Open Access Research article

Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species

Marcela Mendes Salazar1, Leandro Costa Nascimento1, Eduardo Leal Oliveira Camargo1, Danieli Cristina Gonçalves1, Jorge Lepikson Neto1, Wesley Leoricy Marques1, Paulo José Pereira Lima Teixeira1, Piotr Mieczkowski2, Jorge Maurício Costa Mondego3, Marcelo Falsarella Carazzolle1, Ana Carolina Deckmann1 and Gonçalo Amarante Guimarães Pereira1*

Author Affiliations

1 Laboratório de Genômica e Expressão, Departamento de Genética Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Campinas, CEP: 13083-970, Brasil

2 Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, USA

3 Centro de Pesquisa e Desenvolvimento em Recursos Genéticos vegetais, Instituto Agronômico de Campinas, São Paulo, Campinas, CEP: 13001-970, Brasil

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BMC Genomics 2013, 14:201  doi:10.1186/1471-2164-14-201

Published: 22 March 2013

Additional files

Additional file 1:

FASTA-formatted sequences of the 10,398 contigs formed by the de novo assembly.

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Additional file 2: Figure S1:

Distribution of contig lengths: 29,292 EUCANEXT contigs (min: 200, max: 12,053, mean length: 899.5, n50: 1442 bp). Figure S2. Distribution tail of FPKM values vs. the contig frequency for each xylem library.

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Additional file 3: Table S1:

All contigs of the EUCANEXT dataset: Contig names, FPKM values, fold-changes and p-values, BLAST results against NR, TAIR and E. grandis genome scaffolds. Table S2. Cell wall genes: FPKM values, fold-changes and p-values for all genes mentioned in the text. Only isoforms with the most significant expression in the xylem were considered. The dark-gray squares indicate the fold-changes of differentially expressed genes with fold changes>2 and p-values<0.01. The light-gray squares are genes that tended to be differentially expressed, although the fold-change is 2.0>x>1.5 (p-value 0.01)). GL: E. globulus; GR: E. grandis; UR: E. urophylla.Table S3. Other genes: FPKM values, fold-changes and p-values for all genes mentioned in the text. Only isoforms with the most significant expression in the xylems are considered. The dark-gray squares indicate the fold-changes of differentially expressed genes with fold changes >2 and p-values<0.01. The light-gray squares are genes that tended to be differentially expressed, although the fold-change is 2.0>x>1.5 (p-value 0.01)). GL: E. globulus; GR: E. grandis; UR: E. urophylla. Red, green and brown squares indicate contigs belonging to CC, MDR and other NBS resistance gene families respectively (ZIP 6449 kb).

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Additional file 4: Doc file S1:

Pairwise comparisons. Figure S3. Flow diagram of genes expressed in all xylem libraries (group a, Figure 1). The genes were separated as being “non-differentially expressed” and “differentially expressed”. The differentially expressed genes were analyzed by pairwise comparisons between species. Figure S4. GO categories at Biological Process level 3. A: Representative GO categories of genes shared by only two species (groups b, c and d, Figure 2); B: Representative GO categories of genes expressed in only one species (groups e, f and g, Figure 2). A and B: The percentage of contigs in each GO category related to the total number of known function contigs is present on the y-axis. Doc file S2. Validation by Real Time-PCR (RT-qPCR) [51,76-81].

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