title: Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa.
abstract: The generation of genome-scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome-scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high-throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double-digestion RAD sequencing libraries for nine different species and five genera of insects and fish. We found one particular enzyme pair produced consistently higher number of sequence-able fragments across all nine species. Building libraries off this enzyme pair, we found a range of usable SNPs between 4000 and 37 000 SNPS per species and we found a greater number of usable SNPs using reference genomes than de novo pipelines in STACKS. We also found fewer reads in the Read 2 fragments from the paired-end Illumina Hiseq run. Overall, the results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies.
authors.affiliation: Department of Applied Ecology, North Carolina State University, Campus Box 7617, Raleigh, NC, 27695, USA. mbreiski@ncsu.edu.
authors.forename: M O
authors.initials: MO
authors.lastname: Burford Reiskind
authors.affiliation: Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: K
authors.initials: K
authors.lastname: Coyle
authors.affiliation: Department of Applied Ecology, North Carolina State University, Campus Box 7617, Raleigh, NC, 27695, USA.
authors.forename: H V
authors.initials: HV
authors.lastname: Daniels
authors.affiliation: Department of Entomology, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: P
authors.initials: P
authors.lastname: Labadie
authors.affiliation: Department of Entomology, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: M H
authors.initials: MH
authors.lastname: Reiskind
authors.affiliation: Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: N B
authors.initials: NB
authors.lastname: Roberts
authors.affiliation: Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: R B
authors.initials: RB
authors.lastname: Roberts
authors.affiliation: Genomic Sciences Laboratory, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: J
authors.initials: J
authors.lastname: Schaff
authors.affiliation: Department of Entomology, Texas A&M University, College Station, TX, 77843, USA.
authors.forename: E L
authors.initials: EL
authors.lastname: Vargo
mesh_terms: D000818:Animals; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004262:DNA Restriction Enzymes / Q000378:metabolism; D005399:Fishes / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D007313:Insecta / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA; D004262:DNA Restriction Enzymes
keywords: double-digest RAD sequencing; high-throughput sequencing; reduced representation sequencing; restriction enzyme digests