Open Access Method

Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays

Luca Santuari1, Sylvain Pradervand23, Amelia-Maria Amiguet-Vercher1, Jerôme Thomas3, Eavan Dorcey1, Keith Harshman3, Ioannis Xenarios2, Thomas E Juenger4 and Christian S Hardtke1*

Author Affiliations

1 Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland

2 Swiss Institute of Bioinformatics, Genopode Building, CH-1015 Lausanne, Switzerland

3 Lausanne DNA Array Facility, Center for Integrative Genomics, University of Lausanne, Genopode Building, CH-1015 Lausanne, Switzerland

4 Section of Integrative Biology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station C0930, Austin, Texas 78712, USA

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Genome Biology 2010, 11:R4  doi:10.1186/gb-2010-11-1-r4

Published: 12 January 2010

Additional files

Additional file 1:

Distribution of the read coverage for the five Arabidopsis chromosomes across the different accessions.

Format: PDF Size: 365KB Download file

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Additional file 2:

Experimentally tested deletions predicted in Eil-0 and Tsu-1, positions and primer sequences.

Format: XLS Size: 32KB Download file

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Additional file 3:

Number of unique tiles from the Col-0 genome without UHTS coverage in the four accessions for different tiling array signal ratios.

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Additional file 4:

Deletions predicted from paired end reads of the Eil-0 and Lc-0 genomes by the Breakdancer algorithm.

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Additional file 5:

Genes carrying deletions as predicted from intersection of UHTS and tiling arrays.

Format: XLS Size: 149KB Download file

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Additional file 6:

The subset of genes whose coding sequence is carrying deletions as predicted from intersection of UHTS and tiling arrays.

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Additional file 7:

Script for computing the UHTS coverage and signal ratio of array tiles.

Format: R Size: 4KB Download file

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Additional file 8:

Script for deletion prediction based on intersection of UHTS coverage and tiling array signal.

Format: R Size: 3KB Download file

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