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Open Access Highly Accessed Research article

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

Mark TA Donoghue12, Channa Keshavaiah12, Sandesh H Swamidatta2 and Charles Spillane12*

Author Affiliations

1 Genetics & Biotechnology Lab, Department of Biochemistry, Lee Maltings 2.10, University College Cork (UCC), Cork, Ireland

2 Genetics & Biotechnology Lab, Botany & Plant Science, Aras de Brun C306, National University of Ireland Galway (NUIG), Galway, Ireland

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BMC Evolutionary Biology 2011, 11:47  doi:10.1186/1471-2148-11-47

Published: 18 February 2011

Additional files

Additional file 1:

Search schema to identify Brassicaceae LSGs.

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Additional file 2:

The effect of using different E value cut-offs in BLAST. "X" indicates the number of LSGs reported after the InterProScan, here the x axis (E-value cut off) is irrelevant.

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Additional file 3:

Supplementary information: Including genomic feature comparisons between LSGs and non-LSGs.

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Additional file 4:

Table listing all LSGs their gene description and genomic coordinates.

Format: XLSX Size: 140KB Download file

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Additional file 5:

LSGs with overlapping CDS with the CDS of a non-LSG.

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Additional file 6:

Distributions of E-values for LSG non-LSG paralog BLASTP and BLASTN hits.

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Additional file 7:

Details of all LSG non-LSG paralog BLASTP and BLASTN hits.

Format: XLSX Size: 135KB Download file

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Additional file 8:

Percentage of each transposable element super-families contributing DNA to the CDS of LSGs and non-LSGs CDS. Dark gray = percentage of TEs that contribute DNA to LSG CDS content, mid gray = percentage of TEs that contribute DNA to non-LSG CDS content, light gray = percentage of TEs that do not contribute any DNA to any gene model CDS.

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Additional file 9:

LSGs and accessions that were sequenced.

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Additional file 10:

Alignments and gene models of sequenced LSGs in various accessions and sister species. For the multiple sequence alignments: black = identical residues, blue = similar residues, red = other residues (i.e. non-matching). In addition, for the gene model alignments "!" Indicates indel and the number of nucleotides are displayed below. For ambiguous nucleotides; m = A or C, y = C or T and w = A or T and "x" = undetermined peptide.

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Additional file 11:

Stress conditions tested for differential expression of LSGs.

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Additional file 12:

Summary of all stress responsive LSGs. Red = up-regulated genes, blue = down-regulated genes. For the stress conditions listed across the bottom of each table; blue = abiotic, green = biotic, purple = growth conditions, yellow = hormone treatment and red = chemical treatment.

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Additional file 13:

Heatmaps indicating fold change of LSGs expressed under abiotic and biotic stress conditions. Genes highlighted with a p-value indicate significant differential expression. Colour bars at the top of columns indicate an enrichment of LSGs differentially expressed: red = up-regulated, blue = down-regulated, yellow = LSGs are enriched for both up and down-regulated genes.

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Additional file 14:

Details of differentially expressed LSGs for growth condition, treatments, chemical treatments and hormone treatments.

Format: XLSX Size: 38KB Download file

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Additional file 15:

Forward and reverse primers used fro sequencing and Genbank accessions of sequences.

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