[en] 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.
Disciplines :
Zoology
Author, co-author :
Tsangaras, K.; Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife ResearchBerlin, Germany
Wales, N.; Centre for GeoGenetics, Natural History Museum of Denmark, University of CopenhagenCopenhagen, Denmark
Sicheritz-Pontén, T.; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of DenmarkKongens Lyngby, Denmark
Rasmussen, S.; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of DenmarkKongens Lyngby, Denmark
Michaux, Johan ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues
Ishida, Y.; Department of Animal Sciences, University of Illinois at Urbana-ChampaignUrbana, IL, United States
Morand, S.; Institut des Sciences de l'Evolution, Université de Montpellier IIMontpellier Cedex 5, France
Kampmann, M.-L.; Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife ResearchBerlin, Germany
Gilbert, M. T. P.; Centre for GeoGenetics, Natural History Museum of Denmark, University of CopenhagenCopenhagen, Denmark
Greenwood, A. D.; Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife ResearchBerlin, Germany
Title :
Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank)
Publication date :
2014
Journal title :
PLoS ONE
eISSN :
1932-6203
Publisher :
Public Library of Science
Volume :
9
Issue :
10
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
R01GM092706, NIGMS, National Institute of General Medical Sciences
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