Building up resources and knowledge to unravel transcriptomics dynamics underlying Eucalyptus globulus xylogenesis

The economic importance of some Eucalyptus species, including interspecific hybrids, has been extended from the traditional interest of pulp and paper production to the emergent areas of bio-fuels and bio-materials. New genomic resources and high throughput technologies have provided the Eucalyptus research international community with the opportunities to identify genomic regions of interest in order to comprehensively dissect, catalogue and characterize genes involved in the determination of wood formation and quality. Similar strategies can be now applied to identify key regulator genes and better understand the cellular mechanisms by which they modulate the complex molecular events occurring in xylogenesis. The Geneglob project (2006-2010) produced and used a set of genomic tools which, associated with Next Generation Sequencing (NGS) technologies, allowed us to expand the knowledge of the Eucalyptus genome by focusing on regions potentially involved in the determination of wood properties, namely pulp yield and lignin content. We first start to characterize two E. grandis BAC libraries [1] constructed by the Arizona Genome Institute (with DNA from the clone Brasuz S1 whose genome was sequenced recently by the DOE [http:// www.jgi.doe.gov/sequencing/why/99176.html], and two E. globulus BAC libraries made available by RAIZ [http://www.raiz-iifp.pt/]. We than used 3D-pools of BAC libraries and BAC macroarrays to characterize genomic environment of several lignin and lignin-regulator genes (e.g.EguCCR, EguCAD2 and EguRAC1) both in E. grandis and E. globulus. The shotgun sequencing of selected BAC clones containing those genes generated a high amount of sequencing data that made it possible to map the E. globulus BAC sequenced clones against the E. grandis genome (8X coverage). These comparative analyses showed extended microlinearity between both genomes, at least in the studied regions. Additionally, we have sequenced and annotated the chloroplast genome of E. grandis (GeneBank Accession NC_014570) [1]. A global approach to unravel E. globulus transcriptome dynamics has also been included and structured in the Geneglob project, aiming at the identification of genomic hotspots of transcription activity. Various E. globulus xylogenesis “models” have been considered comprising several paired, contrasting wood forming tissues (provided by RAIZ): i) xylem samples collected along the year (season variation); ii) juvenile and adult individuals of a single genotype; iii) contrasting genotypes for pulp yield. Samples from these tissues were used for transcriptome sequencing using IlluminaHi-Seq technology (mRNA-SEQ). The same E. globulus genotype used for both E. globulus BAC libraries (a parent tree used in controlled crosses by RAIZ) has been resequenced (pair-end 100bp), and provided the first draft of an E. globulus genome. This resequencing data was mapped against the E. grandis Brasuz S1 reference genome. Transcriptomic data were also blatted against the gene models annotated in E. grandis genome, to evaluate in silico the expression of each gene. More recently, the microEGo project (2010-2012) started the identification and characterization of Eucalyptus * Correspondence: [email protected] Instituto de Investigação Científica e Tropical (IICT/MCTES) Palácio Burnay Rua da Junqueira, 30, 1349-007 Lisboa, Portugal Instituto de Biologia Experimental e Tecnológica (IBET) Av. da República, Quinta do Marquês, 2781-901 Oeiras, Portugal Full list of author information is available at the end of the article Paiva et al. BMC Proceedings 2011, 5(Suppl 7):O52 http://www.biomedcentral.com/1753-6561/5/S7/O52