Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays.
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.
Santuari
Luca
L
Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland. luca.santuari@unil.ch
Pradervand
Sylvain
S
Amiguet-Vercher
Amelia-Maria
AM
Thomas
Jerôme
J
Dorcey
Eavan
E
Harshman
Keith
K
Xenarios
Ioannis
I
Juenger
Thomas E
TE
Hardtke
Christian S
CS
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
D018744:DNA, Plant; D012333:RNA, Messenger