title: BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design.
abstract: Target DNA enrichment combined with high-throughput sequencing technologies is a powerful approach to probing a large number of loci in genomes of interest. However, software algorithms that explicitly consider nucleotide sequence information of target loci in multiple reference species for optimizing design of target enrichment baits to be applicable across a wide range of species have not been developed. Here we present an algorithm that infers target DNA enrichment baits from multiple nucleotide sequence alignments. By applying clustering methods and the combinatorial 1-center sequence optimization to bait design, we are able to minimize the total number of baits required to efficiently probe target loci in multiple species. Consequently, more loci can be probed across species with a given number of baits. Using transcript sequences of 24 apoid wasps (Hymenoptera: Crabronidae, Sphecidae) from the 1KITE project and the gene models of Nasonia vitripennis, we inferred 57,650, 120-bp-long baits for capturing 378 coding sequence sections of 282 genes in apoid wasps. Illumina reduced-representation library sequencing confirmed successful enrichment of the target DNA when applying these baits to DNA of various apoid wasps. The designed baits furthermore enriched a major fraction of the target DNA in distantly related Hymenoptera, such as Formicidae and Chalcidoidea, highlighting the baits' broad taxonomic applicability. The availability of baits with broad taxonomic applicability is of major interest in numerous disciplines, ranging from phylogenetics to biodiversity monitoring. We implemented our new approach in a software package, called BaitFisher, which is open source and freely available at https://github.com/cmayer/BaitFisher-package.git.
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Mayer
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.
authors.forename: Manuela
authors.initials: M
authors.lastname: Sann
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Donath
authors.affiliation: Services in Molecular Biology GmbH, Rüdersdorf, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Meixner
authors.affiliation: University of Bonn, Institute of Evolutionary Biology and Ecology, Bonn, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Podsiadlowski
authors.affiliation: Department Arthropoda, Zoological Research Museum Alexander Koenig, Bonn, Germany.
authors.forename: Ralph S
authors.initials: RS
authors.lastname: Peters
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany.
authors.forename: Malte
authors.initials: M
authors.lastname: Petersen
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany Australian National Insect Collection, CSIRO National Research Collections Australia, Acton, Canberra, ACT, Australia.
authors.forename: Karen
authors.initials: K
authors.lastname: Meusemann
authors.affiliation: Services in Molecular Biology GmbH, Rüdersdorf, Germany.
authors.forename: Karsten
authors.initials: K
authors.lastname: Liere
authors.affiliation: Zoological Research Museum Alexander Koenig, Bonn, Germany.
authors.forename: Johann-Wolfgang
authors.initials: JW
authors.lastname: Wägele
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Misof
authors.affiliation: Molecular Evolution and Systematics of Animals, Institute for Biology, University of Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), Madrid, Spain.
authors.forename: Christoph
authors.initials: C
authors.lastname: Bleidorn
authors.affiliation: Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany o.niehuis@zfmk.de michael.ohl@mfn-berlin.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Ohl
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany o.niehuis@zfmk.de michael.ohl@mfn-berlin.de.
authors.forename: Oliver
authors.initials: O
authors.lastname: Niehuis
mesh_terms: D004247:DNA / Q000737:chemistry / Q000235:genetics; D015342:DNA Probes / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics*; D015723:Gene Library; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D015342:DNA Probes; D004247:DNA
keywords: Hymenoptera.; comparative genomics; hybrid enrichment; phylogenetics; phylogenomics