) Base calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8:175–185PubMedGoogle Scholar
  13. 13.
    Green P (1994) Phrap.doc. Accessed 10 Sept 2010
  14. 14.
    UniProt Knowledgebase (2002) UniProt Consortium. Accessed 10 Sept 2010
  15. 15.
    The Gene Index Databases (2005) Dana Farber Cancer Institute, BostonGoogle Scholar
  16. 16.
    The Arabidopsis Information Resource (TAIR) (2001) Carnegie Institution for Science, Stanford. Accessed 10 Sept 2010
  17. 17.
    DNA Data Bank of Japan (2001) National Institute of Genetics, Mishima. Accessed 10 Sept 2010
  18. 18.
    National Center for Biotechnology Information (1990) National Library of Medicine, Bethesda. Accessed 10 Sept 2010
  19. 19.
    Wang Y, Chu Y, Liu G, Wang M, Jiang J, Hou Y, Qu G, Yang C (2006) Identification of expressed sequence tags in an alkali grass (Puccinellia tenuiflora) cDNA library. J Plant Res 164:78–89Google Scholar
  20. 20.
    Jin H, Plaha P, Park JY, Hong CP, Lee IS, Yang ZH, Jiang GB, Kwak SS, Liu SK, Lee JS, Kim YA, Lim YP (2006) Comparative EST profiles of leaf and root of Leymus chinensis, a xerophilous grass adapted to high-pH sodic soil. Plant Sci 170:1081–1086CrossRefGoogle Scholar
  21. 21.
    Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J 38:366–379CrossRefPubMedGoogle Scholar
  22. 22.
    Phytozome (2008) Phytozome Team, Oakland. Accessed 10 Sept 2010
  23. 23.
    Stals H, Inzé D (2001) When plant cells decide to divide. Trend Plant Sci 6:359–364CrossRefGoogle Scholar
  24. 24.
    Wang G, Kong H, Sun Y, Zhang X, Zhang W, Altman N, dePamphilis CW, Ma H (2004) Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclinlike proteins. Plant Physiol 135:1084–1099CrossRefPubMedGoogle Scholar
  25. 25.
    Carpita N, MacCann M (2000) The cell wall. In: Buchanan BB, Gruissem W, Jones RL (eds) Biochemistry and molecular biology of plants. The American Society of Plant Biologists, Rockville, pp 52–109Google Scholar
  26. 26.
    Yokoyama R, Nishitani K (2001) A comprehensive expression analysis of all members of a gene family encoding cell-wall enzymes allowed us to predict cis-regulatory regions involved in cell-wall construction in specific organs of Arabidopsis. Plant Cell Physiol 42:1025–1033CrossRefPubMedGoogle Scholar
  27. 27.
    Sanoedro D, Cosgrove DJ (2005) The expansin superfamily. Genome Biol 6:242CrossRefGoogle Scholar
  28. 28.
    Doerner P (2002) Cell division regulation. In: Buchanan BB, Gruissem W, Jones RL (eds) Biochemistry and molecular biology of plants. The American Society of Plant Biologists, Rockville, pp 528–567Google Scholar
  29. 29.
    Zhong R, Ye ZH (2007) Regulation of cell wall biosynthesis. Curr Opin Plant Biol 10:564–572CrossRefPubMedGoogle Scholar
  30. 30.
    Ralph J, Lundquist K, Brunow G, Lu F, Kim H, Schatz PF, Marita JM, Hatfield RD, Ralph SA, Christensen JH, Boerjan W (2004) Lignins: natural polymers from oxidative coupling of 4-hydroxyphenylpropanoids. Phytochem Rev 3:29–60CrossRefGoogle Scholar
  31. 31.
    Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Ann Rev Plant Biol 54:519–546CrossRefGoogle Scholar
  32. 32.
    Raes J, Rohde A, Christensen JH, de Peer YV, Boerjan W (2003) Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol 133:1051–1071CrossRefPubMedGoogle Scholar
  33. 33.
    Goujon T, Sibout R, Eudes A, MacKay J, Jouanin L (2003) Genes involved in the biosynthesis of lignin precursors in Arabidopsis thaliana. Plant Physiol Biochem 41:677–687CrossRefGoogle Scholar
  34. 34.
    Dixon RA, Reddy MSS (2003) Biosynthesis of monolignols. Genomic and reverse genetic approaches. Phytochem Rev 2:289–306CrossRefGoogle Scholar
  35. 35.
    Brown DM, Zeef LAH, Ellis J, Goodacre R, Turner SR (2005) Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17:2281–2295CrossRefPubMedGoogle Scholar
  36. 36.
    Liang M, Davis E, Gardner D, Cai X, Wu Y (2006) Involvement of AtLAC15 in lignin synthesis in seeds and in root elongation of Arabidopsis. Planta 224:1185–1196CrossRefPubMedGoogle Scholar
  37. 37.
    Hoffmann L, Besseau S, Geoffroy P, Ritzenthaler C, Meyer D, Lapierre C, Pollet B, Legrand M (2004) Silencing of hydroxycinnamoyl-coenzyme A shikimate/quinate hydroxycinnamoyl transferase affects phenylpropanoid biosynthesis. Plant Cell 16:1446–1465CrossRefPubMedGoogle Scholar
  38. 38.
    Besseau S, Hoffmann L, Geoffroy P, Lapierre C, Pollet B, Legrand M (2007) Flavonoid accumulation in Arabidopsis repressed in lignin synthesis affects auxin transport and plant growth. Plant Cell 19:148–162CrossRefPubMedGoogle Scholar
  39. 39.
    Bayer E, Bottrill A, Walshaw J, Vigouroux M, Naldrett MJ, Thomas C, Maule A (2006) Cell wall proteome defined using multidimensional protein identification technology. Proteomics 6:301–311CrossRefPubMedGoogle Scholar
  40. 40.
    Kimura S, Laosinchai W, Itoh T, Cui X, Linder CR, Brown RM Jr (1999) Immunogold labeling of rosette terminal cellulose-synthesizing complexes in the vascular plant Vigna angularis. Plant Cell 11:2075–2085CrossRefPubMedGoogle Scholar
  41. 41.
    Mutwil M, Debolt S, Persson S (2008) Cellulose synthesis: a complex complex. Curr Opin Plant Biol 11:252–257CrossRefPubMedGoogle Scholar
  42. 42.
    Doblin MS, Kurek I, Jacob-Wilk D, Delmer DP (2002) Cellulose biosynthesis in plants: from genes to rosettes. Plant Cell Physiol 43:1407–1420CrossRefPubMedGoogle Scholar
  43. 43.
    Pinto PC, Evtuguin DV, Neto CP (2005) Chemical composition and structural features of the macromolecular components of plantation Acacia mangium wood. J Agric Food Chem 53:7856–7862CrossRefPubMedGoogle Scholar
  44. 44.
    York WS, O’Neill MA (2008) Biochemical control of xylan biosynthesis - which end is up? Curr Opin Plant Biol 11:258–265CrossRefPubMedGoogle Scholar
  45. 45.
    Brown DM, Zhang Z, Stephens E, Dupree P, Turner SR (2009) Characterization of IRX10 and IRX10-like reveals an essential role in glucuronoxylan biosynthesis in Arabidopsis. Plant J 57:732–746CrossRefPubMedGoogle Scholar
  46. 46.
    Wu AM, Rihouey C, Seveno M, Hörnblad E, Singh SK, Matsunaga T, Ishii T, Lerouge P, Marchant A (2009) The Arabidopsis IRX10 and IRX10-LIKE glycosyltransferases are critical for glucuronoxylan biosynthesis during secondary cell wall formation. Plant J 57:718–731CrossRefPubMedGoogle Scholar
  47. 47.
    Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics 21:2568–2569CrossRefPubMedGoogle Scholar
  48. 48.
    Mitsuda N, Seki M, Shinozaki K, Ohme-Takagi M (2005) The NAC transcription factors NST1 and NST2 of Arabidopsis regulate secondary wall thickenings and are required for anther dehiscence. Plant Cell 17:2993–3006CrossRefPubMedGoogle Scholar
  49. 49.
    Mitsuda N, Iwase A, Yamamoto H, Yoshida M, Seki M, Shinozaki K, Ohme-Takagi M (2007) NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis. Plant Cell 19:270–280CrossRefPubMedGoogle Scholar
  50. 50.
    Zhong R, Lee C, Zhou J, McCarthy RL, Ye ZH (2008) A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell 20:2763–2782CrossRefPubMedGoogle Scholar
  51. 51.
    Zhao C, Avci U, Grant EH, Haigler CH, Beers EP (2008) XND1, a member of the NAC domain family in Arabidopsis thaliana, negatively regulates lignocellulose synthesis and programmed cell death in xylem. Plant J 53:425–436CrossRefPubMedGoogle Scholar
  52. 52.
    Zhou J, Lee C, Zhong R, Ye ZH (2009) MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis. Plant Cell 21:248–266CrossRefPubMedGoogle Scholar
  53. 53.
    Newman LJ, Perazza DE, Juda L, Campbell MM (2004) Involvement of the R2R3-MYB, AtMYB61, in the ectopic lignification and dark-photomorphogenic components of the det3 mutant phenotype. Plant J 37:239–250CrossRefPubMedGoogle Scholar

Copyright information

© The Japan Wood Research Society 2010

Authors and Affiliations

  • Shiro Suzuki
    • 1
    • 3
  • Kunihiro Suda
    • 2
  • Nozomu Sakurai
    • 2
  • Yoshiyuki Ogata
    • 2
  • Takefumi Hattori
    • 1
  • Hideyuki Suzuki
    • 2
  • Daisuke Shibata
    • 2
  • Toshiaki Umezawa
    • 1
    • 3
  1. 1.Research Institute of Sustainable HumanosphereKyoto UniversityKyotoJapan
  2. 2.Kazusa DNA Research InstituteKisarazu, ChibaJapan
  3. 3.Institute of Sustainability ScienceKyoto UniversityGokasho, Uji, KyotoJapan

Personalised recommendations