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

Joseph DiBattista; Pablo Saenz Agudelo; Marek J. Piatek; Xin Wang; Manuel Aranda; Michael L. Berumen

doi:10.1111/1755-0998.12662

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

Joseph DiBattista, Pablo Saenz Agudelo, Marek J. Piatek, Xin Wang, Manuel Aranda, Michael L. Berumen

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7 Scopus citations

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.

Original language	English (US)
Pages (from-to)	1330-1341
Number of pages	12
Journal	Molecular Ecology Resources
Volume	17
Issue number	6
DOIs	https://doi.org/10.1111/1755-0998.12662
State	Published - Apr 6 2017

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): CRG-1-2012-BER-002
Acknowledgements: 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.

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10.1111/1755-0998.12662

https://repository.kaust.edu.sa/bitstream/10754/622970/1/DiBattista_et_al-2017-Molecular_Ecology_Resources.pdf

Cite this

@article{5ebbe946c72f40cbb74f48e84308d853,

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 (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.",

author = "Joseph DiBattista and {Saenz Agudelo}, Pablo and Piatek, {Marek J.} and Xin Wang and Manuel Aranda and Berumen, {Michael L.}",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): CRG-1-2012-BER-002 Acknowledgements: 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 Pr{\'e}vot 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.",

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doi = "10.1111/1755-0998.12662",

language = "English (US)",

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AU - Saenz Agudelo, Pablo

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AU - Wang, Xin

AU - Aranda, Manuel

AU - Berumen, Michael L.

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): CRG-1-2012-BER-002 Acknowledgements: 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.

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N2 - 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.

AB - 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.

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

Abstract

Bibliographical note

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Chaetodon austriacus Genome sequencing and assembly

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

Abstract

Bibliographical note

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Datasets

Chaetodon austriacus Genome sequencing and assembly

Cite this