Open Access Highly Accessed Research article

RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus

Emilie Villar123, Christophe Klopp4, Céline Noirot4, Evandro Novaes56, Matias Kirst5, Christophe Plomion27 and Jean-Marc Gion12*

Author Affiliations

1 CIRAD, UMR AGAP, Campus de Baillarguet TA 10C, F-34398 Montpellier Cedex 5, France

2 INRA, UMR1202 BIOGECO, F-33610 Cestas, France

3 CRDPI, BP1291, Pointe Noire, République du Congo

4 Plateforme bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France

5 School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA

6 Universidade Federal de Goiás, Caixa Postal 131, CEP 74690-900, Goiânia, Brazil

7 Université de Bordeaux, UMR1202 BIOGECO, F-33610 Cestas, France

For all author emails, please log on.

BMC Genomics 2011, 12:538  doi:10.1186/1471-2164-12-538

Published: 2 November 2011

Additional files

Additional file 1:

Results of the ANOVA for above-ground biomass.

Format: PDF Size: 13KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Distribution of read length for the three half-runs.

Format: PDF Size: 78KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Increasing coverage with successive runs. Number of contigs represented in each half-run or combination of several half-runs. Performing a second half-run increased contig coverage by an average of 18%, and a third half run increased coverage by an average of 6%.

Format: PDF Size: 53KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Comparison of the distribution of Gene Ontology (GO) categories between Eucalyptus spp unigene elements (UE) and Arabidopsis annotated unigenes. Proportion of each GO category (Biological Process, Cellular Component and Molecular Function) found in the E. spp sequencing set and in the annotated Arabidopsis genome.

Format: GIF Size: 64KB Download file

Open Data

Additional file 5:

Differentially expressed contigs displaying significant T and GxT effects. Each contig showing T or GxT is associated with a functional category (as defined by Mercator : http://mapman.gabipd.org/web/guest webcite). Log2-transformed fold change between abundance in irrigated and non irrigated libraries are indicated for each genotype, as well as p-value of T and GxT effects analyzed by the ANOVA.

Format: XLS Size: 96KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Distribution of "G" contigs between functional pathways. Each square represents the log2-transformed fold-change of abundance between genotypes 1-41 and 18-50 for one contig. Contigs in green were overexpressed in genotype 1-41 and contigs in blue were overexpressed in genotype 18-50.

Format: PDF Size: 91KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Significant categories for the Wilcoxon rank sum test, according to Mapman analysis for the pairwise comparison of differentially expressed contigs displaying genotype (G), treatment (T) and genotype × treatment (GxT) effects. ** Categories differentially expressed at an error rate threshold of 0.05 * Categories differentially expressed at an error rate threshold of 0.1

Format: PDF Size: 56KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 8:

Distribution of "T" contigs between several functional pathways. Each square represents the log2-transformed fold-change of abundance between irrigated (IR) and non-irrigated (NI) treatments for one contig. Contigs in blue were overexpressed for the IR treatment and contigs in red were overexpressed for the NI treatment.

Format: PDF Size: 103KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9:

Supporting information: validation of digital profiles by analyzing expression by RT-qPCR on 36 genes.

Format: PDF Size: 114KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data