Data from: 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 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.针对红海与阿拉伯海9种蝴蝶鱼开展的大规模限制性酶切位点相关DNA测序（restriction site associated DNA sequencing, RAD-Seq）研究数据，为检验最新发表的Chaetodon austriacus参考基因组草图的实用性，以及评估该核位点分离方法的潜在偏倚提供了研究基础。本研究对双酶切限制性酶切位点相关DNA测序（double-digest restriction-site associated DNA sequencing, ddRAD）数据进行了分析处理，分别在使用与不使用本研究参考基因组的前提下，识别单核苷酸多态性（single nucleotide polymorphism, SNP）标记及其相关功能，以探究参考基因组是否可提升RAD-Seq标记的质量。本研究的分析结果显示：① 所有物种中未注释与已注释单核苷酸多态性（SNP）的数量存在小幅差距；② 基于为SNP推定基因功能的能力，使用基因组资源对于近缘蝴蝶鱼物种具有显著优势，而对远缘物种则无此效果；③ 蝴蝶鱼姊妹类群中富集了与钙离子跨膜转运及结合相关的基因。上述第三项研究结果表明，通过后续深入研究，该方法有望为揭示红海、阿拉伯海与阿拉伯湾等严苛珊瑚礁生境中栖息种群的适应性机制提供重要学术见解。