Genome Biol.; co-auth.: GTF, I.Xenarios

Genome Biol. 2010 Jan 12;11(1):R4.

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

Santuari L, Pradervand S, Amiguet-Vercher AM, Thomas J, Dorcey E, Harshman K, Xenarios I, Juenger TE, Hardtke CS.

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

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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.