title: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish.
abstract: Data from a large-scale restriction site-associated DNA sequencing (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction site-associated DNA (ddRAD) sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to see whether it improves the quality of RAD-Seq. Our analyses indicate (i) a modest gap between the number of nonannotated versus annotated SNPs across all species, (ii) an advantage of using genomic resources for closely related but not distantly related butterflyfish species based on the ability to assign putative gene function to SNPs and (iii) an enrichment of genes among sister butterflyfish taxa related to calcium transmembrane transport and binding. The latter result highlights the potential for this approach to reveal insights into adaptive mechanisms in populations inhabiting challenging coral reef environments such as the Red Sea, Arabian Sea and Arabian Gulf with further study.
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.|Department of Environment and Agriculture, Curtin University, PO Box U1987, Perth, WA, 6845, Australia.
authors.forename: Joseph D
authors.identifier: http://orcid.org/0000-0002-5696-7574
authors.initials: JD
authors.lastname: DiBattista
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.|Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, 5090000, Chile.
authors.forename: Pablo
authors.initials: P
authors.lastname: Saenz-Agudelo
authors.affiliation: Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Marek J
authors.initials: MJ
authors.lastname: Piatek
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
authors.forename: Manuel
authors.initials: M
authors.lastname: Aranda
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Berumen
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D059001:Aquatic Organisms / Q000145:classification / Q000235:genetics; D060005:Genotyping Techniques / Q000379:methods*; D010473:Perciformes / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: 
  SNP
  ; Chaetodontidae; adaptation; ddRAD; ecological genomics; next-generation sequencing