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Open Access Highly Accessed Research article

Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection

Bala R Thumma1*, Navin Sharma2 and Simon G Southerton1

Author Affiliations

1 CSIRO Plant Industry, Clunies Ross Street, Acton, ACT, 2601, Australia

2 ITC India, R&D Centre, Peenya Industrial Area, No. 3, Bangalore, Karnataka, 560058, India

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BMC Genomics 2012, 13:364  doi:10.1186/1471-2164-13-364

Published: 1 August 2012

Additional files

Additional file 1:

Figure S1. Comparison of biomass traits between treatments. Error bars are standard errors of mean (SEM). K-Katherine; M-Mt Isa; P-Petford.

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Additional file 2:

Read counts and gene identities of the significantly (P ≤ 0.05; bonferroni correction) differentially expressed transcripts between control (C1) and stress (S1) treatments.

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Additional file 3:

Pearson’s correlation coefficients among the reference-guided assembly read counts from 12 libraries.

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Additional file 4:

Gene ontology analysis of differentially expressed transcripts between control samples collected at the beginning (C0) and at the end (C1) of the treatment.

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Additional file 5:

Allele frequencies of the SNPs with significant differential allelic expression between samples collected at the beginning (S0) and at the end (S1) of stress treatments.

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Additional file 6:

Enrichment of functional gene categories among genes with differential allelic expression. a). Gene categories enriched among genes showing differential allelic expression (between S0 and S1samples) and differential total gene expression between control (C1) and stress (S1) treatments. b). Gene categories enriched among genes showing differential allelic expression but similar total gene expression between control (C1) and stress (S1) treatments. FDR < 0.001.

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Additional file 7:

Distribution of Ka/Ks ratios among the genes. Ka/Ks values are based on full length CDS gene annotations from E. grandis.

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Additional file 8:

Gene categories enriched among genes under purifying selection. Genes with Ka/Ks ratio < 0.20 were used in GO analysis.

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Additional file 9:

Differential allelic expression among positively selected genes.

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