EUCATOUL


Eucalyptus species, renowned for their fast growth, valuable wood properties and wide adaptability, are amongst the most planted hardwoods in the world for pulpwood and timber. They are also still at the early stages of domestication because conventional breeding is slow and costly [1]. Thus, there is a huge potential in developing marker-assisted breeding programs most particularly to improve traits such as wood properties and frost tolerance. Frost tolerance is of critical importance for Eucalyptus, which is native to Australia and freezing temperatures limit the geographical distribution of plants and reduce their productivity.
We present here the sequencing, assembly, analysis and annotation of large collections of ESTs related to wood formation and to frost tolerance. To mine this valuable resource, we have created the EUCATOUL database which allows four types of queries:
- Query 1 is a library filter query allowing retrieval of all unigenes or a selection of them from the user-specified libraries. EST assemblies, Blast hits, GO and PFAM annotations can also be retrieved.
- Query 2 retrieves unigenes by name (aliases), PFAM or GO annotations, hits in Blasts (accession number or name).
- Query 3 allows performing Blast of the user-specified sequence against EucaWood and/or EucaCold databases.
- Query 4 gives access to a treeview showing the number of unigenes by GO terms.

EucaWood
"EUCAWOOD" is a dataset of 3928 wood-related unigenes (2479 contigs and 1449 singletons) originating from one normalized differentiating xylem cDNA library [XylcDNA] and four subtractive [SSH] libraries: [Xl] xylem versus leaves[2] ; [Xp], xylem versus phloem [3], [Mj] mature wood versus juvenile wood, [Jm] juvenile versus mature wood [4]. These comprehensive list of unigenes dedicated to wood formation in the genus Eucalyptus are instrumental for candidate gene approaches, custom array development [5] and marker-assisted selection programs aimed at improving and modulating traits of great economic importance.
The list and sequence of 641 putative EST-SSRs can be retrieved as a pdf file.
The cDNA clones are stored at the CNRGV [cnrgv.toulouse.inra.fr] and can be supplied upon request to Hélène Berges [hberges@toulouse.inra.fr]

EucaCold
A cDNA library was constructed from a cold tolerant and acclimated genotype, originating from Tasmania and provided by French breeding programs. From leaves of cold-acclimated plantlets and adult trees, 366,000 clones were isolated and 13,056 were randomly chosen ESTs for sequencing. The distribution of the 11,303 annotated sequences (5,457 unigenes) was studied according to the GO classification [6]. This functional annotation was completed by the global expressional analysis of 2.662 ESTs randomly selected which provided a first molecular picture of the Eucalyptus transcriptome variation under cold acclimation [7]. (www.polebio.lrsv.ups-tlse.fr/eucatoul/coldexpress).

References:
[1] Myburg AA, Potts BM, Marques CMP, Kirst M, Gion J-M, Grattapaglia D, Grima-Pettenati, J. 2007. Eucalyptus. In: Kole CR, Ed. Genome Mapping & Molecular Breeding in Plants. Vol. 7: Forest Trees. Springer, Heidelberg. ISBN: 978-3-540-34540-4

[2] Paux E, Tamasloukht M, Ladouce N, Sivadon P, Grima-Pettenati J: Identification of genes preferentially expressed during wood formation in Eucalyptus. Plant Mol Biol 2004, 55(2):263-280.
[3] Foucart C, Paux E, Ladouce N, San Clemente H, Grima-Pettenati J, Sivadon P: Transcript profiling of a xylem vs phloem cDNA subtractive library identifies new genes expressed during xylogenesis in Eucalyptus. New Phytol 2006, 170(4):739-752.
[4] D Rengel, H San Clemente, F Servant, N Ladouce, E Paux, P Wincker, A Couloux, P Sivadon and J Grima-Pettenati. A new Eucalyptus genomic resource dedicated to wood formation: a comprehensive survey. BMC Plant Biology 2009, 9:36.
[5] Paux E, Carocha V, Marques C, Mendes de Sousa A, Borralho N, Sivadon P, Grima-Pettenati J: Transcript profiling of Eucalyptus xylem genes during tension wood formation. New Phytol 2005, 167(1):89-100.
[6] Keller G, Marchal T.,SanClemente H., Navarro M., Ladouce N., Wincker P., Couloux A., Teulières C.and Marque C., 2009 - Development and functional annotation of a 11303 EST collection from Eucalyptus for studies of cold tolerance, Tree genetics and genome 5 : 317-327.7.
[7] Keller G., El Kayal W., San Clemente H., Ayax C., Teulières C., Marque C., Transcript profiling combined to functional annotation of 1554 genes from Eucalyptus provides a molecular picture of cold acclimation. (submitted).