Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish
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...
| Main Authors: | , , , , , |
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| Format: | Journal Article |
| Published: |
2017
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| Online Access: | http://hdl.handle.net/20.500.11937/51387 |
| _version_ | 1848758685302521856 |
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| author | Di Battista, Joseph Saenz-Agudelo, P. Piatek, M. Wang, X. Aranda, M. Berumen, M. |
| author_facet | Di Battista, Joseph Saenz-Agudelo, P. Piatek, M. Wang, X. Aranda, M. Berumen, M. |
| author_sort | Di Battista, Joseph |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | 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. This article is protected by copyright. All rights reserved. |
| first_indexed | 2025-11-14T09:47:55Z |
| format | Journal Article |
| id | curtin-20.500.11937-51387 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T09:47:55Z |
| publishDate | 2017 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-513872018-04-12T01:32:34Z Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish Di Battista, Joseph Saenz-Agudelo, P. Piatek, M. Wang, X. Aranda, M. Berumen, M. 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. This article is protected by copyright. All rights reserved. 2017 Journal Article http://hdl.handle.net/20.500.11937/51387 10.1111/1755-0998.12662 fulltext |
| spellingShingle | Di Battista, Joseph Saenz-Agudelo, P. Piatek, M. Wang, X. Aranda, M. Berumen, M. Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish |
| title | Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish |
| title_full | Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish |
| title_fullStr | Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish |
| title_full_unstemmed | Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish |
| title_short | Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish |
| title_sort | using a butterflyfish genome as a general tool for rad-seq studies in specialized reef fish |
| url | http://hdl.handle.net/20.500.11937/51387 |