Butterflyfish are among the most iconic of the coral reef fishes and represent a model system to study general questions of biogeography, evolution and population genetics. We assembled and annotated the genome sequence of the blacktail butterflyfish (Chaetodon austriacus), an Arabian region endemic species that is reliant on coral reefs for food and shelter. Using available bony fish (superclass Osteichthyes) genomes as a reference, a total of 28 926 high-quality protein-coding genes were predicted from 13 967 assembled scaffolds. The quality and completeness of the draft genome of C. austriacus suggest that it has the potential to serve as a resource for studies on the co-evolution of reef fish adaptations to the unique Red Sea environment, as well as a comparison of gene sequences between closely related congeneric species of butterflyfish distributed more broadly across the tropical Indo-Pacific. © 2016 John Wiley & Sons Ltd.

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.

Corallimorpharia are the closest non-calcifying relatives of reef-building corals. Aside from their popularity among aquarium hobbyists, their evolutionary position between the Actiniaria (sea anemones) and the Scleractinia (hard corals) makes them ideal candidates for comparative studies aiming at understanding the evolution of hexacorallian orders in general and reef-building corals in particular. Here we have sequenced and assembled two draft genomes for the Corallimorpharia species Amplexidiscus fenestrafer and Discosoma sp.. The draft genomes encompass 370 Mbp and 445 Mbp respectively and encode for 21,372 and 23,199 genes. To facilitate future studies using these resources, we provide annotations for the predicted gene models-not only at gene level, by annotating gene models with the function of the best-matching homolog, and GO terms when available; but also at protein domain level, where gene function can be better verified through the conservation of the sequence and order of protein domains. Further, we provide an online platform (http://corallimorpharia.reefgenomics.org), which includes a BLAST interface as well as a genome browser to facilitate the use of these resources. We believe that these two genomes are important resources for future studies on hexacorallian systematics and the evolutionary basis of their specific traits such as the symbiotic relationship with dinoflagellates of the genus Symbiodinium or the evolution of calcification in reef-building corals. This article is protected by copyright. All rights reserved.