Generation and analysis of an Eucalyptus globulus cDNA library constructed from seedlings subjected to low temperature conditions

Electronic Journal of Biotechnology

Volumn 11, Issue 2, 2008, Pages

  Rasmussen Poblete, Susana ^a   Valdés, Jorge ^a   Gamboa, Maria Cecilia ^a   Valenzuela, Pablo D T ^a   Krauskopf, Erwin ^a  

^a UNIVERSIDAD ANDRÉS BELLO   (Chile)

Author keywords

Cellulose; Cold temperature; EST database; Forest biotechnology; Lignin

Indexed keywords

BIOTECHNOLOGY; CELLULOSE; FORESTRY; LIGNIN;

BIOFUEL PRODUCTION; COLD-TEMPERATURE; EST DATABASE;

DNA;

LIGNIN; PLANT DNA;

ARTICLE; CONTROLLED STUDY; DNA LIBRARY; EUCALYPTUS; EUCALYPTUS GLOBULUS; EXPRESSED SEQUENCE TAG; LOW TEMPERATURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT BIOTECHNOLOGY; PLANT GENETICS; SEEDLING; UNINDEXED SEQUENCE; WOOD;

BIOTECHNOLOGY; CELLULOSE; FORESTRY; LIGNINS; NUCLEIC ACIDS;

EUCALYPTUS; EUCALYPTUS GLOBULUS;

EID: 44349190977     PISSN: None     EISSN: 07173458     Source Type: Journal    
DOI: 10.2225/vol11-issue2-fulltext-14     Document Type: Article

References (39)

1. ALLONA, I.; QUINN, M.; SHOOP, E.; SWOPE, K.; ST. CYR, S.; CARLIS, J.; RIEDL, J.; RETZEL, E.; CAMPBELL, M.; SEDEROFF, R. and WHETTEN, R. Analysis of xylem formation in pine by cDNA sequencing. Proceedings of the National Academy of Sciences of the United States of America, August 1998, vol. 95, no. 16, p. 9693-9698.
2. ALTSCHUL, S.; MADDEN, T.; SCHAFFER, A.; ZHANG, J.; ZHANG, Z.; MILLER, W. and LIPMAN, D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, September 1997, vol. 25, no. 17, p. 3389-3402.
3. ASHBURNER, M.; BALL, C.; BLAKE, J.; BOTSTEIN, D.; BUTLER, H.; CHERRY, J.; DAVIS, A.; DOLINSKI, K.; DWIGHT, S.; EPPIG, J.; HARRIS, M.; HILL, D.; ISSEL-TARVER, L.; KASARSKIS, A.; LEWIS, S.; MATESE, J.; RICHARDSON, J.; RINGWALD, M.; RUBIN, G. and SHERLOCK, G. Gene Ontology: tool for the unification of biology. Nature Genetics, May 2000, vol. 25, p. 25-29.
4. BOERJAN, W.; RALPH, J. and BAUCHER, M. Lignin biosynthesis. Annual Review of Plant Biology, June 2003, vol. 54, p. 519-546.
5. BRAÜTIGAM, M.; LINDLÖF, A.; ZAKHRABETKOVA, S.; GHARTI-CHHETRI, G.; OLSSON, B. and OLSSON, O. Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa. BMC Plant Biology, September 2005, vol. 5, p. 18.
6. CÁNOVAS, F.; DUMAS-GAUDOT, E.; RECORBET, E.; JORRIN, J.; MOCK, H.-P. and ROSSIGNOL, M. Plant proteome analysis. Proteomics 2004, vol. 4, p.285-298.
7. CHANG, S.; PURYEAR, J. and CAIRNEY, J. A simple and efficient method for isolating RNA from pines trees. Plant Molecular Biology Reporter, June 1993, vol. 11, p. 113-116.
8. COOKE, J.; MORSE, A. and DAVIS, J. Forestry. In: KLEE and P. CRISTOU eds. Handbook of Plant Biotechnology. United Kingdom. John Wiley and Sons, 2004, vol. 2, p. 881-904.
9. EWING, B.; HILLIER, L.; WENDL, M. and GREEN, P. Basecalling of automated sequencer traces using phred I. Accuracy Assessment. Genome Research, March 1998, vol. 8, no. 3, p. 175-185.
10. FAO. Progress towards sustainable forest managment. In: FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS eds. Global forest resources assessment. Rome. FAO forestry paper, 2005, p. 147.
11. FLEISCHMANN, W.; MOELLER, S.; GATEAU, A. and APWEILER, R. A novel method for automatic functional annotation of proteins. Bioinformatics, March 1999, vol. 15, no. 3, p. 228-233.
12. FRANKE, R.; HUMPHREYS, J.M.; HEMM, M.R.; DENAULT, J.W.; RUEGGER, M.O.; CUSUMANO, J.C. and CHAPPLE, C. Changes in secondary metabolism and deposition of an unusual lignin in the ref8 mutant of Arabidopsis. The Plant Journal, April 2002, vol. 30, no. 1, p. 33-45.
13. FUKUSHIMA, K. Regulation of syringyl to guaiacyl ratio in lignin biosynthesis. Journal of Plant Research, February 2001, vol. 114, no. 4, p. 499-508.
14. GAO, G.; ZHONG, Y.; GUO, A.; ZHU, Q.; TANG, W.; ZHENG, W.; GU, X.; WEI, L. and LUO, J. DRTF: a database of rice transcription factors. Bioinformatics, March 2006, vol. 22, no. 10, p. 1286-1287.
15. GOICOECHEA, M.; LACOMBE, E.; LEGAY, S.; MIHALJEVIC, S.; RECH, P.; JAUNEAU, A.; LAPIERRE, C.; POLLET, B.; VERHAEGEN, D.; CHAUBET-GIGOT, N. and GRIMA-PETTENATI, J. EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis. The Plant Journal, August 2005, vol. 43, no. 4, p. 553-567.
16. GRATTAPAGLIA, D. Integrating genomics into Eucalyptus breeding. Genetics and Molecular Research, September 2004, vol. 3, no. 3, p. 369-379.
17. GUO, A.; HE, K.; LIU, D.; BAI, S.; GU, X.; WEI, L. and LUO, J. DATF: a database of Arabidopsis transcription factors. Bioinformatics, February 2005, vol. 21, no. 10, p. 2568-2569.
18. HARAKAVA, R. Genes encoding enzymes of the lignin biosynthesis pathways in Eucalyptus. Genetics and Molecular Biology, 2004, vol. 28, no. 3, p. 601-607.
19. HAUSMAN, J.F.; EVERS, D.; THIELLEMENT, H. and JOUVE, L. Compared responses of poplar cuttings and in vitro raised shoots to short-term chilling treatments. Plant Cell Reports, October 2000, vol. 19, no. 10, p. 954-960.
20. HU, W.J.; HARDING, S.A.; LUNG, J.; POPKO, J.L.; RALPH, J.; STOKKE, D.D.; TSAI, C.J. and CHIANG, V.L. Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nature Biotechnology, August 1999, vol. 17, p. 808-812.
21. HUANG, X. and MADAN, A. CAP3 A DNA sequence assembly program. Genome Research, September 1999, vol. 9, no. 9, p. 868-877.
22. ISRAELSSON, M.; ERIKSSON, M.; HERTZBERG, M.; ASPEBORG, H.; NILSSON, H. and MORITZ, T. Changes in gene expression in the wood-forming tissue of transgenic hybrid aspen with increased secondary growth. Plant Molecular Biology, July 2003, vol. 52, no. 4, p. 893-903.
23. JONES, R.C.; STEANE, D.A.; POTTS, B.M. and VAILLANCOURT, R.E. Microsatellite and morphological analysis of Eucalyptus globulus populations. Canadian Journal of Forest Research, January 2002, vol. 32, no. 1, p. 59-66.
24. JUNG, H.-J. and NI, W. Lignification of plant cell walls. Impact of genetic manipulation. Proceedings of the National Academy of Sciences of the United States of America, October 1998, vol. 95, no. 22, p. 12742-12743.
25. KRAUSKOPF, E.; HARRIS, P. and PUTTERILL, J. The cellulose synthase gene PrCESA10 is involved in cellulose biosynthesis in developing tracheids of the gymnosperm Pinus radiata. Gene, May 2005, vol. 350, no. 2, p. 107-116.
26. LI, L.; ZHOU, Y.H.; CHENG, X.F.; SUN, J.Y.; MARITA, J.M.; RALPH, J. and CHIANG V.L. Combinatorial modification of multiple lignin traits in trees through multigene cotransformation. Proceedings of the National Academy of Sciences of the United States of America, April 2003, vol. 100, no. 8, p. 4939-4944.
27. MIRANDA, I. and PEREIRA, H. Variation of pulpwood quality with provenances and site in Eucalyptus globulus. Annals of Forest Science, 2002, vol. 59, p. 283-291.
28. NANJO, T.; FUTAMURA, N.; NISHIGUCHI, M.; IGASAKI, T.; SHINOZAKI, K. and SHINOHARA, K. Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves. Plant and Cell Physiology, 2004, vol. 45, no. 12, p. 1738-1748.
29. OH, S.; PARK, S. and HAN, K.-H. Transcriptional regulation of secondary growth in Arabidopsis thaliana. Journal of Experimental Botany, December 2003, vol. 54, no. 393, p. 2709-2722.
30. PLOMION, C.; LEPROVOST, G. and STOKES, A. Wood formation in trees. Plant Physiology, December 2001, vol. 127, p. 1513-1523.
31. QUACKENBUSH, J.; LIANG, F.; HOLT, I.; PERTEA, G. and UPTON, J. The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Research, 2000, vol. 28, no. 1, p. 141-145.
32. RALPH, J.; AKIYAMA, T.; KIM, H.; LU, F.; SCHATZ, P.F.; MARITA, J.M.; RALPH, S.A.; SRINIVASAREDDY, M.S.; CHEN, F. and DIXON, R.A. Effects of coumarate 3-hydroxylase down-regulation lignin structure. Journal of Biological Chemistry, March 2006, vol. 281, no. 13, p. 8843-8853.
33. RANIK, M. and MYBURG, A. Six new cellulose synthase genes from Eucalyptus are associated with primary and secondary cell wall biosynthesis. Tree Physiology, May 2006, vol. 26, no. 5, p. 545-556.
34. RASTOGI, S. and DWIVEDI, UN. Down-regulation of lignin biosynthesis in transgenic Leucaena leucocephala harboring O-methyltransferase gene. Biotechnology Progress, 2006, vol. 22, p. 609-616.
35. STERKY, F.; REGAN, S.; KARLSSON, J.; HERTZBERG, M.; ROHDE, A.; HOLMBERG, A.; AMINI, B.; BHALERAO, R.; LARSSON, M.; VILLAROEL, R.; VAN MONTAGU, M.; SANDBERG, G.; OLSSON, O.; TEERI, T.; BOERJAN, W.; GUSTAFSSON, P., UHLÉN, M.; SUNDBERG, B. and LUNDEBERG, J. Gene discovery in the wood forming tissues of poplar: analysis of 5,692 expressed sequence tags. Proceedings of the National Academy of Sciences of the United States of America, October 1998, vol.95, no. 22, p. 13330-13335.
36. STERKY, F.; BHALERAO, R.; UNNEBERG, P.; SEGERMAN, B.; NILSSON, P.; BRUNNER, A.; CHARBONNEL-CAMPAA, L.; LINDVALL, J.; TANDRE, K.;STRAUSS, S.; SUNDBERG, B.; GUSTAFSSON, P.; UHLÉN, M.; BHALERAO, R.; NILSSON, O.; SANDBERG, G.; KARLSSON, J.; LUNDEBERG, J. and JANSSON, S. A populus EST resource for plant functional genomics. Proceedings of the National Academy of Sciences of the United States of America, September 2004, vol. 101, no. 38, p. 13951-13956.
37. TAMAGNONE, L.; MERIDA, A.; PARR, A.; MACKAY, S.; CULIANEZ-MACIA, F.; ROBERTS, K. and MARTIN, C. The AmMYB308 and AmMYB330 transcription factors from Antirrhinum regulate phenylpropanoid and lignin biosynthesis in transgenic tobacco. Plant Cell, February 1998, vol. 10, no. 2, p. 135-154.
38. U.S. DEPARTMENT OF ENERGY. OIT Agriculture Plants/crop-based renewable resources 2020. [cited date July 2007], 2007. Available from Internet: http://www.energy.gov.
39. ZDOBNOV, E.M. and APWEILER, R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 2001, vol. 17, no. 9, p. 847-848.