title: Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays.
abstract: 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.
authors.affiliation: Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland. luca.santuari@unil.ch
authors.forename: Luca
authors.initials: L
authors.lastname: Santuari
authors.forename: Sylvain
authors.initials: S
authors.lastname: Pradervand
authors.forename: Amelia-Maria
authors.initials: AM
authors.lastname: Amiguet-Vercher
authors.forename: Jerôme
authors.initials: J
authors.lastname: Thomas
authors.forename: Eavan
authors.initials: E
authors.lastname: Dorcey
authors.forename: Keith
authors.initials: K
authors.lastname: Harshman
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Juenger
authors.forename: Christian S
authors.initials: CS
authors.lastname: Hardtke
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D001671:Biochemistry / Q000379:methods; D019295:Computational Biology / Q000379:methods; D018744:DNA, Plant / Q000235:genetics; D030541:Databases, Genetic; D017353:Gene Deletion; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D008954:Models, Biological; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D012333:RNA, Messenger