[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
Liao GJ, Lun FM, Zheng YW, Chan KC, Leung TY, et al. (2011) Targeted massively parallel sequencing of maternal plasma DNA permits efficient and unbiased detection of fetal alleles Clin Chem, 57: 92-101.
Avila-Arcos MC, Cappellini E, Romero-Navarro JA, Wales N, Moreno-Mayar JV, et al. (2011). Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Sci Rep 1: 74.
Maricic T, Whitten M, Pääbo S (2010). Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One 5: e14004.
Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, et al. (2010). Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328: 723-725.
Duncavage EJ, Magrini V, Becker N, Armstrong JR, Demeter RT, et al. (2011). Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue. J Mol Diagn 13: 325-333.
Herman DS, Hovingh GK, Iartchouk O, Rehm HL, Kucherlapati R, et al. (2009). Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection. Nat Methods 6: 507-510.
Mason VC, Li G, Helgen KM, Murphy WJ (2011). Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens. Genome Res 21: 1695-1704.
Guo Y, Long J, He J, Li CI, Cai Q, et al. (2012). Exome sequencing generates high quality data in non-target regions. BMC Genomics 13: 194.
Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc pdb prot 5448.
Castiglia R, Annesi F, Capanna E (2005). Geographical pattern of genetic variation in the Robertsonian system of Mus musculus domesticus in central Italy. Biol J Linn Soc 84: 395-405.
Cappellini E, Gilbert MT, Geuna F, Fiorentino G, Hall A, et al. (2010). A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 97: 205-217.
Winkelmann I, Campos PF, Strugnell J, Cherel Y, Smith PJ, et al. (2013). Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species. Proc Biol Sci 280: 20130273.
Japelaghi RH, Haddad R, Garoosi GA (2011). Rapid and efficient isolation of high quality nucleic acids from plant tissues rich in polyphenols and polysaccharides. Mol Biotechnol 49: 129-137.
Marcel M (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10-12.
Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: 1303.3997.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009). Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645.
Lanfear R, Calcott B, Ho SY, Guindon S (2012). Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol 29: 1695-1701.
Silvestro D, Michalak I (2012). raxmlGUI: a graphical front-end for RAxML. Org Divers Evol 12: 335-337.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, et al. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61: 539-542.
Tsangaras K, Avila-Arcos MC, Ishida Y, Helgen KM, Roca AL, et al. (2012). Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus). BMC Genet 13: 92.
Avila-Arcos MC, Ho SY, Ishida Y, Nikolaidis N, Tsangaras K, et al. (2013). One hundred twenty years of koala retrovirus evolution determined from museum skins. Mol Biol Evol 30: 299-304.
Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, et al. (2014). Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol 52: 139-146.
Lundrigan BL, Jansa SA, Tucker PK (2002). Phylogenetic relationships in the genus mus, based on paternally, maternally, and biparentally inherited characters. Syst Biol 51: 410-431.
Suzuki H, Shimada T, Terashima M, Tsuchiya K, Aplin K (2004). Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences. Mol Phylogenet Evol 33: 626-646.