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.
Chaetodon_austriacus_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon austriacus
Chaetodon_fasciatus_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon fasciatus
Chaetodon_larvatus_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon larvatus
Chaetodon_melapterus_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon melapterus
Chaetodon_mesoleucos_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon mesoleucos
Chaetodon_paucifasciatus_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon paucifasciatus
Chaetodon_pictus_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon pictus
Chaetodon_semilarvatus_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon semilarvatus
Chaetodon_trifascialis_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon trifascialis
Ctenochaetus_striatus_denovo_batch_1_filtered.vcf
Filtered denovo_map.pl RAD reads in .vcf format for Ctenochaetus striatus
Chaetodon_austriacus_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Chaetodon austriacus
Chaetodon_fasciatus_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Chaetodon fasciatus
Chaetodon_larvatus_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Chaetodon larvatus
Chaetodon_melapterus_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Chaetodon melapterus
Chaetodon_mesoleucos_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Chaetodon mesoleucos
Chaetodon_paucifasciatus_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Chaetodon paucifasciatus
Chaetodon_pictus_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Chaetodon pictus
Chaetodon_semilarvatus_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Chaetodon semilarvatus
Chaetodon_trifascialis_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Chaetodon trifascialis
Ctenochaetus_striatus_refmap_batch_1_filtered.vcf
Filtered ref_map.pl RAD reads in .vcf format for Ctenochaetus striatus