Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish
Data files
Feb 23, 2017 version files 87.65 MB
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Chaetodon_austriacus batch_1_filtered.vcf
10.64 MB
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Chaetodon_fasciatus_batch_1_filtered.vcf
9.38 MB
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Chaetodon_larvatus_batch_1_filtered.vcf
10.79 MB
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Chaetodon_melapterus_batch_1_filtered.vcf
8.29 MB
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Chaetodon_mesoleucos_batch_1_filtered.vcf
9.26 MB
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Chaetodon_paucifasciatus_batch_1_filtered.vcf
8.18 MB
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Chaetodon_pictus_batch_1_filtered.vcf
5.18 MB
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Chaetodon_semilarvatus_batch_1_filtered.vcf
8.46 MB
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Chaetodon_trifascialis_batch_1_filtered.vcf
8.46 MB
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Ctenochaetus_striatus_batch_1_filtered.vcf
9.04 MB
Mar 13, 2017 version files 137.50 MB
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Chaetodon_austriacus_denovo_batch_1_filtered.vcf
19.89 MB
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Chaetodon_austriacus_refmap_batch_1_filtered.vcf
20.08 MB
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Chaetodon_fasciatus_denovo_batch_1_filtered.vcf
5.40 MB
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Chaetodon_fasciatus_refmap_batch_1_filtered.vcf
1.48 MB
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Chaetodon_larvatus_denovo_batch_1_filtered.vcf
15.37 MB
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Chaetodon_larvatus_refmap_batch_1_filtered.vcf
2.68 MB
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Chaetodon_melapterus_denovo_batch_1_filtered.vcf
6.69 MB
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Chaetodon_melapterus_refmap_batch_1_filtered.vcf
12.31 MB
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Chaetodon_mesoleucos_denovo_batch_1_filtered.vcf
10.16 MB
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Chaetodon_mesoleucos_refmap_batch_1_filtered.vcf
1.69 MB
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Chaetodon_paucifasciatus_denovo_batch_1_filtered.vcf
21.85 MB
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Chaetodon_paucifasciatus_refmap_batch_1_filtered.vcf
1.87 MB
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Chaetodon_pictus_denovo_batch_1_filtered.vcf
5.17 MB
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Chaetodon_pictus_refmap_batch_1_filtered.vcf
987.56 KB
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Chaetodon_semilarvatus_denovo_batch_1_filtered.vcf
4.23 MB
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Chaetodon_semilarvatus_refmap_batch_1_filtered.vcf
710.26 KB
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Chaetodon_trifascialis_denovo_batch_1_filtered.vcf
2.85 MB
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Chaetodon_trifascialis_refmap_batch_1_filtered.vcf
760.11 KB
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Ctenochaetus_striatus_denovo_batch_1_filtered.vcf
3.29 MB
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Ctenochaetus_striatus_refmap_batch_1_filtered.vcf
20.57 KB
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.