title: Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank).
abstract: Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information.
authors.affiliation: Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
authors.forename: Kyriakos
authors.initials: K
authors.lastname: Tsangaras
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Nathan
authors.initials: N
authors.lastname: Wales
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Pontén
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.affiliation: Conservation Genetics Unit, Institute of Botany (Bat. 22), University of Liège, Liège, Belgium.
authors.forename: Johan
authors.initials: J
authors.lastname: Michaux
authors.affiliation: Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Yasuko
authors.initials: Y
authors.lastname: Ishida
authors.affiliation: Institut des Sciences de l'Evolution, Université de Montpellier II, Montpellier Cedex 5, France.
authors.forename: Serge
authors.initials: S
authors.lastname: Morand
authors.affiliation: Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
authors.forename: Marie-Louise
authors.initials: ML
authors.lastname: Kampmann
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
authors.affiliation: Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
authors.forename: Alex D
authors.initials: AD
authors.lastname: Greenwood
mesh_terms: D000818:Animals; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016678:Genome; D051379:Mice; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D016133:Polymerase Chain Reaction / Q000379:methods*; D051381:Rats
chemical_list: D004269:DNA, Bacterial