Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

Handle URI:
http://hdl.handle.net/10754/622970
Title:
Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish
Authors:
DiBattista, Joseph ( 0000-0002-5696-7574 ) ; Saenz Agudelo, Pablo; Piatek, Marek J.; Wang, Xin; Aranda, Manuel ( 0000-0001-6673-016X ) ; Berumen, Michael L. ( 0000-0003-2463-2742 )
Abstract:
Data from a large-scale restriction site associated DNA (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 (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to see if it improves the quality of RAD-Seq markers. Our analyses indicate (1) a modest gap between the number of non-annotated versus annotated SNPs across all species, (2) 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 (3) 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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Red Sea Research Center (RSRC); Computational Bioscience Research Center (CBRC)
Citation:
DiBattista JD, Saenz-Agudelo P, Piatek MJ, Wang X, Aranda M, et al. (2017) Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish. Molecular Ecology Resources. Available: http://dx.doi.org/10.1111/1755-0998.12662.
Publisher:
Wiley-Blackwell
Journal:
Molecular Ecology Resources
KAUST Grant Number:
CRG-1-2012-BER-002
Issue Date:
25-Feb-2017
DOI:
10.1111/1755-0998.12662
Type:
Article
ISSN:
1755-098X
Sponsors:
This research was supported by the KAUST Office of Competitive Research Funds (OCRF) under Award No. CRG-1-2012-BER-002 and baseline research funds to M.L.B., as well as a National Geographic Society Grant 9024-11 to J.D.D. For support in Socotra, we kindly thank the Ministry of Water and Environment of Yemen, staff at the Environment Protection Authority (EPA) Socotra, and especially Salah Saeed Ahmed, Fouad Naseeb and Thabet Abdullah Khamis, as well as Ahmed Issa Ali Affrar from Socotra Specialist Tour for handling general logistics. For logistic support elsewhere, we thank Eric Mason at Dream Divers in Saudi Arabia; the Red Sea State Government and The Red Sea University in Sudan, as well as Equipe Cousteau including N. Hussey, S. Kessel, C. Scarpellini, and M. Younis; Nicolas Prévot at Dolphin Divers and the crew of the M/V Deli in Djibouti; the KAUST Coastal and Marine Resources Core Lab and Amr Gusti; and the Ministry of Agriculture and Fisheries in Oman including Abdul Karim. For specimen collections, we thank Tilman Alpermann, Giacomo Bernardi, Brian Bowen, Camrin Braun, Richard Coleman, Michelle Gaither, Jean-Paul Hobbs, Jennifer McIlwain, Gerrit Nanninga, Mark Priest, Luiz Rocha, Tane Sinclair-Taylor, and members of the Reef Ecology Lab at KAUST. For assistance with bench work at KAUST we thank Craig Michell. We also acknowledge important contributions from Luiz Rocha and David Catania for assistance with specimen archiving at the California Academy of Sciences, Tane Sinclair-Taylor for formatting figures at later stages, and the KAUST Bioscience Core Laboratory with Sivakumar Neelamegam and Hicham Mansour for their assistance with Illumina sequencing.
Additional Links:
http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12662/abstract
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorDiBattista, Josephen
dc.contributor.authorSaenz Agudelo, Pabloen
dc.contributor.authorPiatek, Marek J.en
dc.contributor.authorWang, Xinen
dc.contributor.authorAranda, Manuelen
dc.contributor.authorBerumen, Michael L.en
dc.date.accessioned2017-03-06T11:13:35Z-
dc.date.available2017-03-06T11:13:35Z-
dc.date.issued2017-02-25en
dc.identifier.citationDiBattista JD, Saenz-Agudelo P, Piatek MJ, Wang X, Aranda M, et al. (2017) Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish. Molecular Ecology Resources. Available: http://dx.doi.org/10.1111/1755-0998.12662.en
dc.identifier.issn1755-098Xen
dc.identifier.doi10.1111/1755-0998.12662en
dc.identifier.urihttp://hdl.handle.net/10754/622970-
dc.description.abstractData from a large-scale restriction site associated DNA (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 (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to see if it improves the quality of RAD-Seq markers. Our analyses indicate (1) a modest gap between the number of non-annotated versus annotated SNPs across all species, (2) 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 (3) 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.en
dc.description.sponsorshipThis research was supported by the KAUST Office of Competitive Research Funds (OCRF) under Award No. CRG-1-2012-BER-002 and baseline research funds to M.L.B., as well as a National Geographic Society Grant 9024-11 to J.D.D. For support in Socotra, we kindly thank the Ministry of Water and Environment of Yemen, staff at the Environment Protection Authority (EPA) Socotra, and especially Salah Saeed Ahmed, Fouad Naseeb and Thabet Abdullah Khamis, as well as Ahmed Issa Ali Affrar from Socotra Specialist Tour for handling general logistics. For logistic support elsewhere, we thank Eric Mason at Dream Divers in Saudi Arabia; the Red Sea State Government and The Red Sea University in Sudan, as well as Equipe Cousteau including N. Hussey, S. Kessel, C. Scarpellini, and M. Younis; Nicolas Prévot at Dolphin Divers and the crew of the M/V Deli in Djibouti; the KAUST Coastal and Marine Resources Core Lab and Amr Gusti; and the Ministry of Agriculture and Fisheries in Oman including Abdul Karim. For specimen collections, we thank Tilman Alpermann, Giacomo Bernardi, Brian Bowen, Camrin Braun, Richard Coleman, Michelle Gaither, Jean-Paul Hobbs, Jennifer McIlwain, Gerrit Nanninga, Mark Priest, Luiz Rocha, Tane Sinclair-Taylor, and members of the Reef Ecology Lab at KAUST. For assistance with bench work at KAUST we thank Craig Michell. We also acknowledge important contributions from Luiz Rocha and David Catania for assistance with specimen archiving at the California Academy of Sciences, Tane Sinclair-Taylor for formatting figures at later stages, and the KAUST Bioscience Core Laboratory with Sivakumar Neelamegam and Hicham Mansour for their assistance with Illumina sequencing.en
dc.publisherWiley-Blackwellen
dc.relation.urlhttp://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12662/abstracten
dc.rightsThis is the peer reviewed version of the following article: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish, which has been published in final form at http://doi.org/10.1111/1755-0998.12662. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.en
dc.titleUsing a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fishen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalMolecular Ecology Resourcesen
dc.relation.referencesDiBattista, J. D., Saenz-Agudelo, P., Piatek, M. J., Wang, X., Aranda, M., & Berumen, M. L. (2017). Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish (Version 2) [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.f09rhen
dc.relation.referencesDOI:10.5061/DRYAD.F09RHen
dc.relation.referencesHANDLE:http://hdl.handle.net/10754/624180en
dc.eprint.versionPost-printen
dc.contributor.institutionDepartment of Environment and Agriculture; Curtin University; PO Box U1987 Perth WA 6845 Australiaen
dc.contributor.institutionInstituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile; Valdivia 5090000 Chileen
kaust.authorDiBattista, Josephen
kaust.authorSaenz Agudelo, Pabloen
kaust.authorPiatek, Marek J.en
kaust.authorWang, Xinen
kaust.authorAranda, Manuelen
kaust.authorBerumen, Michael L.en
kaust.grant.numberCRG-1-2012-BER-002en
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