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

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Santuari, Luca
Pradervand, Sylvain
Amiguet-Vercher, Amelia-Maria
Thomas, Jerome
Dorcey, Eavan
Harshman, Keith
Xenarios, Ioannis
Juenger, Thomas E.
Hardtke, Christian S.

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Genome Biology


Identification of small polymorphisms from next generation sequencing short read data is relatively easy, but detection of larger deletions is less straightforward. Here, we analyzed four divergent Arabidopsis accessions and found that intersection of absent short read coverage with weak tiling array hybridization signal reliably flags deletions. Interestingly, individual deletions were frequently observed in two or more of the accessions examined, suggesting that variation in gene content partly reflects a common history of deletion events.


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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Santuari, Luca, Sylvain Pradervand, Amelia-Maria Amiguet-Vercher, Jerôme Thomas, Eavan Dorcey, Keith Harshman, Ioannis Xenarios, Thomas E. Juenger, and Christian S. Hardtke. “Substantial Deletion Overlap among Divergent Arabidopsis Genomes Revealed by Intersection of Short Reads and Tiling Arrays.” Genome Biology 11, no. 1 (January 12, 2010): R4. doi:10.1186/gb-2010-11-1-r4.