Tree Genetics & Genomes

, Volume 5, Issue 2, pp 317–327 | Cite as

Development and functional annotation of an 11,303-EST collection from Eucalyptus for studies of cold tolerance

  • Guylaine Keller
  • Thibault Marchal
  • Hélène SanClemente
  • Marie Navarro
  • Nathalie Ladouce
  • Patrick Wincker
  • Arnaud Couloux
  • Chantal Teulières
  • Christiane Marque
Original Paper

Abstract

A cDNA library was constructed from leaves of a cold-acclimated Eucalyptus gunnii elite clone and 13,056 ESTs were sequenced. When the 5,457 unique sequences were compared with Arabidopsis, rice, and poplar datasets, more than 38% of no-hits were found and the best annotation was provided by the woody perennial poplar database. However, among the 62% of sequences that could be annotated, the vast majority (87.5%) was found to be common to the four compared plant species, which shows how highly conserved this gene pool is across the plant kingdom. When the distribution of the annotated sequences was studied according to the Gene Ontology classification, some typical features of the dehydrative stress transcriptome were observed. In particular, genes from sugar metabolism and, above all, those induced by stress or external stimuli were well represented (6% in total). In addition, the library was found to contain a substantial number of ESTs encoding putative transcription factors including CBF (CRT-Binding Factor). The enrichment of this library with stress-related genes was strongly suggested by the high redundancy (up to 300 ESTs) of several genes known to be involved in cell protection such as the PCP (Pollen Coat Protein), Lti6b (Low temperature induced) or metallothionein. It was further confirmed by demonstrating the cold induction of a set of representative genes through Real Time-PCR. All these characteristics make this Eucalyptus EST collection very suitable for investigating the molecular basis of cold tolerance in a woody perennial and for isolating important or new candidate frost tolerance genes.

Keywords

Eucalyptus Expressed sequence tags (EST) Frost tolerance Cold acclimation 

Notes

Acknowledgements

We thank AFOCEL for supplying the Eucalyptus cuttings. Research supports, salaries, and grants were provided by French Ministry of Research and Technology (MNRT), the “Midi Pyrénées French Council” and TEMBEC SA R&D KRAFT (St GAUDENS, France). Thanks to Victoria McBride for accurate English editing of the manuscript.

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410PubMedGoogle Scholar
  2. 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 investigations. Plant Sci 165:415–422CrossRefGoogle Scholar
  3. Benedict C, Skinner JS, Meng R, Chang Y, Bhalerao R, Huner NPA, Finn CE, Chen THH, Hurry V (2006) The CBF1-dependent low temperature signalling pathway, regulon and increase in freeze tolerance are conserved in Populus spp. Plant, Cell and Environ 29:1259–1272CrossRefGoogle Scholar
  4. Brooker MIH (2000) A new classification of the genus Eucalyptus l’Her. (Myrtaceae). Aust Syst Bot 13:79–148CrossRefGoogle Scholar
  5. Cao S, Ye M, Jiang S (2005) Involvement of GIGANTEA gene in the regulation of the cold stress response in Arabidopsis. Plant Cell Reports 25:683–690CrossRefGoogle Scholar
  6. Chinnusamy V, Ohta M, Kanrar S, Lee BH, Hong X, Agarwal M, Zhu JK (2003) ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev 17:1043–1054PubMedCrossRefGoogle Scholar
  7. Choi H, Hong J, Ha J, Kang J, Kim SY (2000) ABFs, a family of ABA-responsive element binding factors. J Biol Chem 275:1723–1730PubMedCrossRefGoogle Scholar
  8. Davletova S, Schlauch K, Coutu J, Mittler R (2005) The zinc-finger protein ZAT12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Physiol 139:847–856PubMedCrossRefGoogle Scholar
  9. El Kayal W, Keller G, Debayles C, Kumar R, Weier D, Teulières C, Marque C (2006a) Regulation of tocopherol biosynthesis through transcriptional control of tocopherol cyclase during cold hardening in Eucalyptus gunnii. Physiol Plant 126:221–223Google Scholar
  10. El Kayal W, Navarro M, Marque G, Keller G, Marque C, Teulières C (2006b) Expression profile of CBF-like transcriptional factor genes from Eucalyptus in response to cold. J Exp Bot 57:2455–2469PubMedCrossRefGoogle Scholar
  11. FAO (2000) Global forest resource assessment, main report. United Nations Food and Agriculture Organisation, RomeGoogle Scholar
  12. Forment J, Gadea J, Huerta L, Abizanda L, Agusti J, Alamar S, Alos E, Andres F, Arribas R, Beltran JP, Berbel A, Blazquez MA, Brumos J, Canas LA, Cercos M, Colmenero-Flores JM, Conesa A, Estables B, Gandia M, Garcia-Martinez JL, Gimeno J, Gisbert A, Gomez G, Gonzalez-Candelas L, Granell A, Guerri J, Lafuente MT, Madueno F, Marcos JF, Marques MC, Martinez F, Martinez-Godoy MA, Miralles S, Moreno P, Navarro L, Pallas V, Perez-Amador MA, Perez-Valle J, Pons C, Rodrigo I, Rodriguez PL, Royo C, Serrano R, Soler G, Tadeo F, Talon M, Terol J, Trenor M, Vaello L, Vicente O, Vidal C, Zacarias L, Conejero V (2005) Development of a Citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol 57:375–391PubMedCrossRefGoogle Scholar
  13. Hjelm U, Ogren E (2003) Is photosynthetic acclimation to low temperature controlled by capacities for storage and growth at low temperature? Results from comparative studies of grasses and trees. Physiol Plant 119:113–120CrossRefGoogle Scholar
  14. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877PubMedCrossRefGoogle Scholar
  15. Ji W, Li Y, Li J, Dai C-h, Wang X, Bai X, Cai H, Yang L, Zhu Y-m (2006) Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja. BMC Plant Biol 6:4PubMedCrossRefGoogle Scholar
  16. Jones J, Dunsmuir P, Bedbrook J (1985) High level expression of introduced chimeric genes in regenerated transformed plants. EMBO J 4:2411–2418PubMedGoogle Scholar
  17. Keller G (2006) Analyse du transcriptome de l’Eucalyptus pendant l’acclimatation au froid. Recherche de gènes candidats de la tolérance au gel. Doctorat de l’Université Paul Sabatier, Toulouse, FranceGoogle Scholar
  18. Kim SY (2006) The role of ABF family bZIP class transcription factors in stress response. Physiol Plant 126:519–527Google Scholar
  19. Kohler A, Blaudez D, Chalot M, Martin F (2004) Cloning and expression of multiple metallothioneins from hybrid poplar. New Phytol 164:83–93CrossRefGoogle Scholar
  20. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-DDCT method. Methods 25:402–408PubMedCrossRefGoogle Scholar
  21. Mehta PA, Sivaprakash K, Parani M, Venkataraman G, Parida AK (2005) Generation and analysis of expressed sequence tags from the salt-tolerant mangrove species Avicennia marina (Forsk) Vierh. Theor Appl Genet 110:416–424PubMedCrossRefGoogle Scholar
  22. Myburg A, Grattapaglia D, Tuskan G, Schmutz J, Rokhsar D, Barry K, Bristow J; The Eucalyptus Genome Network (EUCAGEN) (2008) Eucalyptus: sequencing a global tree genome for energy, fiber and wood, Genomic of energy and environnement, JGI Third Annual Meeting, march 26–28 2008, Walnut Creek, California, USAGoogle Scholar
  23. 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 55:263–280PubMedCrossRefGoogle Scholar
  24. Pavy N, Paule C, Parsons L, Crow JA, Morency M-J, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Butterfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt R, Marra M, Seguin A, Retzel E, Bousquet J, MacKay J (2005) Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 6:144PubMedCrossRefGoogle Scholar
  25. Poke FS, Vaillancourt RE, Potts BM, Reid JB (2005) Genomic research in Eucalyptus. Genetica 125:79–101PubMedCrossRefGoogle Scholar
  26. Porat R, Pasentsis K, Rozentzvieg D, Gerasopoulos D, Falara V, Samach A, Lurie S, Kanellis AK (2004) Isolation of a dehydrin cDNA from orange and grapefruit citrus fruit that is specifically induced by the combination of heat followed by chilling temperatures. Physiol Plant 120:256–264PubMedCrossRefGoogle Scholar
  27. Ruiter RK, van Eldik GJ, van Herpen MMA, Schrauwen JAM, Wullems GJ (1999) Hydration-dependent gene expression in Brassica oleracea anthers. Sex Plant Reprod 12:135–143CrossRefGoogle Scholar
  28. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning, a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, New YorkGoogle Scholar
  29. Savitch LV, Leonardos ED, Krol M, Jansson S, Grodzinski B, Huner NPA, Öquist G (2002) Two different strategies for light utilization in photosynthesis in relation to growth and cold acclimation. Plant Cell Env 25:761–771CrossRefGoogle Scholar
  30. Shinwari ZK, Nakashima K, Miura S, Kasuga M, Seki M, Yamaguchi-Shinozaki K, Shinozaki K (1998) An Arabidopsis gene family encoding DRE/CRT binding proteins involved in low-temperature-responsive gene expression. Biochem Biophys Res Commun 250:161–170PubMedCrossRefGoogle Scholar
  31. Teulières C, Marque C (2007) Eucalyptus. In: Pua EC, Davey MR (eds) Transgenic crops, vol 60. Springer, Berlin, pp 387–406Google Scholar
  32. Teulières C, Bossinger G, Moran G, Marque C (2007) Stress studies in Eucalyptus. In: Plant Stress, Global Science Books (eds),vol I(2), 197–215Google Scholar
  33. Thomashow MF (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Physiol Plant Mol Biol 50:571–599PubMedCrossRefGoogle Scholar
  34. Vannini C, Locatelli F, Bracale M, Magnani E, Marsoni M, Osnato M, Mattana M, Baldoni E, Coraggio I (2004) Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants. Plant J 37:115–127PubMedCrossRefGoogle Scholar
  35. Vogel JT, Zarka DG, Van Buskirk HA, Fowler SG, Thomashow MF (2005) Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 41:195–211PubMedCrossRefGoogle Scholar
  36. Wei H, Dhanaraj AL, Rowland LJ, Fu Y, Krebs SL, Arora R (2005) Comparative analysis of expressed sequence tags from cold-acclimated and non-acclimated leaves of Rhododendron catawbiense Michx. Planta 221:406–416PubMedCrossRefGoogle Scholar
  37. Welling A, Palva ET (2006) Molecular control of cold acclimation in trees. Physiol Plant 127:167–181CrossRefGoogle Scholar
  38. Wissel K, Pettersson F, Berglund A, Jansson S (2003) What affects mRNA levels in leaves of field-grown aspen? A study of developmental and environmental influences. Plant Physiol 133:1190–1197PubMedCrossRefGoogle Scholar
  39. Wong CE, Li Y, Whitty BR, Diaz-Camino C, Akhter SR, Brandle JE, Golding GB, Weretilnyk EA, Moffatt BA, Griffith M (2005) Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap. Plant Mol Biol 58:561–574PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Guylaine Keller
    • 1
  • Thibault Marchal
    • 1
  • Hélène SanClemente
    • 1
  • Marie Navarro
    • 1
  • Nathalie Ladouce
    • 1
  • Patrick Wincker
    • 2
  • Arnaud Couloux
    • 2
  • Chantal Teulières
    • 1
  • Christiane Marque
    • 1
  1. 1.Réponse adaptative au froid, Pôle de Biotechnologie VégétaleUniversité de Toulouse, ERT 1045Castanet-TolosanFrance
  2. 2.GénoscopeCentre National de Séquençage: BPEvryFrance

Personalised recommendations